Psyllid ID: psy7051

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------16
Protein Sequence
MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRDRRYTRSRSFSSRSRSGSKSPRKARSKSIDRDNKHERNGRS
Secondary Structure (PSIPRED)
ccccccccccccccEEEEccccccccHHHHHHHHHccccEEEEEEcccccccccccEEEEEEccHHHHHHHHHHccccEEcccEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccEEEEccccccccHHHHHHHHHHcccEEEEEEEEcccccccccEEEEEEccHHHHHHHHHHHcccEEccEEEEEEEccccccccccccccccccccccccccccHHHcccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
msygrpppriegmvslkvdnltyrttpdDLRRVFERCgevgdiyiprdrftresrgfaFVRFFDKRDAEDALDAMDGRMLDGRELRVQMArygrppsssrsrggrdrdrrrdrsrsrdrrytrsrsfssrsrsgsksprkarsksidrdnkherngrs
Flexible Loop (DISEMBL)
msygrpppriegmvslkvdnltyrttpddlrrVFERcgevgdiyiprdrftresrgfafvrffdkrdaedalDAMDGRMLDGRELRvqmarygrppsssrsrggrdrdrrrdrsrsrdrrytrsrsfssrsrsgsksprkarsksidrdnkherngrs
Low Complexity Region (SEG)
MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMArygrppsssrsrggrdrdrrrdrsrsrdrrytrsrsfssrsrsgsksprkarsksIDRDNKHERNGRS
Disordered region (IsUnstruct)
*************VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKR********************************************************************************************
Disordered Region (DISOPRED)
************MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV***********************************************************************
Disordered Region (DISEMBL)
MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR*******************************************************************
Disordered Region (DISPRO)
****RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARY******************************************************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRDRRYTRSRSFSSRSRSGSKSPRKARSKSIDRDNKHERNGRS
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	158	2.2.26 [Sep-21-2011]
P30352	221	Serine/arginine-rich spli	yes	N/A	0.658	0.470	0.817	1e-44
Q5R1W5	221	Serine/arginine-rich spli	yes	N/A	0.620	0.443	0.836	1e-43
Q06A98	221	Serine/arginine-rich spli	yes	N/A	0.632	0.452	0.82	3e-43
Q6PDU1	221	Serine/arginine-rich spli	yes	N/A	0.632	0.452	0.82	4e-43
Q62093	221	Serine/arginine-rich spli	yes	N/A	0.632	0.452	0.82	4e-43
Q01130	221	Serine/arginine-rich spli	yes	N/A	0.632	0.452	0.82	4e-43
Q3MHR5	221	Serine/arginine-rich spli	yes	N/A	0.632	0.452	0.82	4e-43
Q9BRL6	282	Serine/arginine-rich spli	no	N/A	0.594	0.333	0.723	2e-34
Q09511	196	Probable splicing factor,	yes	N/A	0.575	0.464	0.615	3e-30
Q8WXF0	261	Serine/arginine-rich spli	no	N/A	0.531	0.321	0.460	1e-15

>sp|P30352|SRSF2_CHICK Serine/arginine-rich splicing factor 2 OS=Gallus gallus GN=SRSF2 PE=2 SV=1

 Score =  178 bits (451), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 85/104 (81%), Positives = 93/104 (89%)

Query: 1   MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
           MSYGRPPP +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFV
Sbjct: 1   MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 60

Query: 61  RFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGG 104
           RF DKRDAEDA+DAMDG +LDGRELRVQMARYGRPP S  SR G
Sbjct: 61  RFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPDSHHSRRG 104

Necessary for the splicing of pre-mRNA. It is required for formation of the earliest ATP-dependent splicing complex and interacts with spliceosomal components bound to both the 5'- and 3'-splice sites during spliceosome assembly. It also is required for ATP-dependent interactions of both U1 and U2 snRNPs with pre-mRNA.
Gallus gallus (taxid: 9031)

>sp|Q5R1W5|SRSF2_PANTR Serine/arginine-rich splicing factor 2 OS=Pan troglodytes GN=SRSF2 PE=2 SV=3

 Score =  175 bits (443), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 82/98 (83%), Positives = 90/98 (91%)

Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          MSYGRPPP +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFV
Sbjct: 1  MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 60

Query: 61 RFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSS 98
          RF DKRDAEDA+DAMDG +LDGRELRVQMARYGRPP S
Sbjct: 61 RFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPDS 98

Necessary for the splicing of pre-mRNA. It is required for formation of the earliest ATP-dependent splicing complex and interacts with spliceosomal components bound to both the 5'- and 3'-splice sites during spliceosome assembly. It also is required for ATP-dependent interactions of both U1 and U2 snRNPs with pre-mRNA. Interacts with other spliceosomal components, via the RS domains, to form a bridge between the 5'- and 3'-splice site binding components, U1 snRNP and U2AF. Binds to purine-rich RNA sequences, either 5'-AGSAGAGTA-3' (S=C or G) or 5'-GTTCGAGTA-3'. Can bind to beta-globin mRNA and commit it to the splicing pathway. The phosphorylated form (by SRPK2) is required for cellular apoptosis in response to cisplatin treatment.

Pan troglodytes (taxid: 9598)

>sp|Q06A98|SRSF2_PIG Serine/arginine-rich splicing factor 2 OS=Sus scrofa GN=SRSF2 PE=2 SV=1

 Score =  174 bits (440), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 82/100 (82%), Positives = 90/100 (90%)

Query: 1   MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
           MSYGRPPP +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFV
Sbjct: 1   MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 60

Query: 61  RFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSR 100
           RF DKRDAEDA+DAMDG +LDGRELRVQMARYGRPP S  
Sbjct: 61  RFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPDSHH 100

Necessary for the splicing of pre-mRNA. It is required for formation of the earliest ATP-dependent splicing complex and interacts with spliceosomal components bound to both the 5'- and 3'-splice sites during spliceosome assembly. It also is required for ATP-dependent interactions of both U1 and U2 snRNPs with pre-mRNA. Interacts with other spliceosomal components, via the RS domains, to form a bridge between the 5'- and 3'-splice site binding components, U1 snRNP and U2AF. Binds to purine-rich RNA sequences, either 5'-AGSAGAGTA-3' (S=C or G) or 5'-GTTCGAGTA-3'. Can bind to beta-globin mRNA and commit it to the splicing pathway. The phosphorylated form (by SRPK2) is required for cellular apoptosis in response to cisplatin treatment.

Sus scrofa (taxid: 9823)

>sp|Q6PDU1|SRSF2_RAT Serine/arginine-rich splicing factor 2 OS=Rattus norvegicus GN=Srsf2 PE=1 SV=3

 Score =  173 bits (439), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 82/100 (82%), Positives = 90/100 (90%)

Query: 1   MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
           MSYGRPPP +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFV
Sbjct: 1   MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 60

Query: 61  RFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSR 100
           RF DKRDAEDA+DAMDG +LDGRELRVQMARYGRPP S  
Sbjct: 61  RFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPDSHH 100

Necessary for the splicing of pre-mRNA. It is required for formation of the earliest ATP-dependent splicing complex and interacts with spliceosomal components bound to both the 5'- and 3'-splice sites during spliceosome assembly. It also is required for ATP-dependent interactions of both U1 and U2 snRNPs with pre-mRNA. The phosphorylated form (by SRPK2) is required for cellular apoptosis in response to cisplatin treatment.

Rattus norvegicus (taxid: 10116)

>sp|Q62093|SRSF2_MOUSE Serine/arginine-rich splicing factor 2 OS=Mus musculus GN=Srsf2 PE=1 SV=4

 Score =  173 bits (439), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 82/100 (82%), Positives = 90/100 (90%)

Query: 1   MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
           MSYGRPPP +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFV
Sbjct: 1   MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 60

Query: 61  RFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSR 100
           RF DKRDAEDA+DAMDG +LDGRELRVQMARYGRPP S  
Sbjct: 61  RFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPDSHH 100

Necessary for the splicing of pre-mRNA. It is required for formation of the earliest ATP-dependent splicing complex and interacts with spliceosomal components bound to both the 5'- and 3'-splice sites during spliceosome assembly. It also is required for ATP-dependent interactions of both U1 and U2 snRNPs with pre-mRNA (By similarity). Can bind to the myelin basic protein (MBP) gene MB3 regulatory region and increase transcription of the mbp promoter in cells derived from the CNS. The phosphorylated form (by SRPK2) is required for cellular apoptosis in response to cisplatin treatment.

Mus musculus (taxid: 10090)

>sp|Q01130|SRSF2_HUMAN Serine/arginine-rich splicing factor 2 OS=Homo sapiens GN=SRSF2 PE=1 SV=4

 Score =  173 bits (439), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 82/100 (82%), Positives = 90/100 (90%)

Query: 1   MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
           MSYGRPPP +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFV
Sbjct: 1   MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 60

Query: 61  RFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSR 100
           RF DKRDAEDA+DAMDG +LDGRELRVQMARYGRPP S  
Sbjct: 61  RFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPDSHH 100

Necessary for the splicing of pre-mRNA. It is required for formation of the earliest ATP-dependent splicing complex and interacts with spliceosomal components bound to both the 5'- and 3'-splice sites during spliceosome assembly. It also is required for ATP-dependent interactions of both U1 and U2 snRNPs with pre-mRNA. Interacts with other spliceosomal components, via the RS domains, to form a bridge between the 5'- and 3'-splice site binding components, U1 snRNP and U2AF. Binds to purine-rich RNA sequences, either 5'-AGSAGAGTA-3' (S=C or G) or 5'-GTTCGAGTA-3'. Can bind to beta-globin mRNA and commit it to the splicing pathway. The phosphorylated form (by SRPK2) is required for cellular apoptosis in response to cisplatin treatment.

Homo sapiens (taxid: 9606)

>sp|Q3MHR5|SRSF2_BOVIN Serine/arginine-rich splicing factor 2 OS=Bos taurus GN=SRSF2 PE=2 SV=3

 Score =  173 bits (439), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 82/100 (82%), Positives = 90/100 (90%)

Query: 1   MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
           MSYGRPPP +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFV
Sbjct: 1   MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 60

Query: 61  RFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSR 100
           RF DKRDAEDA+DAMDG +LDGRELRVQMARYGRPP S  
Sbjct: 61  RFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPDSHH 100

Necessary for the splicing of pre-mRNA. It is required for formation of the earliest ATP-dependent splicing complex and interacts with spliceosomal components bound to both the 5'- and 3'-splice sites during spliceosome assembly. It also is required for ATP-dependent interactions of both U1 and U2 snRNPs with pre-mRNA. Interacts with other spliceosomal components, via the RS domains, to form a bridge between the 5'- and 3'-splice site binding components, U1 snRNP and U2AF. Binds to purine-rich RNA sequences, either 5'-AGSAGAGTA-3' (S=C or G) or 5'-GTTCGAGTA-3'. Can bind to beta-globin mRNA and commit it to the splicing pathway. The phosphorylated form (by SRPK2) is required for cellular apoptosis in response to cisplatin treatment.

Bos taurus (taxid: 9913)

>sp|Q9BRL6|SRSF8_HUMAN Serine/arginine-rich splicing factor 8 OS=Homo sapiens GN=SRSF8 PE=1 SV=1

 Score =  144 bits (363), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 68/94 (72%), Positives = 80/94 (85%)

Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          MS GRPPP ++GM++LKVDNLTYRT+PD LRRVFE+ G VGD+YIPR+  T+  RGFAFV
Sbjct: 1  MSCGRPPPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFV 60

Query: 61 RFFDKRDAEDALDAMDGRMLDGRELRVQMARYGR 94
          RF D+RDA+DA  AMDG  LDGRELRVQ+ARYGR
Sbjct: 61 RFHDRRDAQDAEAAMDGAELDGRELRVQVARYGR 94

Involved in pre-mRNA alternative splicing.

Homo sapiens (taxid: 9606)

>sp|Q09511|RSP4_CAEEL Probable splicing factor, arginine/serine-rich 4 OS=Caenorhabditis elegans GN=rsp-4 PE=3 SV=1

 Score =  130 bits (328), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 56/91 (61%), Positives = 78/91 (85%)

Query: 5   RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
           R  P I G+ SLK+DNL+Y+TTP+DLRR FER G++GD++IPRD+++R+S+GF FVRF++
Sbjct: 10  RAAPDINGLTSLKIDNLSYQTTPNDLRRTFERYGDIGDVHIPRDKYSRQSKGFGFVRFYE 69

Query: 65  KRDAEDALDAMDGRMLDGRELRVQMARYGRP 95
           +RDAE ALD  DG+++DGRELRV +A+Y RP
Sbjct: 70  RRDAEHALDRTDGKLVDGRELRVTLAKYDRP 100

May play a functionally redundant role in embryogenesis.

Caenorhabditis elegans (taxid: 6239)

>sp|Q8WXF0|SRS12_HUMAN Serine/arginine-rich splicing factor 12 OS=Homo sapiens GN=SRSF12 PE=2 SV=1

 Score = 82.4 bits (202), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 41/89 (46%), Positives = 57/89 (64%), Gaps = 5/89 (5%)

Query: 3  YGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRF 62
          Y RPP       SL + N+   T P+DLRR F R G + D+YIP D +TR  RGFA+V+F
Sbjct: 4  YTRPP-----NTSLFIRNVADATRPEDLRREFGRYGPIVDVYIPLDFYTRRPRGFAYVQF 58

Query: 63 FDKRDAEDALDAMDGRMLDGRELRVQMAR 91
           D RDAEDAL  ++ + + GR++ +Q A+
Sbjct: 59 EDVRDAEDALYNLNRKWVCGRQIEIQFAQ 87

Splicing factor that seems to antagonize SR proteins in pre-mRNA splicing regulation.

Homo sapiens (taxid: 9606)

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	158
242005811	246	serine/arginine rich splicing factor, pu	0.753	0.483	0.831	5e-49
307169015	208	Splicing factor, arginine/serine-rich 2	0.613	0.466	0.948	7e-48
332373880	168	unknown [Dendroctonus ponderosae]	0.613	0.577	0.979	1e-47
345486316	198	PREDICTED: serine/arginine-rich splicing	0.613	0.489	0.948	6e-47
322789593	175	hypothetical protein SINV_10987 [Solenop	0.613	0.554	0.948	1e-46
307197633	175	Splicing factor, arginine/serine-rich 2	0.613	0.554	0.948	1e-46
110762781	176	PREDICTED: serine/arginine-rich splicing	0.613	0.551	0.948	1e-46
312373610	170	hypothetical protein AND_17210 [Anophele	0.645	0.6	0.901	6e-46
170041667	186	serine/arginine rich splicing factor [Cu	0.620	0.526	0.928	8e-46
240849499	153	serine/arginine rich splicing factor-lik	0.588	0.607	0.967	1e-45

>gi|242005811|ref|XP_002423754.1| serine/arginine rich splicing factor, putative [Pediculus humanus corporis] gi|212506956|gb|EEB11016.1| serine/arginine rich splicing factor, putative [Pediculus humanus corporis]

 Score =  199 bits (505), Expect = 5e-49,   Method: Compositional matrix adjust.
 Identities = 99/119 (83%), Positives = 107/119 (89%)

Query: 1   MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
           +SYGRPPPRI+GMVSLKVDNLT+RTTPDDLRRVFERCGEVGDIYIPRDRF+RESRGFAFV
Sbjct: 48  VSYGRPPPRIDGMVSLKVDNLTFRTTPDDLRRVFERCGEVGDIYIPRDRFSRESRGFAFV 107

Query: 61  RFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRDR 119
           RF+DKRDAEDALDAMDGR+LDGRELRVQMARYGRP S  RSRG R  D  +   R +DR
Sbjct: 108 RFYDKRDAEDALDAMDGRILDGRELRVQMARYGRPSSPYRSRGRRRGDHDQGVVRDQDR 166

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307169015|gb|EFN61874.1| Splicing factor, arginine/serine-rich 2 [Camponotus floridanus]

 Score =  194 bits (494), Expect = 7e-48,   Method: Compositional matrix adjust.
 Identities = 92/97 (94%), Positives = 96/97 (98%)

Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          MSYGRPPPRI+GMVSLKVDNLTYRTTP+DLRRVFERCGEVGDIYIPRDRFTRESRGFAFV
Sbjct: 1  MSYGRPPPRIDGMVSLKVDNLTYRTTPEDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60

Query: 61 RFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPS 97
          RF+DKRDAEDALDAMDGR+LDGRELRVQMARYGRP S
Sbjct: 61 RFYDKRDAEDALDAMDGRLLDGRELRVQMARYGRPTS 97

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332373880|gb|AEE62081.1| unknown [Dendroctonus ponderosae]

 Score =  194 bits (493), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 95/97 (97%), Positives = 96/97 (98%)

Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV
Sbjct: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60

Query: 61 RFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPS 97
          RF+DKRDAEDALDAMDGRMLDGRELRVQMARYGRP S
Sbjct: 61 RFYDKRDAEDALDAMDGRMLDGRELRVQMARYGRPTS 97

Source: Dendroctonus ponderosae

Species: Dendroctonus ponderosae

Genus: Dendroctonus

Family: Curculionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345486316|ref|XP_003425445.1| PREDICTED: serine/arginine-rich splicing factor 2-like [Nasonia vitripennis]

 Score =  191 bits (486), Expect = 6e-47,   Method: Compositional matrix adjust.
 Identities = 92/97 (94%), Positives = 96/97 (98%)

Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          MSYGRPPPRI+GMVSLKVDNLTYRTTP+DLRRVFERCGEVGDIYIPRDRFTRESRGFAFV
Sbjct: 1  MSYGRPPPRIDGMVSLKVDNLTYRTTPEDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60

Query: 61 RFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPS 97
          RF+DKRDAEDALDAMDGRM+DGRELRVQMARYGRP S
Sbjct: 61 RFYDKRDAEDALDAMDGRMVDGRELRVQMARYGRPTS 97

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322789593|gb|EFZ14819.1| hypothetical protein SINV_10987 [Solenopsis invicta] gi|332021256|gb|EGI61641.1| Splicing factor, arginine/serine-rich 2 [Acromyrmex echinatior]

 Score =  191 bits (484), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 92/97 (94%), Positives = 96/97 (98%)

Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          MSYGRPPPRI+GMVSLKVDNLTYRTTP+DLRRVFERCGEVGDIYIPRDRFTRESRGFAFV
Sbjct: 1  MSYGRPPPRIDGMVSLKVDNLTYRTTPEDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60

Query: 61 RFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPS 97
          RF+DKRDAEDALDAMDGR+LDGRELRVQMARYGRP S
Sbjct: 61 RFYDKRDAEDALDAMDGRLLDGRELRVQMARYGRPTS 97

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307197633|gb|EFN78812.1| Splicing factor, arginine/serine-rich 2 [Harpegnathos saltator]

 Score =  191 bits (484), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 92/97 (94%), Positives = 96/97 (98%)

Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          MSYGRPPPRI+GMVSLKVDNLTYRTTP+DLRRVFERCGEVGDIYIPRDRFTRESRGFAFV
Sbjct: 1  MSYGRPPPRIDGMVSLKVDNLTYRTTPEDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60

Query: 61 RFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPS 97
          RF+DKRDAEDALDAMDGR+LDGRELRVQMARYGRP S
Sbjct: 61 RFYDKRDAEDALDAMDGRLLDGRELRVQMARYGRPTS 97

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|110762781|ref|XP_393352.2| PREDICTED: serine/arginine-rich splicing factor 2-like [Apis mellifera] gi|340724784|ref|XP_003400761.1| PREDICTED: serine/arginine-rich splicing factor 2-like [Bombus terrestris] gi|350398198|ref|XP_003485116.1| PREDICTED: serine/arginine-rich splicing factor 2-like [Bombus impatiens] gi|380022396|ref|XP_003695032.1| PREDICTED: serine/arginine-rich splicing factor 2-like [Apis florea] gi|383865619|ref|XP_003708270.1| PREDICTED: serine/arginine-rich splicing factor 2-like [Megachile rotundata]

 Score =  190 bits (483), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 92/97 (94%), Positives = 96/97 (98%)

Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          MSYGRPPPRI+GMVSLKVDNLTYRTTP+DLRRVFERCGEVGDIYIPRDRFTRESRGFAFV
Sbjct: 1  MSYGRPPPRIDGMVSLKVDNLTYRTTPEDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60

Query: 61 RFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPS 97
          RF+DKRDAEDALDAMDGR+LDGRELRVQMARYGRP S
Sbjct: 61 RFYDKRDAEDALDAMDGRLLDGRELRVQMARYGRPTS 97

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|312373610|gb|EFR21320.1| hypothetical protein AND_17210 [Anopheles darlingi]

 Score =  188 bits (478), Expect = 6e-46,   Method: Compositional matrix adjust.
 Identities = 92/102 (90%), Positives = 95/102 (93%)

Query: 3   YGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRF 62
           Y RPPPRI+GM+SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDR TRESRGFAFVRF
Sbjct: 4   YARPPPRIDGMISLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRHTRESRGFAFVRF 63

Query: 63  FDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGG 104
           +DKRDAEDALDAMDGRMLDGRELRVQMARYGRP S  R  GG
Sbjct: 64  YDKRDAEDALDAMDGRMLDGRELRVQMARYGRPTSPQRRGGG 105

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170041667|ref|XP_001848576.1| serine/arginine rich splicing factor [Culex quinquefasciatus] gi|167865236|gb|EDS28619.1| serine/arginine rich splicing factor [Culex quinquefasciatus]

 Score =  187 bits (476), Expect = 8e-46,   Method: Compositional matrix adjust.
 Identities = 91/98 (92%), Positives = 95/98 (96%)

Query: 2   SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
           SYGRPPPRI+GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDR TRESRGFAFVR
Sbjct: 3   SYGRPPPRIDGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRHTRESRGFAFVR 62

Query: 62  FFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSS 99
           F+DKRDA+DALDAMDGRMLDGRELRVQMARYGRP S +
Sbjct: 63  FYDKRDAQDALDAMDGRMLDGRELRVQMARYGRPTSPA 100

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|240849499|ref|NP_001155685.1| serine/arginine rich splicing factor-like [Acyrthosiphon pisum] gi|239790824|dbj|BAH71947.1| ACYPI006902 [Acyrthosiphon pisum]

 Score =  187 bits (475), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 90/93 (96%), Positives = 92/93 (98%)

Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          MSY RPPPRIEGMVSLKVDNLTYRTTP+DLRRVFERCGEVGDIYIPRDRFTRESRGFAFV
Sbjct: 1  MSYSRPPPRIEGMVSLKVDNLTYRTTPEDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60

Query: 61 RFFDKRDAEDALDAMDGRMLDGRELRVQMARYG 93
          RF+DKRDAEDALDAMDGRMLDGRELRVQMARYG
Sbjct: 61 RFYDKRDAEDALDAMDGRMLDGRELRVQMARYG 93

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

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	158
UNIPROTKB|P30352	221	SRSF2 "Serine/arginine-rich sp	0.569	0.407	0.833	1.1e-37
UNIPROTKB|Q3MHR5	221	SRSF2 "Serine/arginine-rich sp	0.569	0.407	0.833	1.1e-37
UNIPROTKB|E2RDB2	221	SRSF2 "Uncharacterized protein	0.569	0.407	0.833	1.1e-37
UNIPROTKB|B4DN89	209	SRSF2 "Serine/arginine-rich-sp	0.569	0.430	0.833	1.1e-37
UNIPROTKB|J3KP15	134	SRSF2 "Serine/arginine-rich-sp	0.569	0.671	0.833	1.1e-37
UNIPROTKB|J3QL05	130	SRSF2 "Serine/arginine-rich-sp	0.569	0.692	0.833	1.1e-37
UNIPROTKB|Q01130	221	SRSF2 "Serine/arginine-rich sp	0.569	0.407	0.833	1.1e-37
UNIPROTKB|Q06A98	221	SRSF2 "Serine/arginine-rich sp	0.569	0.407	0.833	1.1e-37
MGI|MGI:98284	221	Srsf2 "serine/arginine-rich sp	0.569	0.407	0.833	1.1e-37
RGD|1359422	221	Srsf2 "serine/arginine-rich sp	0.569	0.407	0.833	1.1e-37

UNIPROTKB|P30352 SRSF2 "Serine/arginine-rich splicing factor 2" [Gallus gallus (taxid:9031)]

 Score = 404 (147.3 bits), Expect = 1.1e-37, P = 1.1e-37
 Identities = 75/90 (83%), Positives = 83/90 (92%)

Query:     1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
             MSYGRPPP +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFV
Sbjct:     1 MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 60

Query:    61 RFFDKRDAEDALDAMDGRMLDGRELRVQMA 90
             RF DKRDAEDA+DAMDG +LDGRELRVQMA
Sbjct:    61 RFHDKRDAEDAMDAMDGAVLDGRELRVQMA 90

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|Q3MHR5 SRSF2 "Serine/arginine-rich splicing factor 2" [Bos taurus (taxid:9913)]

 Score = 404 (147.3 bits), Expect = 1.1e-37, P = 1.1e-37
 Identities = 75/90 (83%), Positives = 83/90 (92%)

Query:     1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
             MSYGRPPP +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFV
Sbjct:     1 MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 60

Query:    61 RFFDKRDAEDALDAMDGRMLDGRELRVQMA 90
             RF DKRDAEDA+DAMDG +LDGRELRVQMA
Sbjct:    61 RFHDKRDAEDAMDAMDGAVLDGRELRVQMA 90

GO:0016607 "nuclear speck" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|E2RDB2 SRSF2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 404 (147.3 bits), Expect = 1.1e-37, P = 1.1e-37
 Identities = 75/90 (83%), Positives = 83/90 (92%)

Query:     1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
             MSYGRPPP +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFV
Sbjct:     1 MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 60

Query:    61 RFFDKRDAEDALDAMDGRMLDGRELRVQMA 90
             RF DKRDAEDA+DAMDG +LDGRELRVQMA
Sbjct:    61 RFHDKRDAEDAMDAMDGAVLDGRELRVQMA 90

GO:0016607 "nuclear speck" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|B4DN89 SRSF2 "Serine/arginine-rich-splicing factor 2" [Homo sapiens (taxid:9606)]

 Score = 404 (147.3 bits), Expect = 1.1e-37, P = 1.1e-37
 Identities = 75/90 (83%), Positives = 83/90 (92%)

Query:     1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
             MSYGRPPP +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFV
Sbjct:     1 MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 60

Query:    61 RFFDKRDAEDALDAMDGRMLDGRELRVQMA 90
             RF DKRDAEDA+DAMDG +LDGRELRVQMA
Sbjct:    61 RFHDKRDAEDAMDAMDGAVLDGRELRVQMA 90

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|J3KP15 SRSF2 "Serine/arginine-rich-splicing factor 2" [Homo sapiens (taxid:9606)]

 Score = 404 (147.3 bits), Expect = 1.1e-37, P = 1.1e-37
 Identities = 75/90 (83%), Positives = 83/90 (92%)

Query:     1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
             MSYGRPPP +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFV
Sbjct:     1 MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 60

Query:    61 RFFDKRDAEDALDAMDGRMLDGRELRVQMA 90
             RF DKRDAEDA+DAMDG +LDGRELRVQMA
Sbjct:    61 RFHDKRDAEDAMDAMDGAVLDGRELRVQMA 90

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|J3QL05 SRSF2 "Serine/arginine-rich-splicing factor 2" [Homo sapiens (taxid:9606)]

 Score = 404 (147.3 bits), Expect = 1.1e-37, P = 1.1e-37
 Identities = 75/90 (83%), Positives = 83/90 (92%)

Query:     1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
             MSYGRPPP +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFV
Sbjct:     1 MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 60

Query:    61 RFFDKRDAEDALDAMDGRMLDGRELRVQMA 90
             RF DKRDAEDA+DAMDG +LDGRELRVQMA
Sbjct:    61 RFHDKRDAEDAMDAMDGAVLDGRELRVQMA 90

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|Q01130 SRSF2 "Serine/arginine-rich splicing factor 2" [Homo sapiens (taxid:9606)]

 Score = 404 (147.3 bits), Expect = 1.1e-37, P = 1.1e-37
 Identities = 75/90 (83%), Positives = 83/90 (92%)

Query:     1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
             MSYGRPPP +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFV
Sbjct:     1 MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 60

Query:    61 RFFDKRDAEDALDAMDGRMLDGRELRVQMA 90
             RF DKRDAEDA+DAMDG +LDGRELRVQMA
Sbjct:    61 RFHDKRDAEDAMDAMDGAVLDGRELRVQMA 90

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0016605 "PML body" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0003714 "transcription corepressor activity" evidence=NAS

GO:0016607 "nuclear speck" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0006397 "mRNA processing" evidence=TAS

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

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006366 "transcription from RNA polymerase II promoter" evidence=TAS

GO:0006369 "termination of RNA polymerase II transcription" evidence=TAS

GO:0006406 "mRNA export from nucleus" evidence=TAS

GO:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0031124 "mRNA 3'-end processing" evidence=TAS

UNIPROTKB|Q06A98 SRSF2 "Serine/arginine-rich splicing factor 2" [Sus scrofa (taxid:9823)]

 Score = 404 (147.3 bits), Expect = 1.1e-37, P = 1.1e-37
 Identities = 75/90 (83%), Positives = 83/90 (92%)

Query:     1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
             MSYGRPPP +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFV
Sbjct:     1 MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 60

Query:    61 RFFDKRDAEDALDAMDGRMLDGRELRVQMA 90
             RF DKRDAEDA+DAMDG +LDGRELRVQMA
Sbjct:    61 RFHDKRDAEDAMDAMDGAVLDGRELRVQMA 90

GO:0016607 "nuclear speck" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

MGI|MGI:98284 Srsf2 "serine/arginine-rich splicing factor 2" [Mus musculus (taxid:10090)]

 Score = 404 (147.3 bits), Expect = 1.1e-37, P = 1.1e-37
 Identities = 75/90 (83%), Positives = 83/90 (92%)

Query:     1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
             MSYGRPPP +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFV
Sbjct:     1 MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 60

Query:    61 RFFDKRDAEDALDAMDGRMLDGRELRVQMA 90
             RF DKRDAEDA+DAMDG +LDGRELRVQMA
Sbjct:    61 RFHDKRDAEDAMDAMDGAVLDGRELRVQMA 90

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=ISO;IDA

GO:0005681 "spliceosomal complex" evidence=IDA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0016607 "nuclear speck" evidence=ISO;IDA

RGD|1359422 Srsf2 "serine/arginine-rich splicing factor 2" [Rattus norvegicus (taxid:10116)]

 Score = 404 (147.3 bits), Expect = 1.1e-37, P = 1.1e-37
 Identities = 75/90 (83%), Positives = 83/90 (92%)

Query:     1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
             MSYGRPPP +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFV
Sbjct:     1 MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 60

Query:    61 RFFDKRDAEDALDAMDGRMLDGRELRVQMA 90
             RF DKRDAEDA+DAMDG +LDGRELRVQMA
Sbjct:    61 RFHDKRDAEDAMDAMDGAVLDGRELRVQMA 90

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005681 "spliceosomal complex" evidence=IEA;ISO

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA;ISO

GO:0016605 "PML body" evidence=ISO

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q06A98	SRSF2_PIG	No assigned EC number	0.82	0.6329	0.4524	yes	N/A
Q9P383	NCBP2_SCHPO	No assigned EC number	0.3153	0.7088	0.6153	yes	N/A
Q09511	RSP4_CAEEL	No assigned EC number	0.6153	0.5759	0.4642	yes	N/A
P30352	SRSF2_CHICK	No assigned EC number	0.8173	0.6582	0.4705	yes	N/A
Q01130	SRSF2_HUMAN	No assigned EC number	0.82	0.6329	0.4524	yes	N/A
Q6PDU1	SRSF2_RAT	No assigned EC number	0.82	0.6329	0.4524	yes	N/A
Q3MHR5	SRSF2_BOVIN	No assigned EC number	0.82	0.6329	0.4524	yes	N/A
Q62093	SRSF2_MOUSE	No assigned EC number	0.82	0.6329	0.4524	yes	N/A
Q5R1W5	SRSF2_PANTR	No assigned EC number	0.8367	0.6202	0.4434	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	158
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	5e-37
smart00360	73	smart00360, RRM, RNA recognition motif	2e-25
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	3e-23
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-22
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	1e-19
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	1e-19
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	3e-18
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	1e-17
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	2e-17
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	3e-17
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	4e-17
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	8e-17
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	1e-16
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	4e-16
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	1e-15
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	4e-15
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	2e-14
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	2e-14
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	3e-14
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	3e-14
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	4e-14
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	5e-14
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	1e-13
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	2e-13
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	3e-13
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	3e-13
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	4e-13
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	4e-13
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	5e-13
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	6e-13
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	7e-13
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	1e-12
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	1e-12
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	2e-12
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	2e-12
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	3e-12
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	3e-12
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	4e-12
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	5e-12
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	6e-12
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	8e-12
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	2e-11
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	2e-11
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	2e-11
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	3e-11
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	3e-11
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	4e-11
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	6e-11
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	7e-11
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	7e-11
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	1e-10
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	2e-10
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	2e-10
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	2e-10
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	2e-10
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	2e-10
cd12550	76	cd12550, RRM_II_PABPN1, RNA recognition motif in t	2e-10
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	3e-10
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	3e-10
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	4e-10
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	4e-10
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	5e-10
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	6e-10
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	7e-10
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	7e-10
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	8e-10
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	1e-09
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	1e-09
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	1e-09
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	2e-09
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	2e-09
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	2e-09
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	2e-09
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	3e-09
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	3e-09
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	4e-09
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	4e-09
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	4e-09
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	4e-09
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	5e-09
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	6e-09
cd12232	89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	6e-09
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	6e-09
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	6e-09
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	6e-09
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	7e-09
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	7e-09
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	7e-09
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	8e-09
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	8e-09
cd12431	80	cd12431, RRM_ALKBH8, RNA recognition motif in alky	1e-08
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	2e-08
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	2e-08
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	2e-08
cd12527	71	cd12527, RRM2_EAR1_like, RNA recognition motif 2 i	2e-08
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	2e-08
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	4e-08
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	4e-08
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	6e-08
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	6e-08
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	7e-08
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	7e-08
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	7e-08
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	7e-08
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	8e-08
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	8e-08
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	8e-08
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	9e-08
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	1e-07
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	1e-07
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	1e-07
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	1e-07
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	2e-07
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	2e-07
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	2e-07
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	2e-07
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	2e-07
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	2e-07
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	2e-07
cd12422	85	cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition m	2e-07
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	3e-07
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	3e-07
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	3e-07
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	4e-07
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	4e-07
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	4e-07
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	4e-07
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	5e-07
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	5e-07
cd12296	71	cd12296, RRM1_Prp24, RNA recognition motif 1 in fu	5e-07
cd12467	78	cd12467, RRM_Srp1p_like, RNA recognition motif 1 i	6e-07
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	7e-07
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	7e-07
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	8e-07
cd12285	85	cd12285, RRM3_RBM39_like, RNA recognition motif 3	1e-06
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	1e-06
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	1e-06
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	1e-06
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	1e-06
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	1e-06
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	2e-06
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	2e-06
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	2e-06
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	2e-06
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	2e-06
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	3e-06
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	4e-06
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	4e-06
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	4e-06
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	4e-06
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	6e-06
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	6e-06
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	6e-06
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	7e-06
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	7e-06
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	7e-06
cd12646	77	cd12646, RRM_SRSF7, RNA recognition motif in verte	8e-06
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	8e-06
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	1e-05
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	1e-05
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	1e-05
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	1e-05
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	1e-05
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	1e-05
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	1e-05
cd12681	69	cd12681, RRM_SKAR, RNA recognition motif in S6K1 A	2e-05
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	2e-05
cd12282	91	cd12282, RRM2_TatSF1_like, RNA recognition motif 2	2e-05
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	2e-05
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	2e-05
cd12645	81	cd12645, RRM_SRSF3, RNA recognition motif in verte	2e-05
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	2e-05
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	2e-05
cd12360	78	cd12360, RRM_cwf2, RNA recognition motif in yeast	2e-05
cd12496	74	cd12496, RRM3_RBM46, RNA recognition motif 3 in ve	2e-05
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	2e-05
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	2e-05
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	3e-05
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	3e-05
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	3e-05
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	3e-05
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	4e-05
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	4e-05
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	4e-05
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	5e-05
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	5e-05
cd12317	72	cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition mot	5e-05
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	6e-05
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	6e-05
cd12342	71	cd12342, RRM_Nab3p, RNA recognition motif in yeast	7e-05
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	7e-05
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	7e-05
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	8e-05
cd12597	73	cd12597, RRM1_SRSF1, RNA recognition motif 1 in se	8e-05
cd12277	86	cd12277, RRM3_MEI2_EAR1_like, RNA recognition moti	8e-05
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	8e-05
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	9e-05
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	9e-05
cd12423	74	cd12423, RRM3_PTBP1_like, RNA recognition motif 3	9e-05
cd12603	71	cd12603, RRM_hnRNPC, RNA recognition motif in vert	1e-04
cd12369	68	cd12369, RRM4_RBM45, RNA recognition motif 4 in RN	1e-04
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	1e-04
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	1e-04
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	1e-04
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	1e-04
cd12587	71	cd12587, RRM1_PSF, RNA recognition motif 1 in vert	1e-04
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	1e-04
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	2e-04
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	2e-04
cd12396	85	cd12396, RRM1_Nop13p_fungi, RNA recognition motif	2e-04
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	2e-04
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	2e-04
smart00361	70	smart00361, RRM_1, RNA recognition motif	2e-04
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	3e-04
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	3e-04
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	3e-04
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	3e-04
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	4e-04
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	4e-04
cd12498	83	cd12498, RRM3_ACF, RNA recognition motif 3 in vert	4e-04
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	4e-04
cd12482	79	cd12482, RRM1_hnRNPR, RNA recognition motif 1 in v	4e-04
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	4e-04
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	5e-04
cd12497	74	cd12497, RRM3_RBM47, RNA recognition motif 3 in ve	6e-04
cd12693	96	cd12693, RRM2_PTBP1_like, RNA recognition motif 2	6e-04
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	6e-04
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	7e-04
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	8e-04
cd12484	78	cd12484, RRM1_RBM46, RNA recognition motif 1 found	8e-04
cd12351	77	cd12351, RRM4_SHARP, RNA recognition motif 4 in SM	8e-04
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	8e-04
cd12533	84	cd12533, RRM_EWS, RNA recognition motif in vertebr	9e-04
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	0.001
cd12534	83	cd12534, RRM_SARFH, RNA recognition motif in Droso	0.001
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	0.001
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	0.001
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	0.001
cd12662	77	cd12662, RRM3_MYEF2, RNA recognition motif 3 in ve	0.001
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	0.001
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	0.002
cd12259	76	cd12259, RRM_SRSF11_SREK1, RNA recognition motif i	0.002
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	0.002
cd12477	89	cd12477, RRM1_U1A, RNA recognition motif 1 found i	0.002
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	0.002
cd12269	69	cd12269, RRM_Vip1_like, RNA recognition motif in a	0.002
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	0.002
cd12349	74	cd12349, RRM2_SHARP, RNA recognition motif 2 in SM	0.002
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	0.003
cd12303	86	cd12303, RRM_spSet1p_like, RNA recognition motif i	0.003
cd12668	98	cd12668, RRM3_RAVER2, RNA recognition motif 3 foun	0.003
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	0.003
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	0.003
cd12304	93	cd12304, RRM_Set1, RNA recognition motif in the Se	0.003
cd12607	67	cd12607, RRM2_RBM4, RNA recognition motif 2 in ver	0.003
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	0.004
cd12625	77	cd12625, RRM1_IGF2BP1, RNA recognition motif 1 in	0.004
cd12536	85	cd12536, RRM1_RBM39, RNA recognition motif 1 in ve	0.004
cd12755	86	cd12755, RRM2_RBM5, RNA recognition motif 2 in ver	0.004
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	0.004
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	0.004

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

 Score =  121 bits (306), Expect = 5e-37
 Identities = 65/73 (89%), Positives = 71/73 (97%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          LKVDNLTYRTTPDDLRRVFE+ GEVGD+YIPRDR+TRESRGFAFVRF+DKRDAEDA+DAM
Sbjct: 1  LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60

Query: 76 DGRMLDGRELRVQ 88
          DG+ LDGRELRVQ
Sbjct: 61 DGKELDGRELRVQ 73

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

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

 Score = 92.3 bits (230), Expect = 2e-25
 Identities = 34/73 (46%), Positives = 51/73 (69%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          +L V NL   TT ++LR +F + G+V  + + RD+ T +S+GFAFV F  + DAE AL+A
Sbjct: 1  TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 75 MDGRMLDGRELRV 87
          ++G+ LDGR L+V
Sbjct: 61 LNGKELDGRPLKV 73

Length = 73

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

 Score = 86.5 bits (215), Expect = 3e-23
 Identities = 36/71 (50%), Positives = 47/71 (66%), Gaps = 1/71 (1%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V NL   TT +DL+ +F + G +  I I RD  T  S+GFAFV F D+ DAE AL+A+
Sbjct: 1  LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRD-ETGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 76 DGRMLDGRELR 86
          +G+ L GRELR
Sbjct: 60 NGKELGGRELR 70

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

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

 Score = 84.3 bits (209), Expect = 2e-22
 Identities = 35/73 (47%), Positives = 49/73 (67%), Gaps = 1/73 (1%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V NL   TT +DLR +F + GE+  + I RD+   +S+GFAFV F    DAE AL+A+
Sbjct: 1  LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK-DGKSKGFAFVEFESPEDAEKALEAL 59

Query: 76 DGRMLDGRELRVQ 88
          +G+ LDGR+L+V 
Sbjct: 60 NGKELDGRKLKVS 72

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

>gnl|CDD|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 = 77.6 bits (192), Expect = 1e-19
 Identities = 29/76 (38%), Positives = 47/76 (61%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V  L+ RTT  +L  +F + G V ++ + +D  T ESRGF FV F    DA+ A+  +
Sbjct: 4  LFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDL 63

Query: 76 DGRMLDGRELRVQMAR 91
          +G+ L+GR ++V+ A+
Sbjct: 64 NGKELEGRVIKVEKAK 79

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

 Score = 77.8 bits (192), Expect = 1e-19
 Identities = 41/80 (51%), Positives = 53/80 (66%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          SL V N+   T PDDLRR+F + G + D+YIP D +TR  RGFA+V+F D RDAEDAL  
Sbjct: 2  SLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYY 61

Query: 75 MDGRMLDGRELRVQMARYGR 94
          +D     GRE+ +Q A+  R
Sbjct: 62 LDRTRFLGREIEIQFAQGDR 81

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

 Score = 73.8 bits (182), Expect = 3e-18
 Identities = 30/76 (39%), Positives = 40/76 (52%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V NL Y  T +DL+ +F + GEV    +  DR T  SRGF FV      +A  A++ +
Sbjct: 2  LYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEKL 61

Query: 76 DGRMLDGRELRVQMAR 91
          +G    GR L V  AR
Sbjct: 62 NGTDFGGRTLTVNEAR 77

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

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

 Score = 72.2 bits (178), Expect = 1e-17
 Identities = 29/73 (39%), Positives = 40/73 (54%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V  LT     D L+ +F   G V D+ +P DR     RG+A+V F    DAE A+  M
Sbjct: 1  LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 76 DGRMLDGRELRVQ 88
          DG  +DG+E+ V+
Sbjct: 61 DGGQIDGQEVTVE 73

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

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

 Score = 71.8 bits (177), Expect = 2e-17
 Identities = 29/77 (37%), Positives = 47/77 (61%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          +++V NL+     DDLR +F   G +  +Y+ +D+ T +SRGFAFV F  + DAE A++ 
Sbjct: 1  TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60

Query: 75 MDGRMLDGRELRVQMAR 91
          ++G   D   L V+ A+
Sbjct: 61 LNGFGYDNLILSVEWAK 77

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

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

 Score = 71.2 bits (175), Expect = 3e-17
 Identities = 30/72 (41%), Positives = 44/72 (61%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V NL + TT ++LR +FE  GE+ ++++P D+ T+ S+GFAFV F     A  A   +
Sbjct: 2  LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 76 DGRMLDGRELRV 87
          DG +  GR L V
Sbjct: 62 DGSIFQGRLLHV 73

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

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

 Score = 71.2 bits (175), Expect = 4e-17
 Identities = 27/76 (35%), Positives = 48/76 (63%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          ++ V NL +  T +DL ++F + G+V  + I +D+ TR+S+G AF+ F D+ DA   + A
Sbjct: 3  TVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKA 62

Query: 75 MDGRMLDGRELRVQMA 90
          ++ + L GR L+  +A
Sbjct: 63 LNNKELFGRTLKCSIA 78

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

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

 Score = 70.0 bits (172), Expect = 8e-17
 Identities = 30/72 (41%), Positives = 45/72 (62%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V NL +  T DDLR +FE  GE+  + + RD  T  S+G+ F++F D  DA+ AL+ +
Sbjct: 1  LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 76 DGRMLDGRELRV 87
          +G  L GR ++V
Sbjct: 61 NGFELAGRPIKV 72

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

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

 Score = 69.6 bits (171), Expect = 1e-16
 Identities = 28/73 (38%), Positives = 46/73 (63%), Gaps = 1/73 (1%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          S+ V N+ Y TTP++L+  F+ CG +  I I  D+FT + +GFA++ F DK   E+AL  
Sbjct: 1  SIFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENAL-L 59

Query: 75 MDGRMLDGRELRV 87
          ++     GR+++V
Sbjct: 60 LNESEFRGRQIKV 72

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

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

 Score = 68.4 bits (168), Expect = 4e-16
 Identities = 31/75 (41%), Positives = 45/75 (60%), Gaps = 4/75 (5%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESR---GFAFVRFFDKRDAEDALDA 74
          V NL ++   DDLR +F + GEV  I IP+ +  ++ R   GFAFV F D   AE+AL  
Sbjct: 5  VRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL-Q 63

Query: 75 MDGRMLDGRELRVQM 89
          ++G  L GR++ V +
Sbjct: 64 LNGTELGGRKISVSL 78

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

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

 Score = 67.4 bits (165), Expect = 1e-15
 Identities = 26/72 (36%), Positives = 44/72 (61%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V NL Y    DDL ++F + GE+ ++++  D+ + +S+GFA+V F D  DA  A   +
Sbjct: 5  LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64

Query: 76 DGRMLDGRELRV 87
          DG++  GR + +
Sbjct: 65 DGKVFQGRLIHI 76

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

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

 Score = 65.6 bits (161), Expect = 4e-15
 Identities = 28/70 (40%), Positives = 45/70 (64%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V NL++ TT + +  +F RCG++  I +  DRFT+   GF FV ++ + DAE+A+  ++G
Sbjct: 3  VGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYLNG 62

Query: 78 RMLDGRELRV 87
            LD R +RV
Sbjct: 63 TKLDDRIIRV 72

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

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

 Score = 64.2 bits (157), Expect = 2e-14
 Identities = 30/73 (41%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V  L Y TT D LR+ F + GE+ +  +  DR T +SRG+ FV F DK  AE A    + 
Sbjct: 5  VGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKDPN- 63

Query: 78 RMLDGRELRVQMA 90
           ++DGR+  V +A
Sbjct: 64 PIIDGRKANVNLA 76

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

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

 Score = 64.2 bits (156), Expect = 2e-14
 Identities = 38/80 (47%), Positives = 53/80 (66%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          SL V N+   T  +DLRR F R G + D+Y+P D +TR  RGFA+V+F D RDAEDAL  
Sbjct: 2  SLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHN 61

Query: 75 MDGRMLDGRELRVQMARYGR 94
          +D + + GR++ +Q A+  R
Sbjct: 62 LDRKWICGRQIEIQFAQGDR 81

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

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

 Score = 63.9 bits (155), Expect = 3e-14
 Identities = 37/80 (46%), Positives = 54/80 (67%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          SL V N+   T P+DLRR F R G + D+Y+P D +TR  RGFA+++F D RDAEDAL  
Sbjct: 2  SLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYN 61

Query: 75 MDGRMLDGRELRVQMARYGR 94
          ++ + + GR++ +Q A+  R
Sbjct: 62 LNRKWVCGRQIEIQFAQGDR 81

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

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

 Score = 63.4 bits (155), Expect = 3e-14
 Identities = 29/75 (38%), Positives = 45/75 (60%), Gaps = 1/75 (1%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V NL ++ T  DL+++F   G V ++ IPR    +  +GFAFV+F  K DAE A+  +
Sbjct: 2  LIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGK-KKGFAFVQFTSKADAEKAIKGV 60

Query: 76 DGRMLDGRELRVQMA 90
          +G+ + GR + V  A
Sbjct: 61 NGKKIKGRPVAVDWA 75

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

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

 Score = 63.0 bits (154), Expect = 4e-14
 Identities = 31/71 (43%), Positives = 39/71 (54%), Gaps = 2/71 (2%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V NL    T +DLR  F   G+V  + + R+      RGFAFV F    DAE AL  +
Sbjct: 1  LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRN--KDRPRGFAFVEFASPEDAEAALKKL 58

Query: 76 DGRMLDGRELR 86
          +G +LDGR LR
Sbjct: 59 NGLVLDGRTLR 69

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

>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 = 63.3 bits (154), Expect = 5e-14
 Identities = 30/75 (40%), Positives = 50/75 (66%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L +  L++ T    L +VF + G++ ++ + +DR T+ SRGF FV F +  DA+DA+ AM
Sbjct: 3  LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62

Query: 76 DGRMLDGRELRVQMA 90
          +G+ +DGR++RV  A
Sbjct: 63 NGKSVDGRQIRVDQA 77

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

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

 Score = 61.9 bits (151), Expect = 1e-13
 Identities = 29/72 (40%), Positives = 37/72 (51%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V  L        L   F   G++ DI IP D  T++ RGFAFV F +  DA  A+D M
Sbjct: 1  LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 76 DGRMLDGRELRV 87
          +   L GR +RV
Sbjct: 61 NESELFGRTIRV 72

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

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

 Score = 61.6 bits (150), Expect = 2e-13
 Identities = 30/75 (40%), Positives = 43/75 (57%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V NL++    + L+  FE+ G V    +  DR T  SRGF +V F    DA+ A++AM
Sbjct: 2  LFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEAM 61

Query: 76 DGRMLDGRELRVQMA 90
          DG+ LDGR + V  +
Sbjct: 62 DGKELDGRPINVDFS 76

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

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

 Score = 61.3 bits (149), Expect = 3e-13
 Identities = 24/72 (33%), Positives = 42/72 (58%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L + NL Y  T +DL ++F + G + ++++P D+ T++ +GFAFV +     A  A   +
Sbjct: 5  LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAEL 64

Query: 76 DGRMLDGRELRV 87
          DG +  GR L +
Sbjct: 65 DGTVFQGRLLHL 76

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

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

 Score = 60.7 bits (148), Expect = 3e-13
 Identities = 30/74 (40%), Positives = 44/74 (59%), Gaps = 1/74 (1%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L+V NL Y  T +DL  +F R GEV  + I  DR +  S G A V F  + DAE A+   
Sbjct: 3  LRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDR-SGRSEGTADVVFEKREDAERAIKQF 61

Query: 76 DGRMLDGRELRVQM 89
          +G +LDG+ ++V++
Sbjct: 62 NGVLLDGQPMQVEL 75

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

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

 Score = 60.3 bits (147), Expect = 4e-13
 Identities = 31/74 (41%), Positives = 44/74 (59%), Gaps = 5/74 (6%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V NL  R T  +L   FE+ G +  +++      R   GFAFV F D RDAEDA+ A+DG
Sbjct: 4  VGNLGPRATKRELEDEFEKYGPLRSVWV-----ARNPPGFAFVEFEDPRDAEDAVRALDG 58

Query: 78 RMLDGRELRVQMAR 91
          R + G  +RV+++R
Sbjct: 59 RRICGNRVRVELSR 72

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

>gnl|CDD|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 60.7 bits (148), Expect = 4e-13
 Identities = 29/77 (37%), Positives = 45/77 (58%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          + +  L Y  T  D+  VF + GE+ DI + RD+ T +S+GFAF+ + D+R    A+D +
Sbjct: 12 IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71

Query: 76 DGRMLDGRELRVQMARY 92
          +G  L GR +RV   R 
Sbjct: 72 NGIKLLGRTIRVDHVRN 88

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

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

 Score = 60.4 bits (147), Expect = 5e-13
 Identities = 31/74 (41%), Positives = 41/74 (55%), Gaps = 2/74 (2%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V NL++    DDL   F+ CGEV D+ I +D   R S+GF  V F  +  A+ AL    G
Sbjct: 4  VGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGR-SKGFGHVEFATEEGAQKAL-EKSG 61

Query: 78 RMLDGRELRVQMAR 91
            L GRE+RV +A 
Sbjct: 62 EELLGREIRVDLAT 75

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

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

 Score = 60.1 bits (146), Expect = 6e-13
 Identities = 26/75 (34%), Positives = 43/75 (57%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V+ L    T ++LR +FE  G +    I RDR T +S G+ FV + D+ DA+ A++ +
Sbjct: 3  LIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTL 62

Query: 76 DGRMLDGRELRVQMA 90
          +G  +  + L+V  A
Sbjct: 63 NGFEIRNKRLKVSYA 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|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 60.1 bits (146), Expect = 7e-13
 Identities = 28/77 (36%), Positives = 42/77 (54%), Gaps = 4/77 (5%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V  L ++TT  DL+  F   GE+  + + +D  T +S+GF FVRF    D ED +  +
Sbjct: 2  LIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRF---ADYEDQVKVL 58

Query: 76 DGR-MLDGRELRVQMAR 91
            R M+DGR   V++  
Sbjct: 59 SQRHMIDGRWCDVKIPN 75

This subfamily corresponds to the RRM1 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 77

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

 Score = 59.3 bits (144), Expect = 1e-12
 Identities = 26/69 (37%), Positives = 41/69 (59%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V +L+     + LR  F   GE+ D  + +D  T +S+G+ FV F  K DAE+A+ +M+G
Sbjct: 4  VGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSMNG 63

Query: 78 RMLDGRELR 86
          + L GR +R
Sbjct: 64 QWLGGRAIR 72

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

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

 Score = 59.6 bits (145), Expect = 1e-12
 Identities = 30/72 (41%), Positives = 42/72 (58%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V  L+  TT  DLR VF R G +  + +  D+ T  SRGF FV F    DA++A + +
Sbjct: 2  LGVFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERL 61

Query: 76 DGRMLDGRELRV 87
          +G  +DGR +RV
Sbjct: 62 NGMEIDGRRIRV 73

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

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

 Score = 58.4 bits (142), Expect = 2e-12
 Identities = 26/76 (34%), Positives = 41/76 (53%), Gaps = 8/76 (10%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V NL   TT + LR +F   GEV  +   +D        +AFV F ++ DA  A++ M
Sbjct: 4  LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVKAMEEM 55

Query: 76 DGRMLDGRELRVQMAR 91
          +G+ L+G  + V +A+
Sbjct: 56 NGKELEGSPIEVSLAK 71

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

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

 Score = 58.8 bits (143), Expect = 2e-12
 Identities = 25/70 (35%), Positives = 42/70 (60%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V NL  + T + L  +F + G V +++IP+DR T+  +G+ FV F  + DA+ A+  M+ 
Sbjct: 3  VGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIMNM 62

Query: 78 RMLDGRELRV 87
            L G+ +RV
Sbjct: 63 IKLYGKPIRV 72

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

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

 Score = 58.7 bits (143), Expect = 3e-12
 Identities = 27/73 (36%), Positives = 40/73 (54%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          SL V +L    T   L  +F   G V  I + RD  TR S G+A+V F +  DAE ALD 
Sbjct: 1  SLYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDT 60

Query: 75 MDGRMLDGRELRV 87
          ++  ++ G+ +R+
Sbjct: 61 LNFDVIKGKPIRI 73

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

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

 Score = 58.8 bits (143), Expect = 3e-12
 Identities = 31/76 (40%), Positives = 43/76 (56%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V  L Y TT   LRR FE  G +  I + RD+ T + RG+AF+ F  +RD + A    
Sbjct: 4  LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYA 63

Query: 76 DGRMLDGRELRVQMAR 91
          DG+ +DGR + V + R
Sbjct: 64 DGKKIDGRRVLVDVER 79

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

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

 Score = 57.9 bits (141), Expect = 4e-12
 Identities = 27/73 (36%), Positives = 38/73 (52%), Gaps = 5/73 (6%)

Query: 20 NLTYRTTPDDLRRVFERCGEVG--DIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA--- 74
           L   TT +D+ +       V   D+ + RD+ T  SRGFAFV F    DA   +DA   
Sbjct: 9  GLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMDALNN 68

Query: 75 MDGRMLDGRELRV 87
          +D  ++DGR +RV
Sbjct: 69 LDPFVIDGRVVRV 81

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

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

 Score = 57.6 bits (140), Expect = 5e-12
 Identities = 28/71 (39%), Positives = 41/71 (57%), Gaps = 1/71 (1%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V NL +    ++LR+ FE CG+V  + I RDR T   +GF +V F  K     AL  ++G
Sbjct: 4  VGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALAL-KLNG 62

Query: 78 RMLDGRELRVQ 88
            L GR++RV+
Sbjct: 63 IKLKGRKIRVK 73

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

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

 Score = 61.5 bits (148), Expect = 6e-12
 Identities = 41/135 (30%), Positives = 67/135 (49%), Gaps = 1/135 (0%)

Query: 15  SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
           +L V NL Y  T +DLR +F++ G V  + + RDR T +SRGFAFV F  +  AE A++ 
Sbjct: 117 TLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEE 176

Query: 75  MDGRMLDGRELRVQMARYGRPP-SSSRSRGGRDRDRRRDRSRSRDRRYTRSRSFSSRSRS 133
           ++G+ L+GR LRVQ A+    P S   +       ++  R ++     + +    +    
Sbjct: 177 LNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLK 236

Query: 134 GSKSPRKARSKSIDR 148
            ++       KS   
Sbjct: 237 TAEEELADLFKSRGD 251

Length = 306

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

 Score = 57.2 bits (139), Expect = 8e-12
 Identities = 24/73 (32%), Positives = 35/73 (47%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V N+ Y  T + L  +F   G V    +  DR T + +G+ F  F D   A  A+  ++G
Sbjct: 3  VGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLNG 62

Query: 78 RMLDGRELRVQMA 90
             +GR LRV  A
Sbjct: 63 YEFNGRALRVDFA 75

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

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

 Score = 56.0 bits (136), Expect = 2e-11
 Identities = 20/61 (32%), Positives = 31/61 (50%), Gaps = 5/61 (8%)

Query: 30 LRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM 89
          L ++F   G V  I     +  ++  GFAFV F  +  AE A+  ++G +  GR LRV  
Sbjct: 1  LYKLFSPFGNVEKI-----KLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 55

Query: 90 A 90
          +
Sbjct: 56 S 56

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

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

 Score = 56.1 bits (136), Expect = 2e-11
 Identities = 27/65 (41%), Positives = 35/65 (53%), Gaps = 4/65 (6%)

Query: 21 LTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA----MD 76
          L++ TT + LR  F + GEV D  I +D  T  SRGF FV F D    +  L A    +D
Sbjct: 6  LSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAKPHVLD 65

Query: 77 GRMLD 81
          GR +D
Sbjct: 66 GREID 70

This subfamily corresponds to the RRM1 in the hnRNP A subfamily which includes hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The hnRNP D subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus, plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this subfamily contain two putative RRMs and a glycine- and tyrosine-rich C-terminus. The family also contains DAZAP1 (Deleted in azoospermia-associated protein 1), RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins. They all harbor two RRMs. . Length = 72

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

 Score = 56.2 bits (135), Expect = 2e-11
 Identities = 26/73 (35%), Positives = 45/73 (61%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V +L+   T +D++  F   G++ D  + +D  T +S+G+ FV F++K DAE+A+  M G
Sbjct: 6  VGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHMGG 65

Query: 78 RMLDGRELRVQMA 90
          + L GR++R   A
Sbjct: 66 QWLGGRQIRTNWA 78

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

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

 Score = 55.6 bits (135), Expect = 3e-11
 Identities = 27/81 (33%), Positives = 42/81 (51%), Gaps = 7/81 (8%)

Query: 15 SLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
          +L ++NL  +   D+L+R    +F + G V DI       T + RG AFV F D   A +
Sbjct: 1  TLYINNLNEKIKKDELKRSLYALFSQFGPVLDIVA---SKTLKMRGQAFVVFKDVESATN 57

Query: 71 ALDAMDGRMLDGRELRVQMAR 91
          AL A+ G     + +R+Q A+
Sbjct: 58 ALRALQGFPFYDKPMRIQYAK 78

This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding. . Length = 78

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

 Score = 55.7 bits (135), Expect = 3e-11
 Identities = 20/70 (28%), Positives = 39/70 (55%), Gaps = 6/70 (8%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V NL +  T ++L+R F   G + ++ + +D+      G+AFVRF     A  A+ A++G
Sbjct: 5  VGNLPHGLTEEELQRTFSPFGAIEEVRVFKDK------GYAFVRFDTHEAAATAIVAVNG 58

Query: 78 RMLDGRELRV 87
            ++G+ ++ 
Sbjct: 59 TSINGQTVKC 68

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

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

 Score = 55.5 bits (133), Expect = 4e-11
 Identities = 28/73 (38%), Positives = 44/73 (60%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V +L+   T DD++  F   G + D  + +D  T +S+G+ FV FF+K DAE+A+  M G
Sbjct: 6  VGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGG 65

Query: 78 RMLDGRELRVQMA 90
          + L GR++R   A
Sbjct: 66 QWLGGRQIRTNWA 78

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

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

 Score = 54.9 bits (133), Expect = 6e-11
 Identities = 27/80 (33%), Positives = 44/80 (55%), Gaps = 5/80 (6%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDR-----FTRESRGFAFVRFFDKRDAE 69
          +L V NL ++TT + L++ FE+CG V  + I + +         S G+ FV F  K  A+
Sbjct: 2  TLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQ 61

Query: 70 DALDAMDGRMLDGRELRVQM 89
           AL  + G +LDG  L +++
Sbjct: 62 KALKRLQGTVLDGHALELKL 81

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

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

 Score = 54.9 bits (133), Expect = 7e-11
 Identities = 20/52 (38%), Positives = 36/52 (69%)

Query: 26 TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          T +D+R +FE  G + ++ I RD+ T +S+G AFV+F  + +A+ A++A+ G
Sbjct: 12 TEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEALHG 63

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

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

 Score = 56.6 bits (136), Expect = 7e-11
 Identities = 36/89 (40%), Positives = 48/89 (53%), Gaps = 2/89 (2%)

Query: 16  LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
           L +  L++ T    LR  F   G+V D  +  DR T  SRGF FV F D+  A  A+  M
Sbjct: 37  LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEM 96

Query: 76  DGRMLDGRELRVQMARYGRPPSSSRSRGG 104
           DG+ L+GR +RV  A     PS+ R+ GG
Sbjct: 97  DGKELNGRHIRVNPAN--DRPSAPRAYGG 123

Length = 144

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

 Score = 53.8 bits (130), Expect = 1e-10
 Identities = 27/75 (36%), Positives = 45/75 (60%), Gaps = 1/75 (1%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V N+ +  T  +LR +F   G+V  + +P+ +F    RGFAFV F  K++A++A++A+
Sbjct: 3  LIVRNVPFEATKKELRELFSPFGQVKSVRLPK-KFDGSHRGFAFVEFVTKQEAQNAMEAL 61

Query: 76 DGRMLDGRELRVQMA 90
              L GR L ++ A
Sbjct: 62 KSTHLYGRHLVLEYA 76

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

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

 Score = 53.9 bits (130), Expect = 2e-10
 Identities = 27/68 (39%), Positives = 43/68 (63%), Gaps = 2/68 (2%)

Query: 25 TTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRML--DG 82
           T DDLR  F   GE+ DI++ +D+ T+ES+G A+V+F     A  A++ M+G+ L  D 
Sbjct: 14 VTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLGGDT 73

Query: 83 RELRVQMA 90
          + L+V +A
Sbjct: 74 KPLKVLIA 81

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

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

 Score = 53.8 bits (130), Expect = 2e-10
 Identities = 23/74 (31%), Positives = 40/74 (54%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V NL Y TT + L   F   G +   ++ +D+ +++ RGF +V F  + DA+ AL+    
Sbjct: 4  VRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEKKK 63

Query: 78 RMLDGRELRVQMAR 91
              GR++ V+ A+
Sbjct: 64 TKFGGRKIHVEFAK 77

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

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

 Score = 54.1 bits (131), Expect = 2e-10
 Identities = 21/87 (24%), Positives = 48/87 (55%), Gaps = 2/87 (2%)

Query: 10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAE 69
          +EG + + V  +      +D+   F   GE+ ++++  DR T   +G+A + +  K++A+
Sbjct: 4  VEGWI-IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQ 62

Query: 70 DALDAMDGRMLDGRELRVQMARYGRPP 96
           A++ ++G+ L G+ + V  A + + P
Sbjct: 63 AAIEGLNGKELLGQTISVDWA-FVKGP 88

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

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

 Score = 53.5 bits (129), Expect = 2e-10
 Identities = 18/58 (31%), Positives = 31/58 (53%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          V+ L    T + L+ VF + G V  + +PR + T + +GFAF+ F    +A+ A   +
Sbjct: 4  VECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61

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

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

 Score = 53.8 bits (130), Expect = 2e-10
 Identities = 29/78 (37%), Positives = 43/78 (55%), Gaps = 5/78 (6%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA--- 74
          + NL +  T ++L+ +F + GEV    I +D+ T  S+G AFV+F  K  A+  L+A   
Sbjct: 5  IRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAADN 64

Query: 75 --MDGRMLDGRELRVQMA 90
              G  LDGR L V +A
Sbjct: 65 AEDSGLSLDGRRLIVTLA 82

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

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

 Score = 53.7 bits (129), Expect = 2e-10
 Identities = 27/77 (35%), Positives = 42/77 (54%), Gaps = 1/77 (1%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          S+ V N+ Y  T ++L   F  CG V  + I  D+F+   +GFA++ F DK     AL A
Sbjct: 1  SVYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTAL-A 59

Query: 75 MDGRMLDGRELRVQMAR 91
          +D  +  GR+++V   R
Sbjct: 60 LDESLFRGRQIKVMPKR 76

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

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

 Score = 53.3 bits (129), Expect = 3e-10
 Identities = 19/70 (27%), Positives = 40/70 (57%), Gaps = 1/70 (1%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V NL      + L+ +F + G++    + +D    +S+GF FV F +   A+ A++ ++G
Sbjct: 6  VKNLGEDMDDEKLKELFGKYGKITSAKVMKDD-EGKSKGFGFVNFENHEAAQKAVEELNG 64

Query: 78 RMLDGRELRV 87
          + ++G++L V
Sbjct: 65 KEVNGKKLYV 74

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

 Score = 53.0 bits (128), Expect = 3e-10
 Identities = 20/60 (33%), Positives = 34/60 (56%)

Query: 29 DLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ 88
          DL ++F   G V    +  D+ T +S+ F FV + +   A+ A+ AM+G  + G+ L+VQ
Sbjct: 14 DLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAMNGFQVGGKRLKVQ 73

This subgroup corresponds to the RRM3 of the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) proteins, a family of structurally related RNA-binding proteins involved in the regulation of pre-mRNA splicing in the nucleus and in the control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also termed BRUNOL-2, or CUG-BP1, or NAPOR, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6 (also termed BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. . Length = 73

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

 Score = 52.7 bits (127), Expect = 4e-10
 Identities = 24/72 (33%), Positives = 41/72 (56%), Gaps = 6/72 (8%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V NL    T ++ + +F + GEV ++++ +++      GF F+R   + +AE A   +
Sbjct: 4  LFVGNLPNDITEEEFKELFSKYGEVSEVFLNKEK------GFGFIRLDTRTNAEKAKAEL 57

Query: 76 DGRMLDGRELRV 87
          DG M  GR+LRV
Sbjct: 58 DGIMRKGRQLRV 69

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

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

 Score = 52.7 bits (127), Expect = 4e-10
 Identities = 23/63 (36%), Positives = 36/63 (57%)

Query: 25 TTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRE 84
          TT +DL  +F R G++    + RD+ T +S  +AF+ F  K D E+A   MD  ++D R 
Sbjct: 15 TTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKMDNVLIDDRR 74

Query: 85 LRV 87
          + V
Sbjct: 75 IHV 77

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

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

 Score = 52.7 bits (127), Expect = 5e-10
 Identities = 25/74 (33%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          +L V NL  R T + L  +F + G +  + IP+D   +  + FAFV F  +     A+  
Sbjct: 3  TLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGK-PKSFAFVTFKHEVSVPYAIQL 61

Query: 75 MDGRMLDGRELRVQ 88
          ++G  L GRELR++
Sbjct: 62 LNGIRLFGRELRIK 75

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

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

 Score = 52.4 bits (126), Expect = 6e-10
 Identities = 24/72 (33%), Positives = 38/72 (52%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V NL++    D +   F   GE+  + +P D  +   +GF +V F  +  A+ ALDA+
Sbjct: 1  LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 76 DGRMLDGRELRV 87
           G  L GR +R+
Sbjct: 61 GGTDLLGRPVRL 72

This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues. . Length = 73

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

 Score = 52.1 bits (125), Expect = 7e-10
 Identities = 26/73 (35%), Positives = 44/73 (60%), Gaps = 1/73 (1%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V NL +  T  D+R +F   G++  + +P+ +F + +RGFAFV F   ++A +A++A+  
Sbjct: 5  VKNLPFEATKKDVRTLFSSYGQLKSVRVPK-KFDQSARGFAFVEFSTAKEALNAMNALKD 63

Query: 78 RMLDGRELRVQMA 90
            L GR L +Q A
Sbjct: 64 THLLGRRLVLQYA 76

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

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

 Score = 51.9 bits (125), Expect = 7e-10
 Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 5/73 (6%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V N+      ++LR +FE+ G++  +Y        + RGF  V ++D R A  A  A+
Sbjct: 4  LFVRNINSNVEDEELRALFEQFGDIRTLY-----TACKHRGFIMVSYYDIRAARRAKRAL 58

Query: 76 DGRMLDGRELRVQ 88
           G  L GR+L + 
Sbjct: 59 QGTELGGRKLDIH 71

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

>gnl|CDD|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7), and similar proteins

 Score = 51.9 bits (125), Expect = 8e-10
 Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 2/75 (2%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCG--EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
          L V NLT+ TT +DL       G  +V  I     +   +S+GFA+V F  +  A    +
Sbjct: 1  LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60

Query: 74 AMDGRMLDGRELRVQ 88
           ++GR  +G++  V 
Sbjct: 61 KLEGREFNGKKCVVT 75

This subfamily corresponds to the RRM of cleavage factor Im (CFIm) subunits. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. Structurally related CFIm68 and CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59), are functionally redundant. Both contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. Their N-terminal RRM mediates the interaction with CFIm25, and also serves to enhance RNA binding and facilitate RNA looping. . Length = 76

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

 Score = 51.8 bits (124), Expect = 1e-09
 Identities = 26/75 (34%), Positives = 41/75 (54%), Gaps = 1/75 (1%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V NL  R T D L+++F+  G V ++ I  D+   +   + FV +    DAE AL  +
Sbjct: 1  LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDK-NNKGVNYGFVEYHQSHDAEIALQTL 59

Query: 76 DGRMLDGRELRVQMA 90
          +GR ++  E+RV  A
Sbjct: 60 NGRQIENNEIRVNWA 74

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

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

 Score = 51.5 bits (124), Expect = 1e-09
 Identities = 22/66 (33%), Positives = 42/66 (63%), Gaps = 2/66 (3%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V NL Y    D+LR++F +CGE+ D+ + ++   + S+G+A+V F ++   ++AL  +D 
Sbjct: 4  VSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGK-SKGYAYVEFENEESVQEAL-KLDR 61

Query: 78 RMLDGR 83
           ++ GR
Sbjct: 62 ELIKGR 67

This subfamily corresponds to the RRM1 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 72

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

 Score = 52.0 bits (124), Expect = 1e-09
 Identities = 33/75 (44%), Positives = 46/75 (61%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V  L+  TT  DLR VF + G + D+ I  D+ +R SRGFAFV F +  DA++A +  
Sbjct: 12 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 71

Query: 76 DGRMLDGRELRVQMA 90
          +G  LDGR +RV  +
Sbjct: 72 NGMELDGRRIRVDFS 86

This subgroup corresponds to the RRM of TRA2-beta or TRA-2-beta, also termed splicing factor, arginine/serine-rich 10 (SFRS10), or transformer-2 protein homolog B, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. It contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. TRA2-beta specifically binds to two types of RNA sequences, the CAA and (GAA)2 sequences, through the RRMs in different RNA binding modes. . Length = 89

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

 Score = 51.3 bits (122), Expect = 2e-09
 Identities = 25/77 (32%), Positives = 45/77 (58%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          +L V+ L    T ++L+ +F   GE+    + RD+ T +S G+ FV + D +DAE A++ 
Sbjct: 6  NLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 65

Query: 75 MDGRMLDGRELRVQMAR 91
          ++G  L  + ++V  AR
Sbjct: 66 LNGLRLQTKTIKVSYAR 82

This subgroup corresponds to the RRM1 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads and is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 83

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

 Score = 54.6 bits (131), Expect = 2e-09
 Identities = 29/93 (31%), Positives = 50/93 (53%), Gaps = 4/93 (4%)

Query: 11  EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
           E   +L V+ L    T +++R +F   GE+    + RD+ T +S G+ FV +    DAE 
Sbjct: 1   ESKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEK 60

Query: 71  ALDAMDGRMLDGRELRVQMARYGRPPSSSRSRG 103
           A+++++G  L  + ++V  AR    PSS   +G
Sbjct: 61  AVNSLNGLRLQNKTIKVSYAR----PSSDSIKG 89

This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076). Length = 352

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

 Score = 50.9 bits (122), Expect = 2e-09
 Identities = 25/75 (33%), Positives = 42/75 (56%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V+ L    T D++R +F   GE+    + RD+ T +S G+ FV + D  DAE A++ +
Sbjct: 4  LIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTL 63

Query: 76 DGRMLDGRELRVQMA 90
          +G  L  + ++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|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen D (HuD)

 Score = 51.3 bits (122), Expect = 2e-09
 Identities = 27/83 (32%), Positives = 46/83 (55%), Gaps = 3/83 (3%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          +L V+ L    T ++ R +F   GE+    + RD+ T +S G+ FV + D +DAE A++ 
Sbjct: 4  NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 75 MDGRMLDGRELRVQMARYGRPPS 97
          ++G  L  + ++V    Y RP S
Sbjct: 64 LNGLRLQTKTIKVS---YARPSS 83

This subgroup corresponds to the RRM1 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells, as well as the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 83

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

 Score = 50.4 bits (121), Expect = 3e-09
 Identities = 24/71 (33%), Positives = 36/71 (50%), Gaps = 1/71 (1%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V NL Y TT +DL   F+  G    + +  D+ T +S+G AFV F        AL  +  
Sbjct: 5  VGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALK-LHH 63

Query: 78 RMLDGRELRVQ 88
           +L GR++ V+
Sbjct: 64 TLLKGRKINVE 74

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

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

 Score = 49.9 bits (120), Expect = 3e-09
 Identities = 22/71 (30%), Positives = 39/71 (54%), Gaps = 8/71 (11%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V NL   TT ++LR +FE+ G V +  + ++        + FV   ++ DAEDA+ A++G
Sbjct: 4  VGNLPDATTSEELRALFEKYGTVTECDVVKN--------YGFVHMEEEEDAEDAIKALNG 55

Query: 78 RMLDGRELRVQ 88
              G+ + V+
Sbjct: 56 YEFMGKRINVE 66

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

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

 Score = 54.0 bits (130), Expect = 4e-09
 Identities = 31/77 (40%), Positives = 41/77 (53%), Gaps = 1/77 (1%)

Query: 14  VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
           V+L V NL    T + LR +F  CGE+    +  D     SRGF FV F +  +A  A+ 
Sbjct: 286 VNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDE-KGVSRGFGFVCFSNPEEANRAVT 344

Query: 74  AMDGRMLDGRELRVQMA 90
            M GRML G+ L V +A
Sbjct: 345 EMHGRMLGGKPLYVALA 361

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

 Score = 50.2 bits (120), Expect = 4e-09
 Identities = 23/73 (31%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          S+ V N+ Y +T ++L   F  CG +  + I  D+F+   +G+A++  F  RD+ +A  A
Sbjct: 1  SVYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIE-FATRDSVEAAVA 59

Query: 75 MDGRMLDGRELRV 87
          +D     GR ++V
Sbjct: 60 LDESSFRGRVIKV 72

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

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

 Score = 49.9 bits (120), Expect = 4e-09
 Identities = 26/71 (36%), Positives = 40/71 (56%), Gaps = 1/71 (1%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V  L+ +    DL   F + G+V D+ I RDR +R S+G A+V F+D+     AL  + G
Sbjct: 4  VMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL-GLTG 62

Query: 78 RMLDGRELRVQ 88
          + L G+ + VQ
Sbjct: 63 QRLLGQPIMVQ 73

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

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

 Score = 53.7 bits (129), Expect = 4e-09
 Identities = 32/96 (33%), Positives = 54/96 (56%)

Query: 7   PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKR 66
           P  I   + L V NL +  T  +LR++FE  G++ D+ + RD  T  S+GF F++F D  
Sbjct: 180 PGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAE 239

Query: 67  DAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSR 102
           +A++AL+ M+G  L GR ++V  A+       + + 
Sbjct: 240 EAKEALEVMNGFELAGRPIKVGYAQDSTYLLDAANT 275

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

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

 Score = 50.3 bits (121), Expect = 5e-09
 Identities = 28/75 (37%), Positives = 41/75 (54%), Gaps = 3/75 (4%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYI--PRDRFTR-ESRGFAFVRFFDKRDAEDAL 72
          L V NL  + T + L + F R G +  + I  PR    R  +R   FV F ++ DAE AL
Sbjct: 4  LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERAL 63

Query: 73 DAMDGRMLDGRELRV 87
          D +DG+ + G EL++
Sbjct: 64 DELDGKDVMGYELKL 78

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

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

 Score = 49.6 bits (119), Expect = 6e-09
 Identities = 26/74 (35%), Positives = 36/74 (48%), Gaps = 7/74 (9%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V  LT   T +DLR+ F + GEV D+YIP+       R FAFV F D   A+      + 
Sbjct: 5  VGRLTEDMTEEDLRQYFSQFGEVTDVYIPKP-----FRAFAFVTFADPEVAQSLCG--ED 57

Query: 78 RMLDGRELRVQMAR 91
           ++ G  + V  A 
Sbjct: 58 HIIKGVSVHVSNAE 71

This subfamily corresponds to the RRM2 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 71

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

 Score = 49.9 bits (120), Expect = 6e-09
 Identities = 25/86 (29%), Positives = 38/86 (44%), Gaps = 7/86 (8%)

Query: 9  RIEGMVS---LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPR---DRFTRESRGFAFVRF 62
           +  MV+   L+ D   Y    +D++    + G+V  + IPR   +       G  FV F
Sbjct: 5  CLLNMVTPEELEDDE-EYEEILEDVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEF 63

Query: 63 FDKRDAEDALDAMDGRMLDGRELRVQ 88
           D  DA+ A  A+ GR  DGR +   
Sbjct: 64 ADVEDAQKAQLALAGRKFDGRTVVAS 89

This subfamily corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 89

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

 Score = 49.7 bits (119), Expect = 6e-09
 Identities = 24/60 (40%), Positives = 31/60 (51%), Gaps = 1/60 (1%)

Query: 28 DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV 87
            L   F  CGE+  + IP DR T  S+GFA++ F      E AL+ +DG  L G  L V
Sbjct: 18 RSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKALE-LDGSDLGGGNLVV 76

This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 49.9 bits (120), Expect = 6e-09
 Identities = 20/54 (37%), Positives = 36/54 (66%), Gaps = 3/54 (5%)

Query: 30 LRRVFERCG--EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLD 81
          LR++F + G  ++  IY+P D  T +++G+AFV F    +A++A+ A++G  LD
Sbjct: 24 LRKIFSKFGVGKIVGIYMPVDE-TGKTKGYAFVEFATPEEAKEAVKALNGYKLD 76

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

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

 Score = 49.5 bits (119), Expect = 6e-09
 Identities = 18/62 (29%), Positives = 33/62 (53%)

Query: 27 PDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR 86
            +LR+ F + G V  + + R + T +S+G+AFV F     A+   + M+  +L  R L+
Sbjct: 13 EPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETMNNYLLFERLLK 72

Query: 87 VQ 88
           +
Sbjct: 73 CK 74

This subgroup corresponds to the RRM of NIFK and Nop15p. NIFK, also termed MKI67 FHA domain-interacting nucleolar phosphoprotein, or nucleolar phosphoprotein Nopp34, is a putative RNA-binding protein interacting with the forkhead associated (FHA) domain of pKi-67 antigen in a mitosis-specific and phosphorylation-dependent manner. It is nucleolar in interphase but associates with condensed mitotic chromosomes. This family also includes Saccharomyces cerevisiae YNL110C gene encoding ribosome biogenesis protein 15 (Nop15p), also termed nucleolar protein 15. Both, NIFK and Nop15p, contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 74

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

 Score = 49.6 bits (119), Expect = 7e-09
 Identities = 27/72 (37%), Positives = 37/72 (51%), Gaps = 5/72 (6%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEV--GDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          V NL +  T  DL+ +F  CG V   D+    D     S+GF  V F    DA+ A++  
Sbjct: 3  VRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGR---SKGFGTVLFESPEDAQRAIEMF 59

Query: 76 DGRMLDGRELRV 87
          +G  L+GREL V
Sbjct: 60 NGYDLEGRELEV 71

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

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

 Score = 49.4 bits (118), Expect = 7e-09
 Identities = 23/65 (35%), Positives = 36/65 (55%), Gaps = 4/65 (6%)

Query: 21 LTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA----MD 76
          L+++TT + LR  F + GE+ +  + RD  T+ SRGF FV F D    +  L      +D
Sbjct: 6  LSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQGPHELD 65

Query: 77 GRMLD 81
          G+ +D
Sbjct: 66 GKKID 70

This subfamily corresponds to the RRM1 in Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 75

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

 Score = 49.3 bits (118), Expect = 7e-09
 Identities = 18/60 (30%), Positives = 35/60 (58%), Gaps = 4/60 (6%)

Query: 29 DLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ 88
          D++R+FE CG V  + +     +R  +  AF+ F +   A+ A++ ++G  +DG  ++VQ
Sbjct: 15 DVKRLFETCGPVRKVTML----SRTVQPHAFITFENLEAAQLAIETLNGASVDGNCIKVQ 70

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

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

 Score = 49.4 bits (118), Expect = 8e-09
 Identities = 28/68 (41%), Positives = 37/68 (54%), Gaps = 4/68 (5%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA--- 74
          V  L++ TT + LRR F + GEV D  I +D+ T  SRGF FV+F D       L     
Sbjct: 4  VGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAGGPH 63

Query: 75 -MDGRMLD 81
           +DGR +D
Sbjct: 64 TLDGRTID 71

This subfamily corresponds to the RRM1 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated form is predominantly nuclear and the nonacetylated form is in cytoplasm. It also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain. . Length = 82

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

 Score = 49.2 bits (118), Expect = 8e-09
 Identities = 25/75 (33%), Positives = 40/75 (53%), Gaps = 3/75 (4%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V NL    T D L  +F + G +    + R+     +  +AFV ++D R A  AL  M
Sbjct: 1  LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREH---GNDPYAFVEYYDHRSAAAALQTM 57

Query: 76 DGRMLDGRELRVQMA 90
          +GR++ G+E++V  A
Sbjct: 58 NGRLILGQEIKVNWA 72

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

>gnl|CDD|240877 cd12431, RRM_ALKBH8, RNA recognition motif in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins

 Score = 48.8 bits (117), Expect = 1e-08
 Identities = 18/56 (32%), Positives = 31/56 (55%), Gaps = 6/56 (10%)

Query: 26 TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLD 81
          + ++L RVFE+ G V D+ +P  +       + FV +    DA  A DA++G+ L+
Sbjct: 16 SREELLRVFEKYGTVEDLVMPPGK------PYCFVSYSSIEDAAAAYDALNGKELE 65

This subfamily corresponds to the RRM of ALKBH8, also termed alpha-ketoglutarate-dependent dioxygenase ABH8, or S-adenosyl-L-methionine-dependent tRNA methyltransferase ABH8, expressed in various types of human cancers. It is essential in urothelial carcinoma cell survival mediated by NOX-1-dependent ROS signals. ALKBH8 has also been identified as a tRNA methyltransferase that catalyzes methylation of tRNA to yield 5-methylcarboxymethyl uridine (mcm5U) at the wobble position of the anticodon loop. Thus, ALKBH8 plays a crucial role in the DNA damage survival pathway through a distinct mechanism involving the regulation of tRNA modification. ALKBH8 localizes to the cytoplasm. It contains the characteristic AlkB domain that is composed of a tRNA methyltransferase motif, a motif homologous to the bacterial AlkB DNA/RNA repair enzyme, and a dioxygenase catalytic core domain encompassing cofactor-binding sites for iron and 2-oxoglutarate. In addition, unlike other AlkB homologs, ALKBH8 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal S-adenosylmethionine (SAM)-dependent methyltransferase (MT) domain. . Length = 80

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

 Score = 48.7 bits (116), Expect = 2e-08
 Identities = 27/76 (35%), Positives = 39/76 (51%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          +L V NL +  T +DL   F     +    +  D  T ESRG+ FV F    DA++AL  
Sbjct: 1  TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK 60

Query: 75 MDGRMLDGRELRVQMA 90
          +  + L GR LR+ +A
Sbjct: 61 LKNKKLHGRILRLDIA 76

This subgroup corresponds to the RRM1 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate nucleolin

 Score = 48.4 bits (115), Expect = 2e-08
 Identities = 25/74 (33%), Positives = 44/74 (59%), Gaps = 5/74 (6%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V+NL+Y  + D L+ VFE+      I IP++      +G+AFV F    DA++AL++ 
Sbjct: 4  LVVNNLSYSASEDSLQEVFEK---ATSIRIPQNN--GRPKGYAFVEFESAEDAKEALNSC 58

Query: 76 DGRMLDGRELRVQM 89
          +   ++GR +R++ 
Sbjct: 59 NNTEIEGRSIRLEF 72

This subfamily corresponds to the RRM3 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 72

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

 Score = 48.8 bits (117), Expect = 2e-08
 Identities = 27/73 (36%), Positives = 42/73 (57%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          +L V  L+ +TT + LR VF R G++  + + RD  T  S+G+AFV +  +RDA  A   
Sbjct: 5  TLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRD 64

Query: 75 MDGRMLDGRELRV 87
              ++DG E+ V
Sbjct: 65 AHKLVIDGSEIFV 77

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

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

 Score = 47.9 bits (114), Expect = 2e-08
 Identities = 25/74 (33%), Positives = 41/74 (55%), Gaps = 5/74 (6%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          +L + NL    + + LR +F+  G+V ++     R T   R   FV FFD RDA  AL A
Sbjct: 3  TLVIFNLDPTVSSETLRSIFQVYGDVKEL-----RETPCKREQRFVEFFDVRDAAKALRA 57

Query: 75 MDGRMLDGRELRVQ 88
          M+G+ + G+ + ++
Sbjct: 58 MNGKEISGKPVVIE 71

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

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

 Score = 48.0 bits (115), Expect = 2e-08
 Identities = 20/70 (28%), Positives = 35/70 (50%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          +L + +L        +   F  CGEV  + I R++ T +S G+ FV F     AE AL +
Sbjct: 1  TLWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQS 60

Query: 75 MDGRMLDGRE 84
          ++G+ +   +
Sbjct: 61 LNGKPIPNTQ 70

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

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

 Score = 47.4 bits (113), Expect = 4e-08
 Identities = 22/68 (32%), Positives = 33/68 (48%), Gaps = 8/68 (11%)

Query: 24 RTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGR 83
           T  +D+ ++FE  G +    I +         FAFV F D  DA  AL+A+ G  +DG 
Sbjct: 11 TTREEDIEKLFEPFGPLVRCDIRKT--------FAFVEFEDSEDATKALEALHGSRIDGS 62

Query: 84 ELRVQMAR 91
           L V+  +
Sbjct: 63 VLTVEFVK 70

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

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

 Score = 47.6 bits (114), Expect = 4e-08
 Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 2/76 (2%)

Query: 16 LKVDNLTYRTTPDDLRRVFERC-GEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          L V NL    T  +L+  F +  GE+ D+ + R    + SR  AF+ +  + +A+ A D 
Sbjct: 3  LIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGK-SRRIAFIGYKTEEEAQKAKDY 61

Query: 75 MDGRMLDGRELRVQMA 90
           +   ++  ++ V+ A
Sbjct: 62 FNNTYINTSKISVEFA 77

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

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

 Score = 47.0 bits (112), Expect = 6e-08
 Identities = 26/70 (37%), Positives = 41/70 (58%), Gaps = 1/70 (1%)

Query: 21 LTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRML 80
          L+Y TT D L+  F + GE+ D  + +D  T+ SRGF FV F    + + A++A   + +
Sbjct: 7  LSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNARPHK-V 65

Query: 81 DGRELRVQMA 90
          DGRE+  + A
Sbjct: 66 DGREVEPKRA 75

This subfamily corresponds to the RRM1 in hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 78

>gnl|CDD|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate nucleolin

 Score = 47.1 bits (112), Expect = 6e-08
 Identities = 27/73 (36%), Positives = 41/73 (56%), Gaps = 4/73 (5%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          +L V NL Y  T D+L+ VFE   +  DI +P  +    S+G A++ F  + +AE AL+ 
Sbjct: 5  TLFVKNLPYNITVDELKEVFE---DAVDIRLPSGK-DGSSKGIAYIEFKTEAEAEKALEE 60

Query: 75 MDGRMLDGRELRV 87
            G  +DGR + V
Sbjct: 61 KQGAEVDGRSIVV 73

This subfamily corresponds to the RRM2 of ubiquitously expressed protein nucleolin, also termed protein C23, a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.RRM2, together with RRM1, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 77

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

 Score = 46.8 bits (112), Expect = 7e-08
 Identities = 26/77 (33%), Positives = 38/77 (49%), Gaps = 1/77 (1%)

Query: 14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
          V+L V NL      + LR  F   G +    +  D   R S+GF FV F    +A  A+ 
Sbjct: 2  VNLYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGR-SKGFGFVCFSSPEEATKAVT 60

Query: 74 AMDGRMLDGRELRVQMA 90
           M+GR++ G+ L V +A
Sbjct: 61 EMNGRIIGGKPLYVALA 77

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|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen C (HuC)

 Score = 47.0 bits (111), Expect = 7e-08
 Identities = 25/83 (30%), Positives = 45/83 (54%), Gaps = 3/83 (3%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          +L V+ L    T ++ + +F   GE+    + RD+ T +S G+ FV + D  DA+ A++ 
Sbjct: 5  NLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINT 64

Query: 75 MDGRMLDGRELRVQMARYGRPPS 97
          ++G  L  + ++V    Y RP S
Sbjct: 65 LNGLKLQTKTIKVS---YARPSS 84

This subgroup corresponds to the RRM1 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 84

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

 Score = 47.0 bits (111), Expect = 7e-08
 Identities = 26/77 (33%), Positives = 43/77 (55%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          +L V+ L    T D+LR +F   GEV    + RD+    S G+ FV + + +DAE A++ 
Sbjct: 3  NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINT 62

Query: 75 MDGRMLDGRELRVQMAR 91
          ++G  L  + ++V  AR
Sbjct: 63 LNGLRLQSKTIKVSYAR 79

This subgroup corresponds to the RRM1 of HuR, also termed ELAV-like protein 1 (ELAV-1), a ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response; it binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. Meanwhile, HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

>gnl|CDD|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast nucleolar protein 12 (Nop12p) and similar proteins

 Score = 46.8 bits (111), Expect = 7e-08
 Identities = 27/76 (35%), Positives = 39/76 (51%), Gaps = 2/76 (2%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDA--LDAM 75
          V NL +    + L RVF +CG +  + I RD  T   +GFA+V+F D+   E A  L+  
Sbjct: 4  VGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKALLLNEK 63

Query: 76 DGRMLDGRELRVQMAR 91
              +  RELRV   +
Sbjct: 64 KFPPMLPRELRVSRCK 79

This subgroup corresponds to the RRM2 of Nop12p, which is encoded by YOL041C from Saccharomyces cerevisiae. It is a novel nucleolar protein required for pre-25S rRNA processing and normal rates of cell growth at low temperatures. Nop12p shares high sequence similarity with nucleolar protein 13 (Nop13p). Both, Nop12p and Nop13p, are not essential for growth. However, unlike Nop13p that localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent, Nop12p is localized to the nucleolus. Nop12p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 46.7 bits (111), Expect = 8e-08
 Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 8/77 (10%)

Query: 14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
          V + V N+   T+ ++LR +FE  G V    + R         FAFV    +  A+ A++
Sbjct: 1  VKIFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQ--------FAFVHLRGEAAADRAIE 52

Query: 74 AMDGRMLDGRELRVQMA 90
           ++GR L GR+L V+ +
Sbjct: 53 ELNGRELHGRKLVVEHS 69

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

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

 Score = 46.7 bits (111), Expect = 8e-08
 Identities = 22/70 (31%), Positives = 35/70 (50%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V +L+   T   L   F       D  +  D  +  SRG+ FV F  ++DAE+A++ M+G
Sbjct: 4  VGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEMNG 63

Query: 78 RMLDGRELRV 87
          + L  R +R 
Sbjct: 64 KWLGSRPIRC 73

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

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

 Score = 46.6 bits (111), Expect = 8e-08
 Identities = 26/75 (34%), Positives = 44/75 (58%), Gaps = 2/75 (2%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V N+ +R    DLR++F + G + D+ I  +   R S+GF FV F +  DA+ A + +
Sbjct: 3  LHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNE--RGSKGFGFVTFANSADADRAREKL 60

Query: 76 DGRMLDGRELRVQMA 90
           G +++GR++ V  A
Sbjct: 61 HGTVVEGRKIEVNNA 75

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

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

 Score = 46.9 bits (111), Expect = 9e-08
 Identities = 31/72 (43%), Positives = 43/72 (59%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V  L+  TT  DLR VF R G +  + +  D+ T  SRGFAFV F    D+++A++  
Sbjct: 2  LGVFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHA 61

Query: 76 DGRMLDGRELRV 87
          +G  LDGR +RV
Sbjct: 62 NGMELDGRRIRV 73

This subgroup corresponds to the RRM of TRA2-alpha or TRA-2-alpha, also termed transformer-2 protein homolog A, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein (SRp40) that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-alpha contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. . Length = 79

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

 Score = 46.4 bits (111), Expect = 1e-07
 Identities = 18/63 (28%), Positives = 34/63 (53%), Gaps = 6/63 (9%)

Query: 27 PDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR 86
           D+L  +FE+ G + ++ +  D F+  +RG+AFV + +K  A+ A+     + L   E+R
Sbjct: 15 EDELVPLFEKAGPIYELRLMMD-FSGLNRGYAFVTYTNKEAAQRAV-----KQLHNYEIR 68

Query: 87 VQM 89
             
Sbjct: 69 PGK 71

This subfamily corresponds to the RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs); DND1 harbors only two RRMs. . Length = 78

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

 Score = 46.5 bits (111), Expect = 1e-07
 Identities = 24/82 (29%), Positives = 41/82 (50%), Gaps = 9/82 (10%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTR------ESRGFAFVRFFDKRDAE 69
          L + NL  R T   L ++F + G++         F +      + RG+ FV F  K +AE
Sbjct: 2  LWIGNLDSRLTEFHLLKLFSKYGKIKKFDF---LFHKSGPLKGQPRGYCFVTFETKEEAE 58

Query: 70 DALDAMDGRMLDGRELRVQMAR 91
           AL +++G+   G++L V+ A 
Sbjct: 59 KALKSLNGKTALGKKLVVRWAH 80

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

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

 Score = 46.2 bits (110), Expect = 1e-07
 Identities = 25/70 (35%), Positives = 40/70 (57%), Gaps = 2/70 (2%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          + NL +  T DD+R  F+ C E+  + +  D+ T E +GF  V F D+   + AL  +DG
Sbjct: 4  IGNLAWDITEDDVREFFKGC-EITSVRLATDKETGEFKGFGHVDFADEESLDAAL-KLDG 61

Query: 78 RMLDGRELRV 87
           +L GR +R+
Sbjct: 62 TVLCGRPIRI 71

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

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

 Score = 46.1 bits (110), Expect = 1e-07
 Identities = 23/73 (31%), Positives = 36/73 (49%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V NL    T +  R +    G V   ++     T ES+G+ FV +  K  A  A + +
Sbjct: 2  LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61

Query: 76 DGRMLDGRELRVQ 88
          DG+ + GR+L+V 
Sbjct: 62 DGKQIGGRKLQVD 74

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

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

 Score = 45.8 bits (109), Expect = 2e-07
 Identities = 21/71 (29%), Positives = 34/71 (47%), Gaps = 6/71 (8%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V  L    T D+LR +F   GE+  + IP        +G  FV+F  +  AE A+  + G
Sbjct: 6  VGGLDPAVTEDELRSLFGPFGEIVYVKIP------PGKGCGFVQFVHRAAAEAAIQQLQG 59

Query: 78 RMLDGRELRVQ 88
           ++ G  +R+ 
Sbjct: 60 TIIGGSRIRLS 70

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

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

 Score = 45.8 bits (109), Expect = 2e-07
 Identities = 25/74 (33%), Positives = 38/74 (51%), Gaps = 8/74 (10%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          +  L YR    D+ R F+  G + +I +          GF FV F D RDA+DA+  ++G
Sbjct: 4  IGRLPYRARERDVERFFKGYGRIREINL--------KNGFGFVEFEDPRDADDAVYELNG 55

Query: 78 RMLDGRELRVQMAR 91
          + L G  + V+ AR
Sbjct: 56 KELCGERVIVEHAR 69

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

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

 Score = 46.0 bits (109), Expect = 2e-07
 Identities = 24/75 (32%), Positives = 44/75 (58%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          +L V NL  + T D+LR++FE  G +    + RD+ T   RG AFVR+  + +A+ A+ +
Sbjct: 2  NLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISS 61

Query: 75 MDGRMLDGRELRVQM 89
          ++G +  G  + + +
Sbjct: 62 LNGTIPPGSTMPLSV 76

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

 Score = 45.9 bits (109), Expect = 2e-07
 Identities = 20/81 (24%), Positives = 43/81 (53%), Gaps = 4/81 (4%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V  L +  T ++L ++F++ G V  + +  +R + + +G A+V + ++  A  A+  M
Sbjct: 5  LFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNR-SGKPKGLAYVEYENESSASQAVLKM 63

Query: 76 DGRMLDGRELRVQMARYGRPP 96
          DG  +  + + V ++    PP
Sbjct: 64 DGTEIKEKTISVAIS---NPP 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|240973 cd12529, RRM2_MEI2_like, RNA recognition motif 2 in plant Mei2-like proteins

 Score = 45.6 bits (108), Expect = 2e-07
 Identities = 24/74 (32%), Positives = 40/74 (54%), Gaps = 5/74 (6%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          +L V NL    + DDL ++F   GE+ +I     R T   R   F+ F+D R AE AL A
Sbjct: 3  TLVVFNLDPSVSNDDLHQIFGAYGEIKEI-----RETPNKRHHKFIEFYDVRSAEAALKA 57

Query: 75 MDGRMLDGRELRVQ 88
          ++   + G+ ++++
Sbjct: 58 LNRSEIAGKRIKLE 71

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

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

 Score = 45.6 bits (108), Expect = 2e-07
 Identities = 24/76 (31%), Positives = 42/76 (55%), Gaps = 1/76 (1%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
           L V  L  +T+   LRR F R G++ +  +  D  T+ SRGF F+ F    +A++A++A
Sbjct: 4  KLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAMEA 63

Query: 75 MDGRMLDGRELRVQMA 90
               +DG ++ ++ A
Sbjct: 64 Q-PHSIDGNQIELKRA 78

This subfamily corresponds to the RRM1 of hnRNP A0 which is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 79

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

 Score = 45.6 bits (108), Expect = 2e-07
 Identities = 25/64 (39%), Positives = 38/64 (59%), Gaps = 1/64 (1%)

Query: 27 PDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR 86
          P  L+++F R G+V +  IPR R  +   GFAFV    +++AE AL+  +G  +DGR + 
Sbjct: 15 PVKLKKIFGRYGKVREATIPRKRGGKLC-GFAFVTMKKRKNAEIALENTNGLEIDGRPVA 73

Query: 87 VQMA 90
          V  A
Sbjct: 74 VDWA 77

This subgroup corresponds to the RRM2 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 83

>gnl|CDD|240868 cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition motif in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins

 Score = 45.6 bits (109), Expect = 2e-07
 Identities = 25/76 (32%), Positives = 36/76 (47%), Gaps = 6/76 (7%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          + NL Y  T D L +VF   G V  I I    F + +   A V+F     AE+A  A++G
Sbjct: 6  ISNLLYPVTVDVLHQVFSPYGAVEKILI----FEKNTGVQALVQFDSVESAENAKKALNG 61

Query: 78 RML--DGRELRVQMAR 91
          R +      L +Q +R
Sbjct: 62 RNIYDGCCTLDIQFSR 77

This subfamily corresponds to the RRM2 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins, and RRM3 of PTBPH1 and PTBPH2. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. This family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs. . Length = 85

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

 Score = 48.5 bits (115), Expect = 3e-07
 Identities = 28/83 (33%), Positives = 46/83 (55%), Gaps = 5/83 (6%)

Query: 13  MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDAL 72
           M  + V ++++    D +RR F+  G +  I +  D  T + +GFAFV +     A+ AL
Sbjct: 107 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLAL 166

Query: 73  DAMDGRMLDGRELRVQMARYGRP 95
           + M+G+ML GR ++V     GRP
Sbjct: 167 EQMNGQMLGGRNIKV-----GRP 184

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

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

 Score = 45.1 bits (107), Expect = 3e-07
 Identities = 27/73 (36%), Positives = 42/73 (57%), Gaps = 3/73 (4%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V NL++ TT D+LR  F R G +  + +     + + +GFAFV F    + E A +A+ G
Sbjct: 3  VGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDF---EEIEFATNALKG 59

Query: 78 RMLDGRELRVQMA 90
          + L+GR LRV+  
Sbjct: 60 KHLNGRALRVEYG 72

This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

>gnl|CDD|241075 cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif 1 in CUGBP Elav-like family member CELF-1, CELF-2, Drosophila melanogaster Bruno protein and similar proteins

 Score = 45.2 bits (107), Expect = 3e-07
 Identities = 23/65 (35%), Positives = 36/65 (55%), Gaps = 3/65 (4%)

Query: 28 DDLRRVFERCGEVGDIYIPRDRFT--RESRGFAFVRFFDKRDAEDALDAMDG-RMLDGRE 84
           DLR +FE+ G V  I + RDR     +S+G  FV F+ ++ A +A +A+   + L G  
Sbjct: 16 KDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKTLPGMH 75

Query: 85 LRVQM 89
            +QM
Sbjct: 76 HPIQM 80

This subgroup corresponds to the RRM1 of CELF-1, CELF-2 and Bruno protein. CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR) belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in regulation of pre-mRNA splicing, and control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. The human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. This subgroup also includes Drosophila melanogaster Bruno protein, which plays a central role in regulation of Oskar (Osk) expression in flies. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 84

>gnl|CDD|241115 cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins

 Score = 45.2 bits (107), Expect = 4e-07
 Identities = 24/73 (32%), Positives = 39/73 (53%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V N+ Y  T + L+ +F   G V    +  DR T + +G+ F  + D+  A  A+  ++G
Sbjct: 3  VGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNLNG 62

Query: 78 RMLDGRELRVQMA 90
            L+GR+LRV  A
Sbjct: 63 YELNGRQLRVDNA 75

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

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

 Score = 44.9 bits (106), Expect = 4e-07
 Identities = 29/68 (42%), Positives = 36/68 (52%), Gaps = 4/68 (5%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD---- 73
          V  L++ TT  DL+  F + GEV D  I  D  T  SRGF FV F D    E  LD    
Sbjct: 3  VGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQKEH 62

Query: 74 AMDGRMLD 81
           +DGR++D
Sbjct: 63 KLDGRVID 70

This subfamily corresponds to the RRM1 in hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 74

>gnl|CDD|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins

 Score = 44.9 bits (107), Expect = 4e-07
 Identities = 25/74 (33%), Positives = 40/74 (54%), Gaps = 3/74 (4%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V NL ++ + ++L  +F + G +  I   R   T+E+RG AFV + D  DA++A D +
Sbjct: 5  LYVRNLPFKISSEELYDLFGKYGAIRQI---RIGNTKETRGTAFVVYEDIYDAKNACDHL 61

Query: 76 DGRMLDGRELRVQM 89
           G  +  R L V  
Sbjct: 62 SGFNVANRYLVVLY 75

This subfamily corresponds to the RRM of SF3B14 (also termed p14), a 14 kDa protein subunit of SF3B which is a multiprotein complex that is an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA and has been involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B14 associates directly with another SF3B subunit called SF3B155. It is also present in both U2- and U12-dependent spliceosomes and may contribute to branch site positioning in both the major and minor spliceosome. Moreover, SF3B14 interacts directly with the pre-mRNA branch adenosine early in spliceosome assembly and within the fully assembled spliceosome. SF3B14 contains one well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 77

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

 Score = 44.7 bits (106), Expect = 4e-07
 Identities = 27/72 (37%), Positives = 35/72 (48%), Gaps = 3/72 (4%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V NL       D+  +F + G +  I +   +  R    FAFV F D RDAEDA+   DG
Sbjct: 4  VGNLPGDIRERDIEDLFYKYGPIKAIDL---KNRRRGPPFAFVEFEDPRDAEDAVRGRDG 60

Query: 78 RMLDGRELRVQM 89
             DG  LRV+ 
Sbjct: 61 YDFDGYRLRVEF 72

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

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

 Score = 44.6 bits (106), Expect = 5e-07
 Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 8/75 (10%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDI-YIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD 76
          + +L+ + T +DL+ +FE  GE+  I  IP        RG A+V    ++DA  AL  + 
Sbjct: 7  IGHLSKKVTEEDLKNLFEEYGEIQSIDMIP-------PRGCAYVCMETRQDAHRALQKLR 59

Query: 77 GRMLDGRELRVQMAR 91
             L G++++V  A 
Sbjct: 60 NVKLAGKKIKVAWAP 74

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

 Score = 44.7 bits (106), Expect = 5e-07
 Identities = 20/66 (30%), Positives = 34/66 (51%), Gaps = 1/66 (1%)

Query: 25 TTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRE 84
           T ++ +  F + G+V D  + +D  T  SRGF FV  FD   A + + +     L G++
Sbjct: 11 VTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVT-FDSESAVERVFSAGMLELGGKQ 69

Query: 85 LRVQMA 90
          + V+ A
Sbjct: 70 VEVKRA 75

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

>gnl|CDD|240742 cd12296, RRM1_Prp24, RNA recognition motif 1 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 44.5 bits (106), Expect = 5e-07
 Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 9/76 (11%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          ++KV NL   TT + +R+ F+ CGE+ ++ I       E    A + F      ++AL A
Sbjct: 2  TVKVKNLPKDTTENKIRQFFKDCGEIREVKIVES----EGGLVAVIEF---ETEDEALAA 54

Query: 75 M--DGRMLDGRELRVQ 88
          +  D + L G E+ V 
Sbjct: 55 LTKDHKRLGGNEISVS 70

This subfamily corresponds to the RRM1 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 71

>gnl|CDD|240913 cd12467, RRM_Srp1p_like, RNA recognition motif 1 in fission yeast pre-mRNA-splicing factor Srp1p and similar proteins

 Score = 44.4 bits (105), Expect = 6e-07
 Identities = 29/65 (44%), Positives = 34/65 (52%), Gaps = 3/65 (4%)

Query: 29 DLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRE--LR 86
          DL   FER G +    IP  R T +SR FAFV +   RDAEDA + M GR        L 
Sbjct: 15 DLAYEFERYGRLVRCDIPPPR-TFQSRPFAFVEYESHRDAEDAYEEMHGRRFPDTGDTLH 73

Query: 87 VQMAR 91
          VQ A+
Sbjct: 74 VQWAK 78

This subgroup corresponds to the RRM domain in Srp1p encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but not essential for growth. Srp1p is closely related to the SR protein family found in metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. Some family members also contain another RRM domain. Length = 78

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

 Score = 44.2 bits (105), Expect = 7e-07
 Identities = 19/62 (30%), Positives = 38/62 (61%)

Query: 26 TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGREL 85
          + DD++ VFE  G++    +  D  T + +G+ F+ + + + A+DA+ +M+   L G++L
Sbjct: 13 SEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASMNLFDLGGQQL 72

Query: 86 RV 87
          RV
Sbjct: 73 RV 74

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

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

 Score = 44.1 bits (104), Expect = 7e-07
 Identities = 21/72 (29%), Positives = 39/72 (54%), Gaps = 8/72 (11%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V N++   T D+LR +FE  G V +    +D        +AFV    + +A  A++A++G
Sbjct: 5  VGNVSATCTSDELRGLFEEFGRVVECDKVKD--------YAFVHMEREEEALAAIEALNG 56

Query: 78 RMLDGRELRVQM 89
          + + GR + V++
Sbjct: 57 KEVKGRRINVEL 68

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

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

 Score = 44.5 bits (105), Expect = 8e-07
 Identities = 24/62 (38%), Positives = 36/62 (58%), Gaps = 1/62 (1%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V  L  + T  ++  VF   G V DIY+ RD   ++SRG AFV++  K  A+ A+ A+
Sbjct: 2  LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEM-KQSRGCAFVKYSSKEMAQAAIKAL 60

Query: 76 DG 77
          +G
Sbjct: 61 NG 62

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

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

 Score = 44.1 bits (105), Expect = 1e-06
 Identities = 13/53 (24%), Positives = 23/53 (43%), Gaps = 4/53 (7%)

Query: 35 ERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV 87
           + G V  I +          G  +V+F     A+  + A++GR  DGR++  
Sbjct: 33 SKFGPVEHIKV----DKNSPEGVVYVKFKTVEAAQKCIQALNGRWFDGRQITA 81

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

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

 Score = 43.7 bits (104), Expect = 1e-06
 Identities = 20/73 (27%), Positives = 31/73 (42%), Gaps = 3/73 (4%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCG-EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          +++  L +  T +D+R  F         I+I  D   R + G A+V F    DA  AL  
Sbjct: 2  VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPT-GEAYVEFASPEDARRAL-R 59

Query: 75 MDGRMLDGRELRV 87
               + GR + V
Sbjct: 60 KHNNKMGGRYIEV 72

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

>gnl|CDD|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 43.5 bits (103), Expect = 1e-06
 Identities = 25/71 (35%), Positives = 40/71 (56%), Gaps = 1/71 (1%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V  + Y +T D++R  F  CGE+ ++ +     T   RG AF+ F  +  A+ AL A+DG
Sbjct: 3  VGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRAL-ALDG 61

Query: 78 RMLDGRELRVQ 88
            + GR L+V+
Sbjct: 62 EDMGGRFLKVE 72

This subfamily corresponds to the RRM1 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

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

 Score = 43.8 bits (104), Expect = 1e-06
 Identities = 21/70 (30%), Positives = 36/70 (51%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V NL        L ++F   G V ++ + RD  T + +G+ FV   +  +A  A+ +++G
Sbjct: 6  VYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIASLNG 65

Query: 78 RMLDGRELRV 87
            L GR L+V
Sbjct: 66 YRLGGRVLQV 75

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

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

 Score = 43.6 bits (103), Expect = 1e-06
 Identities = 16/60 (26%), Positives = 34/60 (56%)

Query: 29 DLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ 88
          +L++ F + G V ++ + R + T  S+ + F++F +   A  A  +M+  +L G+ L+V 
Sbjct: 15 ELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSMNNYLLMGKVLQVH 74

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

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

 Score = 43.5 bits (103), Expect = 1e-06
 Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 4/75 (5%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDI-YIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
          S+ V  L+   T ++L   F R G++ ++  I R      +  FAF++F  ++ A  A++
Sbjct: 5  SIFVGQLSPDVTKEELNERFSRHGKILEVNLIKR---ANHTNAFAFIKFEREQAAARAVE 61

Query: 74 AMDGRMLDGRELRVQ 88
          + +  ML  + + VQ
Sbjct: 62 SENHSMLKNKTMHVQ 76

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

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

 Score = 43.4 bits (103), Expect = 2e-06
 Identities = 27/73 (36%), Positives = 37/73 (50%), Gaps = 2/73 (2%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V  +   TT ++LR  F R G V D+ I  DR    S+G+ FV F  + DAE  L AM  
Sbjct: 7  VGGIPPDTTEEELRDFFSRFGSVKDVKIITDR-AGVSKGYGFVTFETQEDAEKIL-AMGN 64

Query: 78 RMLDGRELRVQMA 90
              G++L +  A
Sbjct: 65 LNFRGKKLNIGPA 77

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

>gnl|CDD|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR and similar proteins

 Score = 43.2 bits (101), Expect = 2e-06
 Identities = 26/86 (30%), Positives = 45/86 (52%), Gaps = 5/86 (5%)

Query: 15  SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
           +L V NL+   T   + ++F + G      +  +  + +   + FV F++ RDA  AL A
Sbjct: 1   TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAAALAA 58

Query: 75  MDGRMLDGRELRVQMARYGRPPSSSR 100
           M+GR + G+E++V  A     PSS +
Sbjct: 59  MNGRKILGKEVKVNWA---TTPSSQK 81

This subgroup corresponds to the RRM1 of nucleolysin TIAR, also termed TIA-1-related protein, and a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 81

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

 Score = 43.4 bits (103), Expect = 2e-06
 Identities = 20/49 (40%), Positives = 29/49 (59%), Gaps = 4/49 (8%)

Query: 45 IPRDRFTRESRGFAFVRF--FDKRDAEDALDAMDGRMLDGRELRVQMAR 91
          I RD  T  S+GFAF+ +  F+  DA  A++AM+G+ L  R + V  A 
Sbjct: 34 IMRDPDTGNSKGFAFISYDSFEASDA--AIEAMNGQYLCNRPITVSYAF 80

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

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

 Score = 43.1 bits (102), Expect = 2e-06
 Identities = 26/73 (35%), Positives = 40/73 (54%), Gaps = 2/73 (2%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V NL + T   DL  +F+    V  + + RD+ T + +GF +V F D    ++AL+  DG
Sbjct: 6  VGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVESLKEALE-YDG 63

Query: 78 RMLDGRELRVQMA 90
           + D R LRV +A
Sbjct: 64 ALFDDRSLRVDIA 76

This subfamily corresponds to the RRM of eIF-4H, also termed Williams-Beuren syndrome chromosomal region 1 protein, which, together with elf-4B/eIF-4G, serves as the accessory protein of RNA helicase eIF-4A. eIF-4H contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It stimulates protein synthesis by enhancing the helicase activity of eIF-4A in the initiation step of mRNA translation. . Length = 76

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

 Score = 43.0 bits (102), Expect = 2e-06
 Identities = 25/62 (40%), Positives = 34/62 (54%), Gaps = 7/62 (11%)

Query: 28 DDLRRVFERCGEVGDI-YIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR 86
           +LR +F + GEV DI   P     +      FV F+D R AE ALDA++GR   G  L+
Sbjct: 16 QELRSLFSQFGEVKDIRETPLRPSQK------FVEFYDIRAAEAALDALNGRPFLGGRLK 69

Query: 87 VQ 88
          V+
Sbjct: 70 VK 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|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 42.8 bits (101), Expect = 3e-06
 Identities = 14/48 (29%), Positives = 29/48 (60%)

Query: 28 DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
           DLR +FE+ G++ ++ + +D++T   +G AF+ +  +  A  A  A+
Sbjct: 20 KDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQSAL 67

This subfamily corresponds to the RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In additiona to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 87

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

 Score = 45.2 bits (107), Expect = 4e-06
 Identities = 31/87 (35%), Positives = 47/87 (54%), Gaps = 2/87 (2%)

Query: 15  SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
           SL V +L    T   L  +F+  G V  + + RD  TR S G+ +V F +  DAE AL+ 
Sbjct: 2   SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALET 61

Query: 75  MDGRMLDGRELRVQMARYGRPPSSSRS 101
           M+ + L G+ +R+  ++  R PS  RS
Sbjct: 62  MNFKRLGGKPIRIMWSQ--RDPSLRRS 86

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

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

 Score = 42.4 bits (99), Expect = 4e-06
 Identities = 21/55 (38%), Positives = 32/55 (58%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDAL 72
          +  L+++T+PD LR  F + GE+ +  + RD  T+ SRGF FV F D    +  L
Sbjct: 4  IGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVL 58

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 76

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

 Score = 42.3 bits (100), Expect = 4e-06
 Identities = 25/68 (36%), Positives = 33/68 (48%), Gaps = 2/68 (2%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRD-AEDALDA 74
          L V  L    T  +L  +F   G +    I  D  T  SRG  F+R FDKR  AE A+ A
Sbjct: 3  LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIR-FDKRIEAERAIKA 61

Query: 75 MDGRMLDG 82
          ++G +  G
Sbjct: 62 LNGTIPPG 69

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

>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 42.4 bits (100), Expect = 4e-06
 Identities = 26/75 (34%), Positives = 39/75 (52%), Gaps = 2/75 (2%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRES-RGFAFVRFFDKRDAEDALDAM- 75
          V N+ +  T  +LR +F   GE+  + +P+      S RGF FV F  K+DA+ A  A+ 
Sbjct: 5  VRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFKALC 64

Query: 76 DGRMLDGRELRVQMA 90
              L GR L ++ A
Sbjct: 65 HSTHLYGRRLVLEWA 79

This subgroup corresponds to the RRM6 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 41.9 bits (98), Expect = 6e-06
 Identities = 25/73 (34%), Positives = 40/73 (54%), Gaps = 1/73 (1%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          +  L+++TT + LR  F + GEV +  + RD  T+ SRGF FV F D+   +  L A   
Sbjct: 5  IGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQSR 63

Query: 78 RMLDGRELRVQMA 90
            LD + +  ++A
Sbjct: 64 HELDSKTIDPKVA 76

This subgroup corresponds to the RRM1 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). Musashi-1 has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, it represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 77

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

 Score = 41.8 bits (99), Expect = 6e-06
 Identities = 10/35 (28%), Positives = 22/35 (62%)

Query: 53 ESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV 87
           S+G+ FV F  +  A  A++ ++G +L+ +++ V
Sbjct: 41 GSKGYGFVHFETEEAAVRAIEKVNGMLLNDKKVFV 75

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

>gnl|CDD|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 41.4 bits (97), Expect = 6e-06
 Identities = 26/73 (35%), Positives = 43/73 (58%), Gaps = 6/73 (8%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V NL    T +++R++FE+ G+ G+I+I +D      +GF F+R   +  AE A   +
Sbjct: 4  LFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKD------KGFGFIRLETRTLAEIAKAEL 57

Query: 76 DGRMLDGRELRVQ 88
          D   L G++LRV+
Sbjct: 58 DNMPLRGKQLRVR 70

This subgroup corresponds to the RRM1 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. p54nrb binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. It forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manneras well as with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

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

 Score = 44.4 bits (105), Expect = 7e-06
 Identities = 33/114 (28%), Positives = 53/114 (46%), Gaps = 14/114 (12%)

Query: 16  LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
           L V NL      D LR +F + GE+    + +D  +  SRGFAFV F    DA  A++ M
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDG-SGRSRGFAFVNFEKHEDAAKAVEEM 239

Query: 76  DGRMLD----GRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRDRRYTRSR 125
           +G+ +     G++L V  A         + R  R+ + RR     +  R  +++
Sbjct: 240 NGKKIGLAKEGKKLYVGRA---------QKRAEREAELRRKFEELQQERKMKAQ 284

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|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 41.8 bits (98), Expect = 7e-06
 Identities = 28/83 (33%), Positives = 37/83 (44%), Gaps = 5/83 (6%)

Query: 14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYI-----PRDRFTRESRGFAFVRFFDKRDA 68
           +L V NL + TT   L   F+         +     P+      S GF FV F  K  A
Sbjct: 1  ATLFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQA 60

Query: 69 EDALDAMDGRMLDGRELRVQMAR 91
          + AL AMDG +LDG  L V+ + 
Sbjct: 61 QAALKAMDGFVLDGHTLVVKFSH 83

This subfamily corresponds to the RRM4 of MRD1which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 84

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

 Score = 41.6 bits (98), Expect = 7e-06
 Identities = 23/70 (32%), Positives = 39/70 (55%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V ++++    D +R+ F   G +  I +  D  T + +GFAFV +     A+ AL+ M+G
Sbjct: 5  VGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQMNG 64

Query: 78 RMLDGRELRV 87
           ML GR ++V
Sbjct: 65 VMLGGRNIKV 74

This subfamily corresponds to the RRM1 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition. . Length = 76

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

 Score = 41.5 bits (97), Expect = 8e-06
 Identities = 27/73 (36%), Positives = 41/73 (56%), Gaps = 5/73 (6%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V NL       +L R F   G +  ++I R+       GFAFV F D RDAEDA+  +DG
Sbjct: 4  VGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDG 58

Query: 78 RMLDGRELRVQMA 90
          +++ G  +RV+++
Sbjct: 59 KVICGSRVRVELS 71

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

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

 Score = 41.4 bits (97), Expect = 8e-06
 Identities = 23/64 (35%), Positives = 34/64 (53%), Gaps = 3/64 (4%)

Query: 21 LTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA---MDG 77
          L + TT D LR  F + GEV D  + RD  T  SRGF F+ F   +   + +     +DG
Sbjct: 6  LNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKEHILDG 65

Query: 78 RMLD 81
          +++D
Sbjct: 66 KIID 69

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

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

 Score = 41.1 bits (96), Expect = 1e-05
 Identities = 27/68 (39%), Positives = 36/68 (52%), Gaps = 1/68 (1%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V  L++ T+  DL+  F + GEV D  I  D  T  SRGF F+ F D    E  L+  + 
Sbjct: 4  VGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQKEH 63

Query: 78 RMLDGREL 85
          R LDGR +
Sbjct: 64 R-LDGRLI 70

This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 75

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

 Score = 41.5 bits (97), Expect = 1e-05
 Identities = 22/68 (32%), Positives = 38/68 (55%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          +L V  L    T  +L ++F + G +    I RD+ T  SRG  F+RF  + +AE+A+  
Sbjct: 2  NLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKG 61

Query: 75 MDGRMLDG 82
          ++G+  +G
Sbjct: 62 LNGQKPEG 69

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

>gnl|CDD|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 43.9 bits (103), Expect = 1e-05
 Identities = 28/82 (34%), Positives = 44/82 (53%)

Query: 1   MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
           +SY RP        +L V NL    T D L  +F + G++    I RD+ T   RG AFV
Sbjct: 181 VSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFV 240

Query: 61  RFFDKRDAEDALDAMDGRMLDG 82
           RF  + +A++A+ A++  + +G
Sbjct: 241 RFNKREEAQEAISALNNVIPEG 262

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661). Length = 346

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

 Score = 40.8 bits (96), Expect = 1e-05
 Identities = 23/68 (33%), Positives = 36/68 (52%)

Query: 26 TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGREL 85
          T ++ R +F   G V +  I RD+ T  S GF FV +    DA+ A+  ++G  L  + +
Sbjct: 13 TDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNGLQLQNKRI 72

Query: 86 RVQMARYG 93
          +V  AR G
Sbjct: 73 KVAYARPG 80

This subfamily corresponds to the RRM1 of SXL which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 81

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

 Score = 40.9 bits (96), Expect = 1e-05
 Identities = 22/69 (31%), Positives = 31/69 (44%), Gaps = 6/69 (8%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V N+   TT  DL  +F+  G + +     DR      GFAFV+      A  A+  + G
Sbjct: 5  VGNIPPYTTQADLIPLFQNFGYILEFRHQPDR------GFAFVKLDTHEQAAMAIVQLQG 58

Query: 78 RMLDGRELR 86
            + GR LR
Sbjct: 59 FPVHGRPLR 67

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

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

 Score = 40.7 bits (96), Expect = 1e-05
 Identities = 27/73 (36%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V NL    T D LR  FE  GEV D+ + R R   +SR F FV F  + DA+ A+   + 
Sbjct: 5  VKNLPKYVTEDRLREHFESKGEVTDVKVMRTR-DGKSRRFGFVGFKSEEDAQQAVKYFNK 63

Query: 78 RMLDGRELRVQMA 90
            +D  ++ V++A
Sbjct: 64 TFIDTSKISVELA 76

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

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

 Score = 40.8 bits (96), Expect = 1e-05
 Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 8/73 (10%)

Query: 16 LKVDNLTYRTTPDDLRRVF-ERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          L + NL+      DLR++F E    V  + + +        G+AFV   D+  A+ A++ 
Sbjct: 1  LYIGNLSSDVNESDLRQLFEEHKIPVSSVLVKK-------GGYAFVDCPDQSWADKAIEK 53

Query: 75 MDGRMLDGRELRV 87
          ++G++L G+ + V
Sbjct: 54 LNGKILQGKVIEV 66

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

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

 Score = 40.3 bits (95), Expect = 2e-05
 Identities = 21/74 (28%), Positives = 32/74 (43%), Gaps = 7/74 (9%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V NL    T DD+  +F   G +               G A V +  K DA  A+D  
Sbjct: 3  LVVSNLHPSVTEDDIVELFSAIGALKRA-------RLVRPGVAEVVYVRKDDALTAIDKY 55

Query: 76 DGRMLDGRELRVQM 89
          + R LDG+ ++ ++
Sbjct: 56 NNRELDGQPMKCKL 69

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

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

 Score = 40.4 bits (95), Expect = 2e-05
 Identities = 18/56 (32%), Positives = 31/56 (55%), Gaps = 4/56 (7%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
          V  L+  TT + +R  F + G + +I +P D+ T + RGF F+ F    D+E+ + 
Sbjct: 4  VGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITF----DSEEPVK 55

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

>gnl|CDD|240728 cd12282, RRM2_TatSF1_like, RNA recognition motif 2 in HIV Tat-specific factor 1 (Tat-SF1) and similar proteins

 Score = 40.7 bits (96), Expect = 2e-05
 Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 4/61 (6%)

Query: 28 DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV 87
          DDLR   E+ G+V  + +    F R   G A V+F +  +A+  ++A++GR   GR+L  
Sbjct: 27 DDLREECEKFGQVKKVVV----FDRHPDGVASVKFKEPEEADRCIEALNGRWFAGRQLEA 82

Query: 88 Q 88
          +
Sbjct: 83 E 83

This subfamily corresponds to the RRM2 of Tat-SF1 and CUS2. Tat-SF1 is the cofactor for stimulation of transcriptional elongation by human immunodeficiency virus-type 1 (HIV-1) Tat. It is a substrate of an associated cellular kinase. Tat-SF1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a highly acidic carboxyl-terminal half. The family also includes CUS2, a yeast homolog of human Tat-SF1. CUS2 interacts with U2 RNA in splicing extracts and functions as a splicing factor that aids assembly of the splicing-competent U2 snRNP in vivo. CUS2 also associates with PRP11 that is a subunit of the conserved splicing factor SF3a. Like Tat-SF1, CUS2 contains two RRMs as well. . Length = 91

>gnl|CDD|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 40.4 bits (94), Expect = 2e-05
 Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 2/76 (2%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          +L V NL+   T   + ++F + G      +  D  T  +  + FV FF+ R A  +L A
Sbjct: 1  TLYVGNLSRDVTEALILQLFSQIGPCKSCKMIMD--TAGNDPYCFVEFFEHRHAAASLAA 58

Query: 75 MDGRMLDGRELRVQMA 90
          M+GR + G+E++V  A
Sbjct: 59 MNGRKIMGKEVKVNWA 74

This subgroup corresponds to the RRM1 of TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and functions as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 74

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

 Score = 40.3 bits (95), Expect = 2e-05
 Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V NL +  + DD++ +F   G +    +  DR  R S G A V F  + DA  A+   
Sbjct: 3  LLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRSGR-SLGTADVVFERRADALKAMKQY 61

Query: 76 DGRMLDGRELRVQM 89
          +G  LDGR +++Q+
Sbjct: 62 NGVPLDGRPMKIQL 75

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

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

 Score = 40.4 bits (94), Expect = 2e-05
 Identities = 27/73 (36%), Positives = 39/73 (53%), Gaps = 5/73 (6%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V NL       +L R F   G +  +++ R+       GFAFV F D RDA DA+  +DG
Sbjct: 9  VGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDG 63

Query: 78 RMLDGRELRVQMA 90
          R L G  +RV+++
Sbjct: 64 RTLCGCRVRVELS 76

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

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

 Score = 43.0 bits (101), Expect = 2e-05
 Identities = 31/97 (31%), Positives = 39/97 (40%), Gaps = 4/97 (4%)

Query: 66  RDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDR-SRSRDRRYTRS 124
           RD E   +    R  D      +  R  R  S  R R  R R+R     SR RDRR   S
Sbjct: 1   RDEEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDS 60

Query: 125 RSFSSRSRSG---SKSPRKARSKSIDRDNKHERNGRS 158
           RS  S   S    S+   + RS+S+    +H R  R 
Sbjct: 61  RSPRSLRYSSVRRSRDRPRRRSRSVRSIEQHRRRLRD 97

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

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

 Score = 40.4 bits (95), Expect = 2e-05
 Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V NL Y+     L+ VF+  G+V    I  D+   +SRG   V+F    +A  A+   +G
Sbjct: 3  VANLDYKVGWKKLKEVFKLAGKVVRADIKEDK-EGKSRGMGVVQFEHPIEAVQAISMFNG 61

Query: 78 RMLDGRELRVQM 89
          +ML  R +RV+M
Sbjct: 62 QMLFDRPMRVKM 73

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

>gnl|CDD|240806 cd12360, RRM_cwf2, RNA recognition motif in yeast pre-mRNA-splicing factor Cwc2 and similar proteins

 Score = 40.3 bits (95), Expect = 2e-05
 Identities = 23/61 (37%), Positives = 33/61 (54%), Gaps = 8/61 (13%)

Query: 26 TPDDLRRVFERCGEVGDI-YIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRE 84
            + LRR F   G++ DI  +P       S+G AFVR+  +  AE A +AM  + LDG E
Sbjct: 18 IEEILRRHFGEWGDIEDIRVLP-------SKGIAFVRYKYRASAEFAKEAMADQSLDGGE 70

Query: 85 L 85
          +
Sbjct: 71 V 71

This subfamily corresponds to the RRM of yeast protein Cwc2, also termed Complexed with CEF1 protein 2, or PRP19-associated complex protein 40 (Ntc40), or synthetic lethal with CLF1 protein 3, one of the components of the Prp19-associated complex [nineteen complex (NTC)] that can bind to RNA. NTC is composed of the scaffold protein Prp19 and a number of associated splicing factors, and plays a crucial role in intron removal during premature mRNA splicing in eukaryotes. Cwc2 functions as an RNA-binding protein that can bind both small nuclear RNAs (snRNAs) and pre-mRNA in vitro. It interacts directly with the U6 snRNA to link the NTC to the spliceosome during pre-mRNA splicing. In the N-terminal half, Cwc2 contains a CCCH-type zinc finger (ZnF domain), a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and an intervening loop, also termed RNA-binding loop or RB loop, between ZnF and RRM, all of which are necessary and sufficient for RNA binding. The ZnF is also responsible for mediating protein-protein interaction. The C-terminal flexible region of Cwc2 interacts with the WD40 domain of Prp19. Length = 78

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

 Score = 40.4 bits (94), Expect = 2e-05
 Identities = 24/78 (30%), Positives = 42/78 (53%), Gaps = 10/78 (12%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPR--DRFTRESRGFAFVRFFDKRDAEDALD 73
          L V NL   TT + ++  F +       + P   +R  ++ R +AFV FF++ DA  A+ 
Sbjct: 4  LYVRNLMISTTEETIKAEFNK-------FKPGVVER-VKKLRDYAFVHFFNREDAVAAMS 55

Query: 74 AMDGRMLDGRELRVQMAR 91
           M+G+ +DG  + V +A+
Sbjct: 56 VMNGKCIDGASIEVTLAK 73

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

>gnl|CDD|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score = 40.2 bits (94), Expect = 2e-05
 Identities = 27/77 (35%), Positives = 37/77 (48%), Gaps = 1/77 (1%)

Query: 15 SLKVDNLTYRTTPDDLRRVFE-RCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
          S+ V +L+      DL  +F+ R        I  D  T  SRG+ FVRF D+ D + AL 
Sbjct: 3  SIFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALI 62

Query: 74 AMDGRMLDGRELRVQMA 90
           M G    GR +R+  A
Sbjct: 63 EMQGVYCGGRPMRISTA 79

This subgroup corresponds to the RRM2 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both, RNA and single-stranded DNA (ssDNA), in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. . Length = 80

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

 Score = 39.9 bits (93), Expect = 2e-05
 Identities = 27/73 (36%), Positives = 41/73 (56%), Gaps = 6/73 (8%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V NL    T +D +++FE+ GE  +++I RDR      GF F+R   +  AE A   +
Sbjct: 4  LFVGNLPTDITEEDFKKLFEKYGEPSEVFINRDR------GFGFIRLESRTLAEIAKAEL 57

Query: 76 DGRMLDGRELRVQ 88
          DG +L  R LR++
Sbjct: 58 DGTILKNRPLRIR 70

This subgroup corresponds to the RRM1 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Its cellular function remains unknown currently, however, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

>gnl|CDD|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 40.2 bits (95), Expect = 3e-05
 Identities = 20/61 (32%), Positives = 37/61 (60%), Gaps = 1/61 (1%)

Query: 29 DLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ 88
          D+R +FE+ GE+  I  P  RF + +R F +V+F     A  A+  ++G++ +G +L V+
Sbjct: 16 DIRDLFEQYGEILSIRFPSLRFNK-TRRFCYVQFTSPESAAAAVALLNGKLGEGYKLVVK 74

Query: 89 M 89
          +
Sbjct: 75 I 75

This subfamily corresponds to the RRM2 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

>gnl|CDD|240706 cd12260, RRM2_SREK1, RNA recognition motif 2 in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins

 Score = 40.4 bits (95), Expect = 3e-05
 Identities = 27/81 (33%), Positives = 37/81 (45%), Gaps = 15/81 (18%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEV------GDIYIPRDRFTRESRGFAFVRFFDKRDAEDA 71
          V NL   TT D L   F + GEV      GD      + TR    +AFV F ++    +A
Sbjct: 9  VGNLDPTTTADQLLEFFSQAGEVKYVRMAGD----ETQPTR----YAFVEFAEQTSVINA 60

Query: 72 LDAMDGRMLDGRELRVQMARY 92
          L  ++G M  GR L+V  +  
Sbjct: 61 L-KLNGAMFGGRPLKVNHSNN 80

This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site. . Length = 85

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

 Score = 39.7 bits (93), Expect = 3e-05
 Identities = 21/56 (37%), Positives = 32/56 (57%), Gaps = 4/56 (7%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
          V  L+  TT DD+++ F + G+V D  +  D+ T   RGF FV F    ++ED +D
Sbjct: 4  VGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTF----ESEDVVD 55

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

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

 Score = 39.6 bits (93), Expect = 3e-05
 Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 1/71 (1%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V NL +     +L+  F + G+V    +P D+ T  S+G+ FV  F  RD  +       
Sbjct: 4  VGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVS-FSSRDGLENALQKQK 62

Query: 78 RMLDGRELRVQ 88
           +L+G +L+VQ
Sbjct: 63 HILEGNKLQVQ 73

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

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

 Score = 39.9 bits (94), Expect = 4e-05
 Identities = 24/81 (29%), Positives = 38/81 (46%), Gaps = 8/81 (9%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRF------TRESRGFAFVRFFDKRDAE 69
          L V NL+ R T +DL  +F R   V      ++ F          +G AFV F  +  A 
Sbjct: 4  LYVKNLSKRVTEEDLVYIFGR--FVDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIAT 61

Query: 70 DALDAMDGRMLDGRELRVQMA 90
           AL+ ++G +L G+ + +Q  
Sbjct: 62 KALNLVNGYVLKGKPMVIQFG 82

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

 Score = 39.7 bits (93), Expect = 4e-05
 Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 3/73 (4%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          +L + NL   TT  DLR  FER GE+ DI I +      +  +AF+++ D      A+  
Sbjct: 4  TLFIGNLEKTTTYSDLREAFERFGEIIDIDIKK---QGGNPAYAFIQYADIASVVKAMRK 60

Query: 75 MDGRMLDGRELRV 87
          MDG  L    +++
Sbjct: 61 MDGEYLGNNRVKL 73

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

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

 Score = 39.1 bits (92), Expect = 4e-05
 Identities = 20/69 (28%), Positives = 38/69 (55%), Gaps = 9/69 (13%)

Query: 18 VDNL-TYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD 76
          V NL T + + +DL  +F + G++  I +         +G+ FV+F ++ DA  A+   +
Sbjct: 5  VGNLNTDKVSKEDLEEIFSKYGKILGISL--------HKGYGFVQFDNEEDARAAVAGEN 56

Query: 77 GRMLDGREL 85
          GR + G++L
Sbjct: 57 GREIAGQKL 65

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

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

 Score = 39.2 bits (92), Expect = 5e-05
 Identities = 16/58 (27%), Positives = 30/58 (51%)

Query: 21 LTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGR 78
          L   TT +DL ++ +  G++       D+ T + +G+ FV F     A  A++ ++GR
Sbjct: 8  LPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEGLNGR 65

This subfamily corresponds to the RRM1 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus, they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. Moreover, the family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot. . Length = 71

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

 Score = 39.1 bits (91), Expect = 5e-05
 Identities = 21/75 (28%), Positives = 36/75 (48%), Gaps = 8/75 (10%)

Query: 14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
          V L V NL    T  ++R +FE+ G+V +  I ++        + FV   DK  A++A+ 
Sbjct: 1  VKLFVGNLPPEATEQEIRSLFEQYGKVLECDIIKN--------YGFVHMDDKTAADEAIR 52

Query: 74 AMDGRMLDGRELRVQ 88
           +    L G  + V+
Sbjct: 53 NLHHYKLHGVAINVE 67

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

>gnl|CDD|240763 cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition motif 4 in RNA-binding protein 19 (RBM19) and RNA recognition motif 3 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 39.1 bits (92), Expect = 5e-05
 Identities = 20/58 (34%), Positives = 31/58 (53%), Gaps = 6/58 (10%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          V NL + TT ++LR +FE+ G +G + +P       SR  A V F +  DA  A  ++
Sbjct: 5  VKNLPFGTTEEELRELFEKFGSLGRLLLP------PSRTIALVEFLEPSDARKAFKSL 56

This subfamily corresponds to the RRM4 of RBM19 and the RRM3 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologues exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 72

>gnl|CDD|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)

 Score = 39.1 bits (91), Expect = 6e-05
 Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          +L V NL  + T + +  +F + G V  + IP+D+   + + FAFV F  +     A++ 
Sbjct: 3  TLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDK-DGKPKQFAFVNFKHEVSVPYAMNL 61

Query: 75 MDGRMLDGRELRVQ 88
          ++G  L GR L +Q
Sbjct: 62 LNGIKLYGRPLNIQ 75

This subfamily corresponds to the RRM of RBM7, a ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM7 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. . Length = 75

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

 Score = 39.1 bits (92), Expect = 6e-05
 Identities = 18/73 (24%), Positives = 36/73 (49%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          +  L    + D ++ + E  G++    + +D  T  S+G+AF  + D    + A+  ++G
Sbjct: 5  IGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAGLNG 64

Query: 78 RMLDGRELRVQMA 90
            L  ++L VQ A
Sbjct: 65 MQLGDKKLTVQRA 77

This subfamily corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 77

>gnl|CDD|240788 cd12342, RRM_Nab3p, RNA recognition motif in yeast nuclear polyadenylated RNA-binding protein 3 (Nab3p) and similar proteins

 Score = 39.0 bits (91), Expect = 7e-05
 Identities = 18/70 (25%), Positives = 36/70 (51%), Gaps = 8/70 (11%)

Query: 22 TYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLD 81
          T R + +DL R+F   GE+  I +           + FV+F       +A++   G+M+ 
Sbjct: 9  TKRVSKEDLFRIFSTYGELAQIVL--------KNAYGFVQFDSPESCANAINCEQGKMIR 60

Query: 82 GRELRVQMAR 91
          GR+L +++++
Sbjct: 61 GRKLHLEVSK 70

This subfamily corresponds to the RRM of Nab3p, an acidic nuclear polyadenylated RNA-binding protein encoded by Saccharomyces cerevisiae NAB3 gene that is essential for cell viability. Nab3p is predominantly localized within the nucleoplasm and essential for growth in yeast. It may play an important role in packaging pre-mRNAs into ribonucleoprotein structures amenable to efficient nuclear RNA processing. Nab3p contains an N-terminal aspartic/glutamic acid-rich region, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal region rich in glutamine and proline residues. . Length = 71

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

 Score = 38.8 bits (90), Expect = 7e-05
 Identities = 22/71 (30%), Positives = 37/71 (52%), Gaps = 4/71 (5%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD---- 73
          +  L++ TT  DL+  F + GEV D  +  D  T  SRGF FV F +    +  +D    
Sbjct: 3  IGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEH 62

Query: 74 AMDGRMLDGRE 84
           ++G+++D + 
Sbjct: 63 KLNGKVIDPKR 73

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

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

 Score = 38.8 bits (90), Expect = 7e-05
 Identities = 20/56 (35%), Positives = 33/56 (58%), Gaps = 4/56 (7%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
          V  L+  TT +D+++ FE+ G+V D  +  D+ T   RGF FV F    ++ED ++
Sbjct: 4  VGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTF----ESEDIVE 55

This subgroup corresponds to the RRM2 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1) and has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. It represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

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

 Score = 41.2 bits (96), Expect = 8e-05
 Identities = 17/60 (28%), Positives = 32/60 (53%)

Query: 28  DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV 87
            D++ VFE  GE+    + R    R  +G+ F+ + + +   +A+ +M+   L G+ LRV
Sbjct: 219 TDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRV 278

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

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

 Score = 38.6 bits (90), Expect = 8e-05
 Identities = 30/74 (40%), Positives = 36/74 (48%), Gaps = 4/74 (5%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V NL       D+  +F + G + DI    D   R    FAFV F D RDAEDA+   DG
Sbjct: 4  VGNLPPDIRTKDIEDLFYKYGAIRDI----DLKNRRGPPFAFVEFEDPRDAEDAVYGRDG 59

Query: 78 RMLDGRELRVQMAR 91
             DG  LRV+  R
Sbjct: 60 YDYDGYRLRVEFPR 73

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

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

 Score = 39.1 bits (92), Expect = 8e-05
 Identities = 16/70 (22%), Positives = 33/70 (47%), Gaps = 3/70 (4%)

Query: 20 NLTYRTTPDDLRRVFERCGEVGDI---YIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD 76
          N+  + T + L ++ +  G+ G     Y+P D   + + G+AF+ F +   AE    A +
Sbjct: 5  NIPNKYTQEMLLQLLDEHGKGGAYDFLYLPIDFKNKCNVGYAFINFVNPEYAEKFYKAFN 64

Query: 77 GRMLDGRELR 86
          G+     + +
Sbjct: 65 GKKWKNFKSK 74

This subfamily corresponds to the RRM3 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 = 86

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

 Score = 39.2 bits (92), Expect = 8e-05
 Identities = 29/82 (35%), Positives = 41/82 (50%), Gaps = 4/82 (4%)

Query: 16 LKVDNL--TYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
          L VD L  T+R     LR++F + G+     +       + RGFAFV +    DAE+A  
Sbjct: 5  LFVDRLPKTFRDV-SILRKLFSQVGKPTFCQLAIAP-NGQPRGFAFVEYATAEDAEEAQQ 62

Query: 74 AMDGRMLDGRELRVQMARYGRP 95
          A++G  L G  +RV     GRP
Sbjct: 63 ALNGHSLQGSPIRVSFGNPGRP 84

This subfamily corresponds to the RRM3 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only. . Length = 92

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

 Score = 38.4 bits (90), Expect = 9e-05
 Identities = 18/40 (45%), Positives = 23/40 (57%)

Query: 25 TTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
           T +DLR  F + G V  + I  D+ T + RGFAFV F D
Sbjct: 11 VTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDD 50

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

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

 Score = 38.9 bits (91), Expect = 9e-05
 Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 4/49 (8%)

Query: 26 TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          T  DLR+ F + G V ++ +  D   +  RGF F+ F    ++ED++D 
Sbjct: 15 TETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITF----ESEDSVDQ 59

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

>gnl|CDD|240869 cd12423, RRM3_PTBP1_like, RNA recognition motif 3 in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins

 Score = 38.4 bits (90), Expect = 9e-05
 Identities = 24/78 (30%), Positives = 39/78 (50%), Gaps = 6/78 (7%)

Query: 16 LKVDNLT-YRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          L V NL     TPD L   F   G  GD+   R +     +  A ++  D + A+ AL  
Sbjct: 2  LLVSNLNEEMVTPDAL---FTLFGVYGDVV--RVKILFNKKDTALIQMADPQQAQTALTH 56

Query: 75 MDGRMLDGRELRVQMARY 92
          ++G  L G++LRV ++++
Sbjct: 57 LNGIRLHGKKLRVTLSKH 74

This subfamily corresponds to the RRM3 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), and similar proteins found in Metazoa. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 also contains four RRMs. ROD1 coding protein Rod1 is a mammalian PTB homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It may play a role controlling differentiation in mammals. All members in this family contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 74

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

 Score = 38.4 bits (89), Expect = 1e-04
 Identities = 15/36 (41%), Positives = 26/36 (72%)

Query: 55 RGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA 90
          +GFAFV++ ++R+A  A+   DGRM+ G+ L + +A
Sbjct: 36 KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLA 71

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

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

 Score = 38.4 bits (90), Expect = 1e-04
 Identities = 17/62 (27%), Positives = 33/62 (53%), Gaps = 7/62 (11%)

Query: 27 PDD-LRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGREL 85
          PD  L  VF R G + D+Y+   +       + + ++ D+  AE A+  + G+ ++G +L
Sbjct: 12 PDYILEDVFCRFGGLIDVYLVPGK------NYGYAKYADRESAERAITTLHGKEVNGVKL 65

Query: 86 RV 87
          +V
Sbjct: 66 KV 67

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

>gnl|CDD|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP DL) and similar proteins

 Score = 38.5 bits (89), Expect = 1e-04
 Identities = 19/57 (33%), Positives = 31/57 (54%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          V  L+  TT + ++  F   GE+ +I +P D  T E RGF FV + D+   +  L++
Sbjct: 4  VGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKLLES 60

This subgroup corresponds to the RRM2 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 75

>gnl|CDD|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 38.4 bits (90), Expect = 1e-04
 Identities = 25/77 (32%), Positives = 36/77 (46%), Gaps = 1/77 (1%)

Query: 15 SLKVDNLTYRTTPDDLRRVF-ERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
          S+ V +L    T   L+  F  R   V    +  D  T  S+G+ FVRF D+ + + AL 
Sbjct: 3  SIFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALT 62

Query: 74 AMDGRMLDGRELRVQMA 90
           M+G     R +RV  A
Sbjct: 63 EMNGVYCSSRPMRVSPA 79

This subfamily corresponds to the RRM2 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs. . Length = 80

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

 Score = 38.4 bits (89), Expect = 1e-04
 Identities = 24/73 (32%), Positives = 36/73 (49%), Gaps = 4/73 (5%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD---- 73
          +  L++ T+  DL     R GEV D  I  D  T  SRGF FV F D    +  L+    
Sbjct: 4  IGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELKEH 63

Query: 74 AMDGRMLDGRELR 86
           +DG+++D +  +
Sbjct: 64 KLDGKLIDPKRAK 76

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

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

 Score = 38.1 bits (89), Expect = 1e-04
 Identities = 18/71 (25%), Positives = 26/71 (36%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V NL +  T D+L+  F+  G V ++ I           F FV F D    +  L     
Sbjct: 8  VGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILANKPI 67

Query: 78 RMLDGRELRVQ 88
                 L V+
Sbjct: 68 YFRGDHRLNVE 78

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

>gnl|CDD|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

 Score = 38.0 bits (88), Expect = 1e-04
 Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 6/73 (8%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V NL    T D+ +++F + GE G+++I       + +GF F++   +  AE A   +
Sbjct: 4  LFVGNLPADITEDEFKKLFAKYGEPGEVFI------NKGKGFGFIKLESRALAEIAKAEL 57

Query: 76 DGRMLDGRELRVQ 88
          D   + GR+LRV+
Sbjct: 58 DDTPMRGRQLRVR 70

This subgroup corresponds to the RRM1 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. Besides, it promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. Additionally, PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules. . Length = 71

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

 Score = 38.2 bits (89), Expect = 1e-04
 Identities = 25/66 (37%), Positives = 36/66 (54%), Gaps = 1/66 (1%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          +L V NL    T ++LRR FER G V D+ I R    + +  +AFV+F +   A  A  A
Sbjct: 4  TLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGN-AYAFVKFLNLDMAHRAKVA 62

Query: 75 MDGRML 80
          M G+ +
Sbjct: 63 MSGQYI 68

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

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

 Score = 38.1 bits (88), Expect = 2e-04
 Identities = 24/70 (34%), Positives = 41/70 (58%), Gaps = 4/70 (5%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA- 74
          L +  L++ TT + LR  FE+ G + D  + RD  T+ SRGF FV +    + + A++A 
Sbjct: 5  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMNAR 64

Query: 75 ---MDGRMLD 81
             +DGR+++
Sbjct: 65 PHKVDGRVVE 74

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

>gnl|CDD|240671 cd12225, RRM1_2_CID8_like, RNA recognition motif 1 and 2 (RRM1, RRM2) in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 37.7 bits (88), Expect = 2e-04
 Identities = 27/70 (38%), Positives = 35/70 (50%), Gaps = 3/70 (4%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V  +    + DDL+  F  CGEV  + +  DR  + S  FAFV F D   A  AL  + G
Sbjct: 5  VGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDR--QHSARFAFVEFADAESALSAL-NLSG 61

Query: 78 RMLDGRELRV 87
           +L G  LRV
Sbjct: 62 TLLGGHPLRV 71

This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 77

>gnl|CDD|240842 cd12396, RRM1_Nop13p_fungi, RNA recognition motif 1 in yeast nucleolar protein 13 (Nop13p) and similar proteins

 Score = 37.9 bits (88), Expect = 2e-04
 Identities = 21/79 (26%), Positives = 43/79 (54%), Gaps = 12/79 (15%)

Query: 18 VDNLTYRTTPDDLRRVFER-------CGEVGDIYIPRDRFTR----ESRGFAFVRFFDKR 66
          + NL++ TT + LR+ F           ++  +++P  +  R    +++GFA+V  F  +
Sbjct: 3  IGNLSFTTTKEMLRQFFVSKSGDRITDEQITRVHMPDSKAKRKGVKQNKGFAYV-DFTSQ 61

Query: 67 DAEDALDAMDGRMLDGREL 85
          +A  A  A+  ++L+GR+L
Sbjct: 62 EATKAAIALSEKILNGRKL 80

This subfamily corresponds to the RRM1 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both, Nop12p and Nop13p, are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 85

>gnl|CDD|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 37.8 bits (88), Expect = 2e-04
 Identities = 19/51 (37%), Positives = 30/51 (58%)

Query: 26 TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD 76
          T +DLR  F+  G++  + I +D+ T ES+GF +V+F     A  AL+  D
Sbjct: 13 TEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVALENCD 63

This subfamily corresponds to the RRM2 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

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

 Score = 37.2 bits (87), Expect = 2e-04
 Identities = 16/66 (24%), Positives = 33/66 (50%), Gaps = 6/66 (9%)

Query: 26 TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGREL 85
          T + L++ F   G + +I + +++         FV F     A+ A+  ++G  + G +L
Sbjct: 15 TEEILKKAFSPFGNIINISMEKEK------NCGFVTFEKMESADRAIAELNGTTVQGVQL 68

Query: 86 RVQMAR 91
          +V +AR
Sbjct: 69 KVSLAR 74

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

>gnl|CDD|214637 smart00361, RRM_1, RNA recognition motif

 Score = 37.4 bits (87), Expect = 2e-04
 Identities = 15/49 (30%), Positives = 25/49 (51%)

Query: 38 GEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR 86
          G++  IYI    +    RG  ++ F    DA  A+  ++GR  DGR ++
Sbjct: 20 GKINKIYIDDVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRLVK 68

Length = 70

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

 Score = 37.4 bits (86), Expect = 3e-04
 Identities = 25/70 (35%), Positives = 40/70 (57%), Gaps = 4/70 (5%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA- 74
          L +  L++ TT D LR  FE+ G + D  + RD  T+ SRGF FV +    + + A+ A 
Sbjct: 5  LFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMSAR 64

Query: 75 ---MDGRMLD 81
             +DGR+++
Sbjct: 65 PHKVDGRVVE 74

This subgroup corresponds to the RRM1 of hnRNP A3 which is a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

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

 Score = 37.3 bits (87), Expect = 3e-04
 Identities = 21/75 (28%), Positives = 39/75 (52%), Gaps = 5/75 (6%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRES--RGFAFVRFFDKRDAEDALD 73
          L V NL      D LR++FE  G + D+ +   ++T++   R F FV +  + +A+ AL 
Sbjct: 3  LIVKNLPKGIKEDKLRKLFEAFGTITDVQL---KYTKDGKFRKFGFVGYKTEEEAQKALK 59

Query: 74 AMDGRMLDGRELRVQ 88
            +   +D  ++ V+
Sbjct: 60 HFNNSFIDTSKITVE 74

This subgroup corresponds to the RRM1 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

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

 Score = 37.1 bits (86), Expect = 3e-04
 Identities = 18/34 (52%), Positives = 24/34 (70%)

Query: 56 GFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM 89
          G+AF+ F D RDAEDA+   DG   DG+ LRV++
Sbjct: 39 GYAFIEFEDARDAEDAIRGRDGYDFDGQRLRVEL 72

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

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

 Score = 37.2 bits (87), Expect = 3e-04
 Identities = 20/71 (28%), Positives = 36/71 (50%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V +L    T + L R F +        + RD+ T +S+G+ FV F D  D   A+  M+G
Sbjct: 11 VGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKEMNG 70

Query: 78 RMLDGRELRVQ 88
          + +  R ++++
Sbjct: 71 KYVGNRPIKLR 81

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

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

 Score = 39.1 bits (91), Expect = 4e-04
 Identities = 27/71 (38%), Positives = 39/71 (54%), Gaps = 1/71 (1%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
           V  L  +    DL   F + G+V D+   +DR +R S+G A+V F+D      AL A+ G
Sbjct: 94  VLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKAL-ALTG 152

Query: 78  RMLDGRELRVQ 88
           +ML GR + VQ
Sbjct: 153 QMLLGRPIIVQ 163

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

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

 Score = 39.1 bits (91), Expect = 4e-04
 Identities = 24/61 (39%), Positives = 29/61 (47%), Gaps = 1/61 (1%)

Query: 95  PPSSSRSRGGRDRDRRRDRS-RSRDRRYTRSRSFSSRSRSGSKSPRKARSKSIDRDNKHE 153
             S       R R R RDRS R RDR Y R R   SRSRS ++  R    +S  RD++  
Sbjct: 15  RRSDKGRERSRRRSRSRDRSRRRRDRDYYRGRRGRSRSRSPNRYYRPRGDRSYRRDDRRS 74

Query: 154 R 154
            
Sbjct: 75  G 75

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

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

 Score = 37.3 bits (86), Expect = 4e-04
 Identities = 15/40 (37%), Positives = 30/40 (75%)

Query: 52 RESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR 91
          ++ R +AFV F ++ DA DA++A++G+++DG  + V +A+
Sbjct: 41 KKIRDYAFVHFSNREDAVDAMNALNGKVIDGSPIEVTLAK 80

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

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

 Score = 39.2 bits (91), Expect = 4e-04
 Identities = 29/95 (30%), Positives = 46/95 (48%), Gaps = 12/95 (12%)

Query: 16  LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
           L V NL   TT + + + F    E     + R    ++ R +AFV F D+ DA  A+D +
Sbjct: 236 LYVRNLMTTTTEEIIEKSF---SEFKPGKVER---VKKIRDYAFVHFEDREDAVKAMDEL 289

Query: 76  DGRMLDGRELRVQMAR------YGRPPSSSRSRGG 104
           +G+ L+G E+ V +A+      Y R    +  RG 
Sbjct: 290 NGKELEGSEIEVTLAKPVDKKSYVRYTRGTGGRGK 324

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

>gnl|CDD|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 36.9 bits (85), Expect = 4e-04
 Identities = 18/59 (30%), Positives = 35/59 (59%), Gaps = 5/59 (8%)

Query: 28 DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR 86
          D+L  +FE+ G + D+ +  D  + ++RG+AF+ F  K  A++A+     ++ D  E+R
Sbjct: 16 DELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAV-----KLCDNYEIR 69

This subgroup corresponds to the RRM1 of hnRNP R, which is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. It is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, and in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; it binds RNA through its RRM domains. . Length = 79

>gnl|CDD|241083 cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 36.8 bits (85), Expect = 4e-04
 Identities = 20/60 (33%), Positives = 33/60 (55%)

Query: 29 DLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ 88
          +L ++F   G V    +  DR T +S+ F FV F +   A+ A+ AM+G  +  + L+VQ
Sbjct: 20 ELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQ 79

This subgroup corresponds to the RRM3 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contains three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. Both, RRM1 and RRM2 of CELF-4, can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 79

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

 Score = 37.0 bits (85), Expect = 5e-04
 Identities = 23/70 (32%), Positives = 41/70 (58%), Gaps = 4/70 (5%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA- 74
          L +  L++ TT + LR  +E+ G++ D  + RD  ++ SRGF FV F    + + A+ A 
Sbjct: 5  LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAMAAR 64

Query: 75 ---MDGRMLD 81
             +DGR+++
Sbjct: 65 PHTIDGRVVE 74

This subgroup corresponds to the RRM1 of hnRNP A2/B1 which is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Moreover, the overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

>gnl|CDD|240941 cd12497, RRM3_RBM47, RNA recognition motif 3 in vertebrate RNA-binding protein 47 (RBM47)

 Score = 36.5 bits (84), Expect = 6e-04
 Identities = 22/76 (28%), Positives = 40/76 (52%), Gaps = 6/76 (7%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V NL   T+ D +++ F   G+     + R    ++ R +AFV F  + DA  A++ +
Sbjct: 4  LYVRNLMIETSEDTIKKTF---GQFNPGCVER---VKKIRDYAFVHFTSREDAVHAMNNL 57

Query: 76 DGRMLDGRELRVQMAR 91
          +G  L+G  + V +A+
Sbjct: 58 NGTELEGSCIEVTLAK 73

This subgroup corresponds to the RRM3 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

>gnl|CDD|241137 cd12693, RRM2_PTBP1_like, RNA recognition motif 2 in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins

 Score = 37.0 bits (86), Expect = 6e-04
 Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 4/61 (6%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V+N+TY  T D L ++F + G V  I      FT+ ++  A ++F D   A+ A  ++DG
Sbjct: 8  VENMTYPVTLDVLHQIFSKFGTVLKIIT----FTKNNQFQALIQFADAVSAQAAKLSLDG 63

Query: 78 R 78
          +
Sbjct: 64 Q 64

This subfamily corresponds to the RRM2 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), and similar proteins found in Metazoa. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 also contains four RRMs. ROD1 coding protein Rod1 is a mammalian PTB homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It may play a role controlling differentiation in mammals. All members in this family contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 96

>gnl|CDD|241056 cd12612, RRM2_SECp43, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 36.5 bits (85), Expect = 6e-04
 Identities = 17/39 (43%), Positives = 24/39 (61%), Gaps = 1/39 (2%)

Query: 53 ESRGFAFVRFFDKRDAEDALDAMDG-RMLDGRELRVQMA 90
           SRG+ FVRF D+ + + AL  M G   L G+ +RV +A
Sbjct: 41 NSRGYGFVRFSDESEQKRALTEMQGASGLGGKPIRVSLA 79

This subgroup corresponds to the RRM2 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. . Length = 82

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

 Score = 36.6 bits (85), Expect = 7e-04
 Identities = 20/81 (24%), Positives = 37/81 (45%), Gaps = 7/81 (8%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRD--RFTRESR----GFAFVRFFDKRDA 68
           + + NL+Y ++ +DL    +    V  + IP    R  R  R    G A+  F     A
Sbjct: 1  RVYISNLSYSSSEEDLEEFLKDFEPV-SVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQA 59

Query: 69 EDALDAMDGRMLDGRELRVQM 89
          E  +  ++G++   R+L V++
Sbjct: 60 EKVVKDLNGKVFKNRKLFVKL 80

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

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

 Score = 36.2 bits (83), Expect = 8e-04
 Identities = 17/45 (37%), Positives = 26/45 (57%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRF 62
          V  L+  T  +D+++ FE+ G+V D  +  D+ T   RGF FV F
Sbjct: 8  VGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTF 52

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 79

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

 Score = 36.0 bits (83), Expect = 8e-04
 Identities = 20/59 (33%), Positives = 37/59 (62%), Gaps = 6/59 (10%)

Query: 28 DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR 86
          D+L  +FER G++ +  +  + F+ E+RG+AFV +  K +A+ A+     R+L+  E+R
Sbjct: 16 DELVPLFERAGKIYEFRLMME-FSGENRGYAFVMYTTKEEAQLAI-----RILNNYEIR 68

This subgroup corresponds to the RRM1 of RBM46, also termed cancer/testis antigen 68 (CT68), a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM46 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

>gnl|CDD|240797 cd12351, RRM4_SHARP, RNA recognition motif 4 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 36.1 bits (84), Expect = 8e-04
 Identities = 29/71 (40%), Positives = 37/71 (52%), Gaps = 8/71 (11%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRD-AEDALDAMD 76
          +D L    T   L R F R G V  + I R       RG A V FFDK + A+ A++ M 
Sbjct: 12 LDGLDESVTEQYLTRHFSRYGPVVHVVIDR------QRGQALV-FFDKVEAAQAAVNEMK 64

Query: 77 GRMLDGRELRV 87
          GR L GR+L+V
Sbjct: 65 GRKLGGRKLQV 75

This subfamily corresponds to the RRM of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, is an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 77

>gnl|CDD|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 36.8 bits (85), Expect = 8e-04
 Identities = 18/58 (31%), Positives = 25/58 (43%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDAL 72
          +L V NL Y  T + L   F + G V       D+ T  ++G  FV F D+      L
Sbjct: 3  TLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACL 60

This subgroup corresponds to the RRM3 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 107

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

 Score = 36.0 bits (83), Expect = 9e-04
 Identities = 22/83 (26%), Positives = 39/83 (46%), Gaps = 8/83 (9%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVG--------DIYIPRDRFTRESRGFAFVRFFDKR 66
          ++ V  L    T ++L   F+ CG V          + I  D+ T + +G A V + D  
Sbjct: 2  TIYVQGLNDNVTLEELADFFKHCGVVKINKRTGQPMVNIYTDKETGKPKGDATVSYEDPP 61

Query: 67 DAEDALDAMDGRMLDGRELRVQM 89
           A+ A++  DG+   G +L+V +
Sbjct: 62 SAKAAVEWFDGKDFQGSKLKVSL 84

This subgroup corresponds to the RRM of EWS, also termed Ewing sarcoma breakpoint region 1 protein, a member of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a multifunctional protein and may play roles in transcription and RNA processing. EWS is involved in transcriptional regulation by interacting with the preinitiation complex TFIID and the RNA polymerase II (RNAPII) complexes. It is also associated with splicing factors, such as the U1 snRNP protein U1C, suggesting its implication in pre-mRNA splicing. Additionally, EWS has been shown to regulate DNA damage-induced alternative splicing (AS). Like other members in the FET family, EWS contains an N-terminal Ser, Gly, Gln and Tyr-rich region composed of multiple copies of a degenerate hexapeptide repeat motif. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a C2/C2 zinc-finger motif, a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and at least 1 arginine-glycine-glycine (RGG)-repeat region. EWS specifically binds to poly G and poly U RNA. It also binds to the proximal-element DNA of the macrophage-specific promoter of the CSF-1 receptor gene. . Length = 84

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

 Score = 38.0 bits (88), Expect = 0.001
 Identities = 35/105 (33%), Positives = 53/105 (50%), Gaps = 5/105 (4%)

Query: 1   MSYGRPPP-RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAF 59
           +SY RP    I+G  +L V  L    T  +L  +F   G++    I  D  T  S+G  F
Sbjct: 77  VSYARPSSDSIKG-ANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGF 135

Query: 60  VRFFDKRD-AEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRG 103
           +R FDKRD A+ A+  ++G    G    + + ++   PSSS S+G
Sbjct: 136 IR-FDKRDEADRAIKTLNGTTPSGCTEPITV-KFANNPSSSNSKG 178

This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076). Length = 352

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

 Score = 35.9 bits (83), Expect = 0.001
 Identities = 23/84 (27%), Positives = 37/84 (44%), Gaps = 14/84 (16%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVG-----------DIYIPRDRFTRESRGFAFVRFFDKR 66
          V NL   TT  DL   F   G +G            I++ +D+ T E +G A V + D  
Sbjct: 3  VSNLPPNTTEQDLAEHF---GSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPH 59

Query: 67 DAEDALDAMDGRMLDGRELRVQMA 90
           A  A++  + +   G  ++V +A
Sbjct: 60 AASAAIEWFNNKDFMGNTIKVSLA 83

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

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

 Score = 35.8 bits (83), Expect = 0.001
 Identities = 19/74 (25%), Positives = 34/74 (45%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          +L V  L+  T   DL+++F + G+V    I  +  +  +R F FV      +A   +  
Sbjct: 1  NLWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQH 60

Query: 75 MDGRMLDGRELRVQ 88
          +    L GR + V+
Sbjct: 61 LHRTELHGRVISVE 74

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

>gnl|CDD|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 36.1 bits (84), Expect = 0.001
 Identities = 20/87 (22%), Positives = 36/87 (41%), Gaps = 18/87 (20%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYI---------PRDRFTRESRGF--------AFV 60
          V NL   T   DL+++F++ G +  +              +     + F        A+V
Sbjct: 5  VGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNVNAYV 64

Query: 61 RFFDKRDAEDALDAMDGRMLDGRELRV 87
           F ++  AE AL  ++G   +G  +RV
Sbjct: 65 VFKEEESAEKAL-KLNGTEFEGHHIRV 90

This subfamily corresponds to the RRM1 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 91

>gnl|CDD|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 35.8 bits (83), Expect = 0.001
 Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 5/69 (7%)

Query: 30 LRRVFERCGE-VGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDG----RE 84
          ++R F   GE V  + I R++ T    G+ FV F D+  AE  L  ++G+ + G    + 
Sbjct: 16 IKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLHKLNGKPIPGSNPPKR 75

Query: 85 LRVQMARYG 93
           ++  A YG
Sbjct: 76 FKLNRATYG 84

This subgroup corresponds to the RRM1 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. . Length = 84

>gnl|CDD|241106 cd12662, RRM3_MYEF2, RNA recognition motif 3 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 35.8 bits (82), Expect = 0.001
 Identities = 24/74 (32%), Positives = 37/74 (50%), Gaps = 2/74 (2%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V NL +  T   L+  F +CG V  ++        +S+G   VRF     AE A   M+G
Sbjct: 4  VRNLPFDLTWQKLKEKFSQCGHV--MFAEIKMENGKSKGCGTVRFDSPESAEKACRLMNG 61

Query: 78 RMLDGRELRVQMAR 91
            ++GRE+ V++ R
Sbjct: 62 IKINGREIDVRLDR 75

This subgroup corresponds to the RRM3 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 77

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

 Score = 35.4 bits (81), Expect = 0.001
 Identities = 20/76 (26%), Positives = 40/76 (52%), Gaps = 8/76 (10%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V NL    T + L + F   G++  +        ++ + +AFV F ++  A  A+D M
Sbjct: 4  LFVRNLATTVTEEILEKSFSEFGKLERV--------KKLKDYAFVHFEERDAAVRAMDEM 55

Query: 76 DGRMLDGRELRVQMAR 91
          +G+ ++G E+ + +A+
Sbjct: 56 NGKEIEGEEIEIVLAK 71

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

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

 Score = 35.3 bits (81), Expect = 0.002
 Identities = 26/77 (33%), Positives = 42/77 (54%), Gaps = 3/77 (3%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          +L V  L+  TT + L+  F+  G +    I  DR T  S+GF FV F  + DA+ A +A
Sbjct: 2  TLFVKGLSEDTTEETLKESFD--GSI-AARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEA 58

Query: 75 MDGRMLDGRELRVQMAR 91
          M+   +DG ++ +  A+
Sbjct: 59 MEDGEIDGNKVTLDFAK 75

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

>gnl|CDD|240705 cd12259, RRM_SRSF11_SREK1, RNA recognition motif in serine/arginine-rich splicing factor 11 (SRSF11), splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins

 Score = 35.3 bits (82), Expect = 0.002
 Identities = 15/60 (25%), Positives = 31/60 (51%), Gaps = 4/60 (6%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYI-PRDRFTRE--SRGFAFVRFFDKRDAEDAL 72
          ++V N++ + T + +R +F   G++ ++ + P D       S+   FV++ D  D   AL
Sbjct: 2  VQVTNVSPQATEEQMRTLFGFLGKIEELRLYPSDDDLAPVLSK-VCFVKYEDPEDVGVAL 60

This subfamily corresponds to the RRM domain of SRSF11 (SRp54 or p54), SREK1 ( SFRS12 or SRrp86) and similar proteins, a group of proteins containing regions rich in serine-arginine dipeptides (SR protein family). These are involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. SR proteins have been identified as crucial regulators of alternative splicing. Different SR proteins display different substrate specificity, have distinct functions in alternative splicing of different pre-mRNAs, and can even negatively regulate splicing. All SR family members are characterized by the presence of one or two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and the C-terminal regions rich in serine and arginine dipeptides (SR domains). The RRM domain is responsible for RNA binding and specificity in both alternative and constitutive splicing. In contrast, SR domains are thought to be protein-protein interaction domains that are often interchangeable. . Length = 76

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

 Score = 34.9 bits (81), Expect = 0.002
 Identities = 23/78 (29%), Positives = 34/78 (43%), Gaps = 8/78 (10%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V  L   T+  +L R F+R G +  I           R +A++ +     A+ A +A+
Sbjct: 1  LWVGGLGPWTSLAELEREFDRFGAIRRI------DYDPGRNYAYIEYESIEAAQAAKEAL 54

Query: 76 DGRML--DGRELRVQMAR 91
           G  L   GR LRV  A 
Sbjct: 55 RGFPLGGPGRRLRVDFAD 72

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

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

 Score = 35.4 bits (81), Expect = 0.002
 Identities = 24/81 (29%), Positives = 45/81 (55%), Gaps = 7/81 (8%)

Query: 15 SLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
          ++ ++NL  +   D+L++    +F R G++ DI + R   + + RG AFV F +   A +
Sbjct: 5  TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 61

Query: 71 ALDAMDGRMLDGRELRVQMAR 91
          AL +M G     + +R+Q A+
Sbjct: 62 ALRSMQGFPFYDKPMRIQYAK 82

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

>gnl|CDD|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic activator RIM4 and similar proteins

 Score = 35.1 bits (81), Expect = 0.002
 Identities = 22/63 (34%), Positives = 36/63 (57%), Gaps = 3/63 (4%)

Query: 32 RVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR 91
            F + G +  + + RD   R+ R +AFV+F +  DA++AL    G +LDGR +R + A+
Sbjct: 25 EHFSKYGTLVFVKVLRD--WRQ-RPYAFVQFTNDDDAKNALAKGQGTILDGRHIRCERAK 81

Query: 92 YGR 94
            R
Sbjct: 82 VNR 84

This subfamily corresponds to the RRM1 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 86

>gnl|CDD|240715 cd12269, RRM_Vip1_like, RNA recognition motif in a group of uncharacterized plant proteins similar to fission yeast Vip1

 Score = 34.7 bits (80), Expect = 0.002
 Identities = 18/68 (26%), Positives = 32/68 (47%), Gaps = 3/68 (4%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          ++V NL+ + T  D+   F   G++  + I R     +S+  A+V F D +  E AL   
Sbjct: 1  VEVTNLSPKATERDIYDFFSFSGDIEYVEIQRSGE--QSQ-TAYVTFKDPQAQETALLLS 57

Query: 76 DGRMLDGR 83
             ++D  
Sbjct: 58 GATIVDQS 65

This subfamily corresponds to the Vip1-like, uncharacterized proteins found in plants. Although their biological roles remain unclear, these proteins show high sequence similarity to the fission yeast Vip1. Like Vip1 protein, members in this family contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 69

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

 Score = 35.0 bits (80), Expect = 0.002
 Identities = 19/59 (32%), Positives = 34/59 (57%), Gaps = 5/59 (8%)

Query: 28 DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR 86
          D+L  +FE+ G + D+ +  D  T  +RG+AFV F  K  A++A+     ++ +  E+R
Sbjct: 16 DELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAV-----KLYNNHEIR 69

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

>gnl|CDD|240795 cd12349, RRM2_SHARP, RNA recognition motif 2 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 34.6 bits (80), Expect = 0.002
 Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 8/78 (10%)

Query: 15 SLKVDNLTYRTTPDDLR----RVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
           + V NL  R++   L+      F++ G+V  + +     T   R +A V F    DAE 
Sbjct: 1  GIIVKNLPLRSSDTSLKDGLFHEFKKHGKVTSVKV---HGTGSER-YAIVFFRKPEDAEK 56

Query: 71 ALDAMDGRMLDGRELRVQ 88
          AL+   G++  G E+ V 
Sbjct: 57 ALEVSKGKLFFGAEIEVT 74

This subfamily corresponds to the RRM2 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 74

>gnl|CDD|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen D (HuD)

 Score = 35.1 bits (80), Expect = 0.003
 Identities = 21/71 (29%), Positives = 36/71 (50%), Gaps = 4/71 (5%)

Query: 21 LTYRTTPDD----LRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD 76
            Y  +PD     L ++F   G V ++ + RD  T + +GF FV   +  +A  A+ +++
Sbjct: 7  FVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASLN 66

Query: 77 GRMLDGRELRV 87
          G  L  R L+V
Sbjct: 67 GYRLGDRVLQV 77

This subgroup corresponds to the RRM3 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells. And it also regulates the neurite elongation and morphological differentiation. HuD specifically bound poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

>gnl|CDD|240749 cd12303, RRM_spSet1p_like, RNA recognition motif in fission yeast Schizosaccharomyces pombe SET domain-containing protein 1 (spSet1p) and similar proteins

 Score = 34.6 bits (80), Expect = 0.003
 Identities = 24/84 (28%), Positives = 40/84 (47%), Gaps = 8/84 (9%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRD--------AE 69
          +  L+  TTP  +R  F   GE+ +  +  D  T +S G   V F             A+
Sbjct: 3  ITGLSPLTTPKQIRMHFRPFGEIEESELKLDPRTGQSLGICRVTFRGDPLRPSAAHEAAK 62

Query: 70 DALDAMDGRMLDGRELRVQMARYG 93
           A+D ++GR + G+ +RV++ R G
Sbjct: 63 AAVDGLNGRRIGGKRVRVELDRDG 86

This subfamily corresponds to the RRM of spSet1p, also termed H3 lysine-4 specific histone-lysine N-methyltransferase, or COMPASS component SET1, or lysine N-methyltransferase 2, or Set1 complex component, is encoded by SET1 from the fission yeast S. pombe. It is essential for the H3 lysine-4 methylation. in vivo, and plays an important role in telomere maintenance and DNA repair in an ATM kinase Rad3-dependent pathway. spSet1p is the homology counterpart of Saccharomyces cerevisiae Set1p (scSet1p). However, it is more closely related to Set1 found in mammalian. Moreover, unlike scSet1p, spSet1p is not required for heterochromatin assembly in fission yeast. spSet1p contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a conserved SET domain that may play a role in DNA repair and telomere function. . Length = 86

>gnl|CDD|241112 cd12668, RRM3_RAVER2, RNA recognition motif 3 found in vertebrate ribonucleoprotein PTB-binding 2 (raver-2)

 Score = 34.9 bits (80), Expect = 0.003
 Identities = 14/45 (31%), Positives = 21/45 (46%)

Query: 55 RGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSS 99
           GFA V +     AE+   AMDG  + G  +++     G P  S+
Sbjct: 44 GGFAVVEYETAEQAEEVQLAMDGTTIKGSRIQLSFCAPGAPGRST 88

This subgroup corresponds to the RRM3 of raver-2, a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It is present in vertebrates and shows high sequence homology to raver-1, a ubiquitously expressed co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. In contrast, raver-2 exerts a distinct spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Raver-2 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. Raver-2 binds to PTB through the SLLGEPP motif only, and binds to RNA through its RRMs. . Length = 98

>gnl|CDD|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 34.6 bits (79), Expect = 0.003
 Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 1/62 (1%)

Query: 29 DLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ 88
           LR  FE+ G++  I +  DR + + RGFAFV  FD  D  D +       ++G    V+
Sbjct: 16 HLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVT-FDDHDTVDKIVVQKYHTINGHNCEVK 74

Query: 89 MA 90
           A
Sbjct: 75 KA 76

This subgroup corresponds to the RRM2 of hnRNP A3, a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

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

 Score = 34.1 bits (78), Expect = 0.003
 Identities = 23/74 (31%), Positives = 39/74 (52%), Gaps = 8/74 (10%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          +  L+Y     D++R F   G++ +I +          G+ FV F D RDA+DA+  ++G
Sbjct: 4  IGRLSYHVREKDIQRFFGGYGKLLEIDL--------KNGYGFVEFEDSRDADDAVYELNG 55

Query: 78 RMLDGRELRVQMAR 91
          + L G  + V+ AR
Sbjct: 56 KDLCGERVIVEHAR 69

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

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

 Score = 34.6 bits (80), Expect = 0.003
 Identities = 15/75 (20%), Positives = 33/75 (44%), Gaps = 5/75 (6%)

Query: 28 DDLRRVF-----ERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDG 82
          D++   F     ++ GEV ++ I     T +  G A V F   + A+  ++ ++   + G
Sbjct: 12 DNIDEGFLKDMCKKYGEVEEVKIYFHPKTNKHLGLARVVFDSVKSAKRCVEKLNQTSVMG 71

Query: 83 RELRVQMARYGRPPS 97
          + ++V +   G    
Sbjct: 72 KIIKVFLDPKGEIRK 86

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

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

 Score = 34.2 bits (78), Expect = 0.003
 Identities = 22/73 (30%), Positives = 33/73 (45%), Gaps = 8/73 (10%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V N++   T  +LR  FE  G V +  I +D        +AFV      DA +A+  +
Sbjct: 3  LHVGNISSSCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIRGL 54

Query: 76 DGRMLDGRELRVQ 88
          D     G+ + VQ
Sbjct: 55 DNTEFQGKRMHVQ 67

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

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

 Score = 36.1 bits (83), Expect = 0.004
 Identities = 22/70 (31%), Positives = 37/70 (52%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
           V NL+  T    L ++F   G V ++ I RD  T + +G+ FV   +  +A  A+ +++G
Sbjct: 274 VYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNG 333

Query: 78  RMLDGRELRV 87
             L  R L+V
Sbjct: 334 YTLGNRVLQV 343

This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076). Length = 352

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

 Score = 34.2 bits (78), Expect = 0.004
 Identities = 26/78 (33%), Positives = 40/78 (51%), Gaps = 9/78 (11%)

Query: 13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIP-RDRFTRESRGFAFVRFFDKRDAEDA 71
          M  L + NL    TP DL +VFE      D  I    +F  +S G+AFV   D++ A  A
Sbjct: 1  MNKLYIGNLNESVTPADLEKVFE------DHKISYSGQFLVKS-GYAFVDCPDEQWAMKA 53

Query: 72 LDAMDGRM-LDGRELRVQ 88
          ++   G++ L G+ L ++
Sbjct: 54 IETFSGKVELHGKRLEIE 71

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

>gnl|CDD|240980 cd12536, RRM1_RBM39, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39)

 Score = 34.6 bits (79), Expect = 0.004
 Identities = 21/60 (35%), Positives = 29/60 (48%)

Query: 21 LTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRML 80
          L  R  P DL   F   G+V D+ +  DR +R S+G A+V F D      A+     R+L
Sbjct: 9  LAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSVPLAIGLTGQRVL 68

This subgroup corresponds to the RRM1 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor HCC1, a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Based on the specific domain composition, RBM39 has been classified into a family of non-snRNP (small nuclear ribonucleoprotein) splicing factors that are usually not complexed to snRNAs. . Length = 85

>gnl|CDD|241199 cd12755, RRM2_RBM5, RNA recognition motif 2 in vertebrate RNA-binding protein 5 (RBM5)

 Score = 34.5 bits (79), Expect = 0.004
 Identities = 16/56 (28%), Positives = 30/56 (53%), Gaps = 4/56 (7%)

Query: 40 VGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRM----LDGRELRVQMAR 91
          V +I + +D+ T+++RGFAFV+     +A   L  +        +DG+ + V  A+
Sbjct: 31 VNNIRLIKDKQTQQNRGFAFVQLSSALEASQLLQILQSLHPPLKIDGKTIGVDFAK 86

This subgroup corresponds to the RRM2 of RBM5, also termed protein G15, or putative tumor suppressor LUCA15, or renal carcinoma antigen NY-REN-9, a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM5 shows high sequence similarity to RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). Both, RBM5 and RBM6, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain. . Length = 86

>gnl|CDD|241105 cd12661, RRM3_hnRNPM, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 34.2 bits (78), Expect = 0.004
 Identities = 26/74 (35%), Positives = 36/74 (48%), Gaps = 2/74 (2%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V NL +  T   L+  F  CG V  +Y        +S+G   VRF     AE A   M+G
Sbjct: 4  VRNLPFDFTWKMLKDKFNECGHV--LYADIKMENGKSKGCGVVRFESPEVAERACRMMNG 61

Query: 78 RMLDGRELRVQMAR 91
            L+GRE+ V++ R
Sbjct: 62 YKLNGREIDVRIDR 75

This subgroup corresponds to the RRM3 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 77

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

 Score = 34.3 bits (78), Expect = 0.004
 Identities = 21/68 (30%), Positives = 36/68 (52%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          +L V  L    T  +L ++F + G +    I  D+ T  SRG  F+RF  + +AE+A+  
Sbjct: 4  NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 63

Query: 75 MDGRMLDG 82
          ++G+   G
Sbjct: 64 LNGQKPSG 71

This subgroup corresponds to the RRM2 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells and also regulates the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	158
KOG4207|consensus	256		99.95
KOG0107|consensus	195		99.92
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.9
KOG0113|consensus	335		99.87
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.8
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.8
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.8
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.79
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.79
KOG0130|consensus	170		99.78
KOG0105|consensus	241		99.75
KOG0122|consensus	270		99.75
KOG0149|consensus	247		99.75
KOG0121|consensus	153		99.73
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.73
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.72
PLN03120	260	nucleic acid binding protein; Provisional	99.72
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.7
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.7
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.69
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.68
smart00362	72	RRM_2 RNA recognition motif.	99.68
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.68
KOG0117|consensus	506		99.68
KOG0111|consensus	298		99.67
PLN03121	243	nucleic acid binding protein; Provisional	99.66
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.66
PLN03213	759	repressor of silencing 3; Provisional	99.66
KOG0125|consensus	376		99.65
KOG0131|consensus	203		99.65
KOG0148|consensus	321		99.64
smart00360	71	RRM RNA recognition motif.	99.64
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.64
KOG0126|consensus	219		99.63
KOG0415|consensus	479		99.63
KOG0114|consensus	124		99.63
KOG0148|consensus	321		99.63
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.63
KOG0145|consensus	360		99.62
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.62
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.62
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.61
KOG0108|consensus	435		99.59
KOG0145|consensus	360		99.59
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.58
KOG0144|consensus	510		99.57
KOG0109|consensus	346		99.55
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.54
KOG0127|consensus	678		99.53
KOG0117|consensus	506		99.52
KOG0127|consensus	678		99.51
smart00361	70	RRM_1 RNA recognition motif.	99.51
KOG0147|consensus	549		99.51
KOG4212|consensus	608		99.5
KOG0144|consensus	510		99.5
KOG0109|consensus	346		99.44
KOG0124|consensus	544		99.44
KOG0131|consensus	203		99.41
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.41
KOG0146|consensus	371		99.37
KOG0153|consensus	377		99.34
KOG4206|consensus	221		99.34
KOG4208|consensus	214		99.3
KOG0132|consensus	894		99.3
KOG4661|consensus	940		99.29
KOG0123|consensus	369		99.29
KOG0116|consensus	419		99.23
KOG4212|consensus	608		99.23
KOG0106|consensus	216		99.22
KOG0533|consensus	243		99.22
KOG4209|consensus	231		99.21
KOG0146|consensus	371		99.2
KOG0124|consensus	544		99.2
KOG0110|consensus	725		99.18
KOG4454|consensus	267		99.18
KOG0123|consensus	369		99.18
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	99.16
KOG0110|consensus	725		99.14
KOG4660|consensus	549		99.13
KOG4205|consensus	311		99.12
KOG4205|consensus	311		99.09
KOG1457|consensus	284		99.08
KOG0106|consensus	216		99.05
KOG1548|consensus	382		99.04
KOG4211|consensus	510		99.0
KOG1995|consensus	351		98.89
KOG0120|consensus	500		98.86
KOG0151|consensus	877		98.83
KOG0226|consensus	290		98.83
KOG0105|consensus	241		98.8
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.75
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.65
KOG0147|consensus	549		98.64
KOG4211|consensus	510		98.63
KOG4206|consensus	221		98.61
KOG1190|consensus	492		98.61
KOG2202|consensus	260		98.5
KOG1457|consensus	284		98.44
KOG4849|consensus	498		98.43
KOG4210|consensus	285		98.41
COG5175	480	MOT2 Transcriptional repressor [Transcription]	98.36
KOG0129|consensus	520		98.36
KOG1365|consensus	508		98.34
KOG1456|consensus	494		98.33
KOG4307|consensus	944		98.32
KOG2416|consensus	718		98.24
KOG2314|consensus	698		98.22
KOG1190|consensus	492		98.22
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	98.2
KOG1548|consensus	382		98.15
KOG3152|consensus	278		98.06
KOG0120|consensus	500		98.01
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.99
KOG4676|consensus	479		97.96
KOG1365|consensus	508		97.93
KOG1456|consensus	494		97.93
KOG4676|consensus	479		97.92
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	97.9
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.81
KOG0112|consensus	975		97.79
KOG0129|consensus	520		97.79
KOG1996|consensus	378		97.79
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	97.76
KOG1855|consensus	484		97.75
KOG0128|consensus	881		97.46
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	97.36
KOG0128|consensus	881		97.3
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	97.28
KOG4307|consensus	944		97.26
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	97.2
KOG4660|consensus	549		97.18
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	97.15
KOG0115|consensus	275		97.09
KOG2193|consensus	584		97.03
KOG2135|consensus	526		96.97
KOG2253|consensus	668		96.92
KOG0112|consensus	975		96.82
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	96.72
KOG4285|consensus	350		96.61
KOG2591|consensus	684		96.61
KOG2068|consensus	327		96.58
KOG0804|consensus	493		96.3
KOG4574|consensus	1007		95.96
KOG4210|consensus	285		95.76
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	95.51
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	94.99
KOG2318|consensus	650		94.4
KOG2193|consensus	584		94.37
KOG4207|consensus	256		94.29
KOG4483|consensus	528		94.21
KOG0835|consensus	367		93.58
smart00596	69	PRE_C2HC PRE_C2HC domain.	92.92
KOG4019|consensus	193		92.49
PF07530	68	PRE_C2HC: Associated with zinc fingers; InterPro:	92.14
KOG4410|consensus	396		90.49
KOG0107|consensus	195		88.22
KOG1295|consensus	376		86.88
KOG2295|consensus	648		85.94
PRK14548	84	50S ribosomal protein L23P; Provisional	85.32
PF03468	116	XS: XS domain; InterPro: IPR005380 The XS (rice ge	84.51
KOG4365|consensus	572		84.23
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	83.95
TIGR03636	77	L23_arch archaeal ribosomal protein L23. This mode	81.44
KOG4454|consensus	267		80.78
COG0724	306	RNA-binding proteins (RRM domain) [General functio	80.12

>KOG4207|consensus

Probab=99.95  E-value=1.8e-27  Score=166.00  Aligned_cols=95  Identities=86%  Similarity=1.431  Sum_probs=93.2

Q ss_pred             CCCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCccc
Q psy7051           1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRML   80 (158)
Q Consensus         1 ~~~~~p~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i   80 (158)
                      |+||.+||+++++++|.|-||..-++.++|..+|++||.|..|.|+.|..|....|||||.|....+|+.|++.|+|..|
T Consensus         1 MS~g~~PPdv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~l   80 (256)
T KOG4207|consen    1 MSYGRPPPDVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVL   80 (256)
T ss_pred             CCCCCCCCCcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceee
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCceEEEEeeecCCC
Q psy7051          81 DGRELRVQMARYGRP   95 (158)
Q Consensus        81 ~g~~i~v~~a~~~~~   95 (158)
                      +|+.|.|++|+++++
T Consensus        81 dgRelrVq~arygr~   95 (256)
T KOG4207|consen   81 DGRELRVQMARYGRP   95 (256)
T ss_pred             ccceeeehhhhcCCC
Confidence            999999999998876

>KOG0107|consensus

Probab=99.92  E-value=9.6e-24  Score=143.82  Aligned_cols=76  Identities=37%  Similarity=0.640  Sum_probs=71.5

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeec
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARY   92 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~   92 (158)
                      .++||||||+..+++.||+.+|..||.|..|+|-.+     +.|||||||+++.+|+.|+..|+|..|+|..|.|++++.
T Consensus        10 ~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn-----PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G   84 (195)
T KOG0107|consen   10 NTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN-----PPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTG   84 (195)
T ss_pred             CceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec-----CCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecC
Confidence            478999999999999999999999999999999776     479999999999999999999999999999999999984


Q ss_pred             C
Q psy7051          93 G   93 (158)
Q Consensus        93 ~   93 (158)
                      .
T Consensus        85 ~   85 (195)
T KOG0107|consen   85 R   85 (195)
T ss_pred             C
Confidence            3

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

Probab=99.90  E-value=2.2e-22  Score=137.30  Aligned_cols=84  Identities=37%  Similarity=0.525  Sum_probs=78.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ..++|||+|||+.+++++|+++|++||.|+.|.|+.+..+++++|||||+|.+.++|+.||+.||+..|+|+.|+|+++.
T Consensus        33 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a~  112 (144)
T PLN03134         33 MSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPAN  112 (144)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeCC
Confidence            35789999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             cCCC
Q psy7051          92 YGRP   95 (158)
Q Consensus        92 ~~~~   95 (158)
                      ....
T Consensus       113 ~~~~  116 (144)
T PLN03134        113 DRPS  116 (144)
T ss_pred             cCCC
Confidence            5433

>KOG0113|consensus

Probab=99.87  E-value=5.8e-21  Score=139.80  Aligned_cols=87  Identities=34%  Similarity=0.587  Sum_probs=81.5

Q ss_pred             CCCCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCce
Q psy7051           5 RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRE   84 (158)
Q Consensus         5 ~p~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~   84 (158)
                      .|....++-.||||+-|+..++|..|+..|+.||+|+.|.|+.++.||+++|||||+|+.+-++..|++..+|..|+|+.
T Consensus        93 dp~a~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrr  172 (335)
T KOG0113|consen   93 DPNAIGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRR  172 (335)
T ss_pred             CCcccCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcE
Confidence            44445577799999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEeee
Q psy7051          85 LRVQMAR   91 (158)
Q Consensus        85 i~v~~a~   91 (158)
                      |.|.+..
T Consensus       173 i~VDvER  179 (335)
T KOG0113|consen  173 ILVDVER  179 (335)
T ss_pred             EEEEecc
Confidence            9999865

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.80  E-value=5.5e-19  Score=136.68  Aligned_cols=79  Identities=28%  Similarity=0.387  Sum_probs=76.2

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeec
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARY   92 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~   92 (158)
                      .+|||+|||+.+++++|.++|++||.|+.|.|+.+..++.++|||||+|.+.++|..|++.|||..|.|+.|+|.|...
T Consensus       270 ~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~  348 (352)
T TIGR01661       270 YCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTN  348 (352)
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccC
Confidence            4799999999999999999999999999999999998999999999999999999999999999999999999999873

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

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.80  E-value=4.8e-19  Score=136.38  Aligned_cols=82  Identities=29%  Similarity=0.400  Sum_probs=77.6

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      ....++|||+|||+++++++|+++|+.||+|+.|+|+.+..+++.+|||||+|.++++|+.||+.||+..|.++.|+|.+
T Consensus       104 ~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~  183 (346)
T TIGR01659       104 NNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSY  183 (346)
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeec
Confidence            34568999999999999999999999999999999999988999999999999999999999999999999999999998


Q ss_pred             ee
Q psy7051          90 AR   91 (158)
Q Consensus        90 a~   91 (158)
                      ++
T Consensus       184 a~  185 (346)
T TIGR01659       184 AR  185 (346)
T ss_pred             cc
Confidence            75

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.80  E-value=4.4e-19  Score=137.24  Aligned_cols=81  Identities=30%  Similarity=0.540  Sum_probs=77.4

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      +..+|||+|||..+++++|+++|+.||+|..|.|+.++.+++++|||||+|.+.++|+.||+.|||..|.|+.|.|.+++
T Consensus         2 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~   81 (352)
T TIGR01661         2 SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYAR   81 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeec
Confidence            45789999999999999999999999999999999998899999999999999999999999999999999999999986


Q ss_pred             c
Q psy7051          92 Y   92 (158)
Q Consensus        92 ~   92 (158)
                      .
T Consensus        82 ~   82 (352)
T TIGR01661        82 P   82 (352)
T ss_pred             c
Confidence            3

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

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.79  E-value=1.9e-18  Score=133.08  Aligned_cols=90  Identities=32%  Similarity=0.506  Sum_probs=79.5

Q ss_pred             CCCCCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCC-
Q psy7051           4 GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDG-   82 (158)
Q Consensus         4 ~~p~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g-   82 (158)
                      ..|.......++|||+|||..+++++|+++|++||+|+.|.|+.++.++++++||||+|.+.++|++||+.||+..|.+ 
T Consensus       184 a~p~~~~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~  263 (346)
T TIGR01659       184 ARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGG  263 (346)
T ss_pred             ccccccccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCC
Confidence            3343333446789999999999999999999999999999999998899999999999999999999999999998866 


Q ss_pred             -ceEEEEeeecC
Q psy7051          83 -RELRVQMARYG   93 (158)
Q Consensus        83 -~~i~v~~a~~~   93 (158)
                       ..|+|.+++..
T Consensus       264 ~~~l~V~~a~~~  275 (346)
T TIGR01659       264 SQPLTVRLAEEH  275 (346)
T ss_pred             ceeEEEEECCcc
Confidence             68999998754

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

>PF00076 RRM_1: RNA recognition motif

Probab=99.79  E-value=9.5e-19  Score=104.91  Aligned_cols=70  Identities=37%  Similarity=0.695  Sum_probs=66.3

Q ss_pred             EEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEE
Q psy7051          16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR   86 (158)
Q Consensus        16 l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~   86 (158)
                      |||+|||+.+++++|.++|++||.|..+.+..+ .++...++|||+|.+.++|+.|++.|+|..|+|+.|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999999999887 5788899999999999999999999999999999875

(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 ....

>KOG0130|consensus

Probab=99.78  E-value=1.4e-18  Score=114.04  Aligned_cols=84  Identities=25%  Similarity=0.357  Sum_probs=78.8

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      -....|||+++...+++++|.+.|..||+|+++.|..+..||..+|||+|+|++.+.|++|+..|||..|.|+.|.|.|+
T Consensus        70 VEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~  149 (170)
T KOG0130|consen   70 VEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWC  149 (170)
T ss_pred             eeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEE
Confidence            34567999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ecCC
Q psy7051          91 RYGR   94 (158)
Q Consensus        91 ~~~~   94 (158)
                      -...
T Consensus       150 Fv~g  153 (170)
T KOG0130|consen  150 FVKG  153 (170)
T ss_pred             EecC
Confidence            7443

>KOG0105|consensus

Probab=99.75  E-value=1.5e-17  Score=114.83  Aligned_cols=83  Identities=35%  Similarity=0.502  Sum_probs=73.4

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeec
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARY   92 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~   92 (158)
                      ..+|||+|||..|.+.+|+++|.+||.|.+|.|...   ..+..||||+|+++.+|+.||..-+|..++|+.|.|+++..
T Consensus         6 ~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r---~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprg   82 (241)
T KOG0105|consen    6 SRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNR---PGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRG   82 (241)
T ss_pred             cceEEecCCCcchhhccHHHHHhhhcceEEEEeccC---CCCCCeeEEEecCccchhhhhhcccccccCcceEEEEeccC
Confidence            468999999999999999999999999999988443   22467999999999999999999999999999999999997


Q ss_pred             CCCCCC
Q psy7051          93 GRPPSS   98 (158)
Q Consensus        93 ~~~~~~   98 (158)
                      +++...
T Consensus        83 gr~s~~   88 (241)
T KOG0105|consen   83 GRSSSD   88 (241)
T ss_pred             CCcccc
Confidence            764433

>KOG0122|consensus

Probab=99.75  E-value=8.3e-18  Score=120.34  Aligned_cols=82  Identities=33%  Similarity=0.546  Sum_probs=78.5

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      ....+|-|.||+.++++.+|+++|.+||.|..|.|..++.||.++|||||.|.+.++|+.||+.|||.-++.-.|.|+|+
T Consensus       187 ~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEws  266 (270)
T KOG0122|consen  187 DDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWS  266 (270)
T ss_pred             CccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEec
Confidence            34578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ec
Q psy7051          91 RY   92 (158)
Q Consensus        91 ~~   92 (158)
                      ++
T Consensus       267 kP  268 (270)
T KOG0122|consen  267 KP  268 (270)
T ss_pred             CC
Confidence            84

>KOG0149|consensus

Probab=99.75  E-value=6.1e-18  Score=120.46  Aligned_cols=80  Identities=30%  Similarity=0.513  Sum_probs=74.7

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ..++||||||+|.+..++|.++|++||+|.+..|+.|+.+++++||+||+|.+.+.|+.||+. ....|+|++..|.+|-
T Consensus        11 ~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnlA~   89 (247)
T KOG0149|consen   11 TFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNLAS   89 (247)
T ss_pred             eEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccchhh
Confidence            347899999999999999999999999999999999999999999999999999999999964 4668999999999987


Q ss_pred             c
Q psy7051          92 Y   92 (158)
Q Consensus        92 ~   92 (158)
                      .
T Consensus        90 l   90 (247)
T KOG0149|consen   90 L   90 (247)
T ss_pred             h
Confidence            6

>KOG0121|consensus

Probab=99.73  E-value=1.2e-17  Score=108.77  Aligned_cols=80  Identities=34%  Similarity=0.690  Sum_probs=76.1

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ...||||+||+..++|++|.++|+++|+|..|.|-.|..+..+-|||||+|.+.++|+.|++.++|..|+.+.|.|.|..
T Consensus        35 ~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D~  114 (153)
T KOG0121|consen   35 KSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWDA  114 (153)
T ss_pred             hcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeeccc
Confidence            35799999999999999999999999999999999998888889999999999999999999999999999999999875

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.73  E-value=3.2e-17  Score=98.55  Aligned_cols=70  Identities=41%  Similarity=0.721  Sum_probs=64.3

Q ss_pred             EEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEE
Q psy7051          16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR   86 (158)
Q Consensus        16 l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~   86 (158)
                      |||+|||+.+++++|.++|+.||.|..+.+..++. +..+++|||+|.++++|..|++.+++..|+|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            79999999999999999999999999999999876 88899999999999999999999999999999874

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 ....

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

Probab=99.72  E-value=7.4e-17  Score=130.39  Aligned_cols=84  Identities=24%  Similarity=0.387  Sum_probs=78.5

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      +...+|||+|||..+++++|+++|+.||.|..+.|+.+..++..+|||||+|.+.++|+.||+.|||..|.|..|.|.++
T Consensus       293 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a  372 (509)
T TIGR01642       293 DSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRA  372 (509)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            34578999999999999999999999999999999999889999999999999999999999999999999999999998


Q ss_pred             ecCC
Q psy7051          91 RYGR   94 (158)
Q Consensus        91 ~~~~   94 (158)
                      ....
T Consensus       373 ~~~~  376 (509)
T TIGR01642       373 CVGA  376 (509)
T ss_pred             ccCC
Confidence            7543

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

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.72  E-value=7.9e-17  Score=117.90  Aligned_cols=76  Identities=22%  Similarity=0.400  Sum_probs=70.1

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeec
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARY   92 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~   92 (158)
                      ..+|||+||++.+++++|+++|+.||+|+.|.|+.+..   ..|||||+|.++++|+.|| .|||..|.|+.|.|.++..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~Al-lLnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETAL-LLSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHH-HhcCCeeCCceEEEEeccC
Confidence            47899999999999999999999999999999988753   4689999999999999999 5999999999999999863

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

Probab=99.70  E-value=8.4e-17  Score=130.35  Aligned_cols=87  Identities=30%  Similarity=0.558  Sum_probs=76.1

Q ss_pred             CCCCCCC-----CCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCC
Q psy7051           3 YGRPPPR-----IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG   77 (158)
Q Consensus         3 ~~~p~~~-----~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g   77 (158)
                      ||.||+.     .+..++|||+|||.+++|++|.++|++||.|..|.|+.+ .++.++|||||+|.+.++|+.||+.||+
T Consensus        43 ~g~Pp~~~~~~~p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng  121 (578)
T TIGR01648        43 YGGPPPGWSGVQPGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNN  121 (578)
T ss_pred             CCCCCCcccCCCCCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCC
Confidence            7766653     233489999999999999999999999999999999999 6899999999999999999999999999


Q ss_pred             cccC-CceEEEEee
Q psy7051          78 RMLD-GRELRVQMA   90 (158)
Q Consensus        78 ~~i~-g~~i~v~~a   90 (158)
                      ..|. ++.|.|..+
T Consensus       122 ~~i~~Gr~l~V~~S  135 (578)
T TIGR01648       122 YEIRPGRLLGVCIS  135 (578)
T ss_pred             CeecCCcccccccc
Confidence            9884 677766654

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

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

Probab=99.70  E-value=1.3e-16  Score=129.64  Aligned_cols=80  Identities=23%  Similarity=0.372  Sum_probs=76.7

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeec
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARY   92 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~   92 (158)
                      ..+|||+||+..+++++|+++|+.||.|..|.|+.+..++..+|||||+|.+.++|..||+.||+..|+|+.|.|.++..
T Consensus       204 ~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi~  283 (612)
T TIGR01645       204 FNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVT  283 (612)
T ss_pred             cceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecCC
Confidence            46899999999999999999999999999999999988899999999999999999999999999999999999998874

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.

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

Probab=99.69  E-value=1.4e-16  Score=127.34  Aligned_cols=79  Identities=38%  Similarity=0.714  Sum_probs=76.2

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ..+|||+|||..+++++|+++|++||.|..|.|+.+..++..+|||||+|.+.++|..|++.|||..|.|+.|.|.++.
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            5789999999999999999999999999999999998888999999999999999999999999999999999999976

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.

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

Probab=99.68  E-value=1.6e-16  Score=129.12  Aligned_cols=79  Identities=32%  Similarity=0.553  Sum_probs=75.3

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      ...+|||+||++.+++++|+++|.+||.|..|.|+.++.+++++|||||+|.+.++|+.|++.|||..|.|+.|+|...
T Consensus       106 ~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp  184 (612)
T TIGR01645       106 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  184 (612)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeeccc
Confidence            4578999999999999999999999999999999999999999999999999999999999999999999999999854

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.

>smart00362 RRM_2 RNA recognition motif

Probab=99.68  E-value=4e-16  Score=93.01  Aligned_cols=72  Identities=43%  Similarity=0.757  Sum_probs=66.5

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEE
Q psy7051          15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ   88 (158)
Q Consensus        15 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~   88 (158)
                      +|+|+|||..+++++|+++|.+||.|..+.+..+.  +...++|||+|.+.++|+.|++.|++..|.|..|.|.
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            58999999999999999999999999999888775  6678999999999999999999999999999998873

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

Probab=99.68  E-value=2.4e-16  Score=128.96  Aligned_cols=77  Identities=34%  Similarity=0.518  Sum_probs=74.6

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        15 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      +|||+|||.++++++|.++|.+||.|..|.|+.+..+++++|||||+|.+.++|+.||+.||+..|.|+.|.|.|+.
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            69999999999999999999999999999999999889999999999999999999999999999999999999875

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

>KOG0117|consensus

Probab=99.68  E-value=3.8e-16  Score=120.03  Aligned_cols=89  Identities=30%  Similarity=0.588  Sum_probs=80.0

Q ss_pred             CCCCCCCCCC-----CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCC
Q psy7051           3 YGRPPPRIEG-----MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG   77 (158)
Q Consensus         3 ~~~p~~~~~~-----~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g   77 (158)
                      ||.|||.-+.     .+-||||.||.++.|++|..+|++.|+|-++.|++++.+|.++|||||+|.+.++|+.||+.||+
T Consensus        68 ~ggPpP~weg~~p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn  147 (506)
T KOG0117|consen   68 YGGPPPGWEGPPPPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNN  147 (506)
T ss_pred             cCCCCCcccCCCCCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhC
Confidence            5666664332     46899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccc-CCceEEEEeee
Q psy7051          78 RML-DGRELRVQMAR   91 (158)
Q Consensus        78 ~~i-~g~~i~v~~a~   91 (158)
                      .+| .|+.|.|+.+-
T Consensus       148 ~Eir~GK~igvc~Sv  162 (506)
T KOG0117|consen  148 YEIRPGKLLGVCVSV  162 (506)
T ss_pred             ccccCCCEeEEEEee
Confidence            998 68888888764

>KOG0111|consensus

Probab=99.67  E-value=5.2e-17  Score=114.92  Aligned_cols=82  Identities=35%  Similarity=0.519  Sum_probs=78.8

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeec
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARY   92 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~   92 (158)
                      ..+||||+|...+++.-|...|-+||.|+.|.++.|.++++.+||+||+|...|+|.+||..||+.+|.|+.|.|.+|++
T Consensus        10 KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~AkP   89 (298)
T KOG0111|consen   10 KRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAKP   89 (298)
T ss_pred             ceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecCC
Confidence            47899999999999999999999999999999999999999999999999999999999999999999999999999986


Q ss_pred             CC
Q psy7051          93 GR   94 (158)
Q Consensus        93 ~~   94 (158)
                      .+
T Consensus        90 ~k   91 (298)
T KOG0111|consen   90 EK   91 (298)
T ss_pred             cc
Confidence            54

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.66  E-value=8.3e-16  Score=111.01  Aligned_cols=76  Identities=24%  Similarity=0.336  Sum_probs=69.1

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ...+|||+||++.+++++|++||+.||+|..|.|+.+..   ..++|||+|.++++|+.|+ .|+|..|.++.|.|....
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~e---t~gfAfVtF~d~~aaetAl-lLnGa~l~d~~I~It~~~   79 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGE---YACTAYVTFKDAYALETAV-LLSGATIVDQRVCITRWG   79 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCC---cceEEEEEECCHHHHHHHH-hcCCCeeCCceEEEEeCc
Confidence            358999999999999999999999999999999998743   3579999999999999999 699999999999998754

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

Probab=99.66  E-value=6.9e-16  Score=123.32  Aligned_cols=80  Identities=33%  Similarity=0.509  Sum_probs=75.2

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ...+|||+|||..+++++|+++|++||.|..|.|+.++.++..+|||||+|.+.++|+.||. |+|..|.|..|.|.++.
T Consensus        88 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~~~  166 (457)
T TIGR01622        88 DDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQSSQ  166 (457)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEeecc
Confidence            35789999999999999999999999999999999999899999999999999999999995 89999999999998875


Q ss_pred             c
Q psy7051          92 Y   92 (158)
Q Consensus        92 ~   92 (158)
                      .
T Consensus       167 ~  167 (457)
T TIGR01622       167 A  167 (457)
T ss_pred             h
Confidence            3

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

>PLN03213 repressor of silencing 3; Provisional

Probab=99.66  E-value=6.1e-16  Score=120.59  Aligned_cols=76  Identities=28%  Similarity=0.456  Sum_probs=70.4

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCH--HHHHHHHHHhCCcccCCceEEEEe
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK--RDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~--~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      ...+||||||++.+++++|..+|..||.|..|.|+.  .+|  +|||||+|.+.  .++..||..|||..|.|+.|+|..
T Consensus         9 ~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpR--ETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNK   84 (759)
T PLN03213          9 GGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVR--TKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEK   84 (759)
T ss_pred             cceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEec--ccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEee
Confidence            347899999999999999999999999999999984  466  89999999987  689999999999999999999999


Q ss_pred             ee
Q psy7051          90 AR   91 (158)
Q Consensus        90 a~   91 (158)
                      |+
T Consensus        85 AK   86 (759)
T PLN03213         85 AK   86 (759)
T ss_pred             cc
Confidence            86

>KOG0125|consensus

Probab=99.65  E-value=4.1e-16  Score=115.88  Aligned_cols=80  Identities=34%  Similarity=0.553  Sum_probs=73.8

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      ...+.|+|.|||...-+.||..+|++||.|..|+|+.+.  .-++||+||+|++.+||+.|-++|||..|.|++|.|..|
T Consensus        94 ~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE--RGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~A  171 (376)
T KOG0125|consen   94 DTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE--RGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNA  171 (376)
T ss_pred             CCCceeEeecCCccccCccHHHHHHhhCceeeEEEEecc--CCCCccceEEecChhhHHHHHHHhhcceeeceEEEEecc
Confidence            345789999999999999999999999999999999873  447999999999999999999999999999999999998


Q ss_pred             ec
Q psy7051          91 RY   92 (158)
Q Consensus        91 ~~   92 (158)
                      +.
T Consensus       172 Ta  173 (376)
T KOG0125|consen  172 TA  173 (376)
T ss_pred             ch
Confidence            73

>KOG0131|consensus

Probab=99.65  E-value=3.8e-16  Score=107.47  Aligned_cols=82  Identities=30%  Similarity=0.483  Sum_probs=77.6

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      .....||||+||+..++++.|.++|-+.|+|..+.++.+..++..+|||||+|.++|+|+-||+.||...|.|++|+|..
T Consensus         6 rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~k   85 (203)
T KOG0131|consen    6 RNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNK   85 (203)
T ss_pred             cCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEe
Confidence            34568999999999999999999999999999999999999999999999999999999999999998899999999988


Q ss_pred             ee
Q psy7051          90 AR   91 (158)
Q Consensus        90 a~   91 (158)
                      +.
T Consensus        86 as   87 (203)
T KOG0131|consen   86 AS   87 (203)
T ss_pred             cc
Confidence            75

>KOG0148|consensus

Probab=99.64  E-value=4.8e-16  Score=112.89  Aligned_cols=80  Identities=35%  Similarity=0.543  Sum_probs=77.4

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ....|||+.|...|+-++|++.|.+||+|.+++|+.|..|++.+||+||.|.+.++|+.||..|||.+|+++.|...||.
T Consensus        61 ~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWAT  140 (321)
T KOG0148|consen   61 QHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWAT  140 (321)
T ss_pred             cceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccccc
Confidence            35679999999999999999999999999999999999999999999999999999999999999999999999999997

>smart00360 RRM RNA recognition motif

Probab=99.64  E-value=1.5e-15  Score=90.19  Aligned_cols=71  Identities=44%  Similarity=0.759  Sum_probs=66.1

Q ss_pred             EeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEE
Q psy7051          18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ   88 (158)
Q Consensus        18 V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~   88 (158)
                      |+|||..+++++|+++|++||.|..+.+..++.++.+.++|||+|.+.++|..|++.|++..+.|..|.|.
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            57999999999999999999999999998887778889999999999999999999999999999998873

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

Probab=99.64  E-value=1.7e-15  Score=123.94  Aligned_cols=80  Identities=39%  Similarity=0.586  Sum_probs=75.3

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ...+|||+||+..+++++|+++|++||.|+.|.++.+ .++..+|||||+|.+.++|++|+..|||..|+|+.|.|.++.
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 QGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQ  362 (562)
T ss_pred             CCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEEC-CCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEecc
Confidence            3468999999999999999999999999999999988 588899999999999999999999999999999999999987


Q ss_pred             c
Q psy7051          92 Y   92 (158)
Q Consensus        92 ~   92 (158)
                      .
T Consensus       363 ~  363 (562)
T TIGR01628       363 R  363 (562)
T ss_pred             C
Confidence            3

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

>KOG0126|consensus

Probab=99.63  E-value=2.5e-17  Score=113.30  Aligned_cols=79  Identities=34%  Similarity=0.544  Sum_probs=75.3

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ..-|||||||...||.+|..+|++||+|+.|.++.|+.||+++||||+.|++..+..-|+..|||..|.|+.|+|...-
T Consensus        35 sA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~  113 (219)
T KOG0126|consen   35 SAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVS  113 (219)
T ss_pred             ceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeecc
Confidence            3569999999999999999999999999999999999999999999999999999999999999999999999999753

>KOG0415|consensus

Probab=99.63  E-value=4.8e-16  Score=116.70  Aligned_cols=81  Identities=32%  Similarity=0.434  Sum_probs=77.0

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      ++...|||..|++-++.++|+-+|+.||.|..|.|+.+..||....||||+|++.++++.|+-+|++..|..+.|+|.|+
T Consensus       237 PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFS  316 (479)
T KOG0415|consen  237 PPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFS  316 (479)
T ss_pred             CCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeehh
Confidence            44467999999999999999999999999999999999999999999999999999999999999999999999999996


Q ss_pred             e
Q psy7051          91 R   91 (158)
Q Consensus        91 ~   91 (158)
                      .
T Consensus       317 Q  317 (479)
T KOG0415|consen  317 Q  317 (479)
T ss_pred             h
Confidence            4

>KOG0114|consensus

Probab=99.63  E-value=3.2e-15  Score=94.10  Aligned_cols=77  Identities=31%  Similarity=0.422  Sum_probs=70.4

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ....|||.|||..+|.+++.++|.+||.|.+|.+-..+.|   +|.|||.|++..+|..|+.+|+|..+.+..+.|-+-.
T Consensus        17 vnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~T---rGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq   93 (124)
T KOG0114|consen   17 VNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKET---RGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQ   93 (124)
T ss_pred             hheeEEEecCCccccHHHHHHHhhcccceEEEEecCccCc---CceEEEEehHhhhHHHHHHHhcccccCCceEEEEecC
Confidence            3478999999999999999999999999999999766544   6999999999999999999999999999999998754

>KOG0148|consensus

Probab=99.63  E-value=1.7e-15  Score=110.07  Aligned_cols=78  Identities=28%  Similarity=0.468  Sum_probs=72.4

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      +..++|||||++..+++++|++.|++||+|.+|.+.++      +|||||.|.+.|.|..||..+|+.+|.|..|++.|-
T Consensus       162 p~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~------qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsWG  235 (321)
T KOG0148|consen  162 PDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD------QGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWG  235 (321)
T ss_pred             CCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc------cceEEEEecchhhHHHHHHHhcCceeCceEEEEecc
Confidence            44589999999999999999999999999999999887      589999999999999999999999999999999998


Q ss_pred             ecCC
Q psy7051          91 RYGR   94 (158)
Q Consensus        91 ~~~~   94 (158)
                      +...
T Consensus       236 Ke~~  239 (321)
T KOG0148|consen  236 KEGD  239 (321)
T ss_pred             ccCC
Confidence            7543

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

Probab=99.63  E-value=3.9e-15  Score=120.77  Aligned_cols=74  Identities=34%  Similarity=0.521  Sum_probs=68.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhc--CceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERC--GEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~--G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      ..++|||+||+..+++++|+++|++|  |+|+.|.++        ++||||+|.+.++|++|++.||+.+|.|+.|+|.+
T Consensus       232 ~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~--------rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~  303 (578)
T TIGR01648       232 KVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI--------RDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTL  303 (578)
T ss_pred             cccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee--------cCeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            35789999999999999999999999  999999875        35999999999999999999999999999999999


Q ss_pred             eecC
Q psy7051          90 ARYG   93 (158)
Q Consensus        90 a~~~   93 (158)
                      ++..
T Consensus       304 Akp~  307 (578)
T TIGR01648       304 AKPV  307 (578)
T ss_pred             ccCC
Confidence            9854

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.

>KOG0145|consensus

Probab=99.62  E-value=1.7e-15  Score=109.68  Aligned_cols=84  Identities=32%  Similarity=0.548  Sum_probs=79.3

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      .+..+.|.|.-||..+|++||+.+|...|+|+.|+++.|+.+|.+.||+||.|..++||+.|+..|||..|..+.|+|.|
T Consensus        38 ~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSy  117 (360)
T KOG0145|consen   38 DESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSY  117 (360)
T ss_pred             CcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEe
Confidence            34457899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecC
Q psy7051          90 ARYG   93 (158)
Q Consensus        90 a~~~   93 (158)
                      |++.
T Consensus       118 ARPS  121 (360)
T KOG0145|consen  118 ARPS  121 (360)
T ss_pred             ccCC
Confidence            9844

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

Probab=99.62  E-value=3.5e-15  Score=120.04  Aligned_cols=78  Identities=24%  Similarity=0.290  Sum_probs=71.6

Q ss_pred             CCCcEEEEeCCCC-CCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          11 EGMVSLKVDNLTY-RTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        11 ~~~~~l~V~nl~~-~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      .+..+|||+||++ .+++++|.++|+.||.|..|+++.++     +|+|||+|.+.++|+.|++.|||..|.|+.|.|.+
T Consensus       273 ~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~  347 (481)
T TIGR01649       273 GPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK-----KETALIEMADPYQAQLALTHLNGVKLFGKPLRVCP  347 (481)
T ss_pred             CCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEE
Confidence            3557999999998 69999999999999999999998763     58999999999999999999999999999999999


Q ss_pred             eecC
Q psy7051          90 ARYG   93 (158)
Q Consensus        90 a~~~   93 (158)
                      ++..
T Consensus       348 s~~~  351 (481)
T TIGR01649       348 SKQQ  351 (481)
T ss_pred             cccc
Confidence            8754

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

>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=99.62  E-value=6.6e-15  Score=88.11  Aligned_cols=74  Identities=49%  Similarity=0.773  Sum_probs=67.8

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        15 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      +|+|+|||..+++++|.++|..||.|..+.+..+..+ ...++|||+|.+.++|..|++.+++..+.|..|.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~-~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDT-KSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCC-CcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            4899999999999999999999999999999877644 5688999999999999999999999999999998864

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).

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

Probab=99.61  E-value=4.7e-15  Score=109.49  Aligned_cols=79  Identities=46%  Similarity=0.723  Sum_probs=76.2

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ..+|||+|||..+++++|.++|.+||.|..+.+..++.++..+|||||+|.+.++|..|++.+++..|.|+.|.|.++.
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~  193 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQ  193 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeeccc
Confidence            5899999999999999999999999999999999998899999999999999999999999999999999999999975

>KOG0108|consensus

Probab=99.59  E-value=3.7e-15  Score=116.95  Aligned_cols=82  Identities=32%  Similarity=0.532  Sum_probs=78.8

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeecC
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARYG   93 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~~   93 (158)
                      ..|||||+|+++++++|.++|+..|.|..++++.|..+|+.+|||||+|.+.++|+.|++.|||.++.|++|+|.|+...
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~   98 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNR   98 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccccc
Confidence            78999999999999999999999999999999999999999999999999999999999999999999999999998755


Q ss_pred             CC
Q psy7051          94 RP   95 (158)
Q Consensus        94 ~~   95 (158)
                      ..
T Consensus        99 ~~  100 (435)
T KOG0108|consen   99 KN  100 (435)
T ss_pred             ch
Confidence            43

>KOG0145|consensus

Probab=99.59  E-value=1.2e-14  Score=105.32  Aligned_cols=80  Identities=28%  Similarity=0.392  Sum_probs=76.6

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ....|||-||.++++|..|+++|.+||.|..|+++.|..+.+++||+||.+.+.++|..||..|||..+.++.|.|.|..
T Consensus       277 ~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFKt  356 (360)
T KOG0145|consen  277 GGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKT  356 (360)
T ss_pred             CeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEec
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999865

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

Probab=99.58  E-value=9.7e-15  Score=117.52  Aligned_cols=74  Identities=18%  Similarity=0.186  Sum_probs=67.7

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHh--CCcccCCceEEEEee
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM--DGRMLDGRELRVQMA   90 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l--~g~~i~g~~i~v~~a   90 (158)
                      ..+|||+|||+.+++++|.++|++||.|..|.++.+      ++||||+|.+.++|+.|++.|  ++..|.|+.|.|.++
T Consensus         2 s~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~------k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s   75 (481)
T TIGR01649         2 SPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPG------KRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYS   75 (481)
T ss_pred             ccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECC------CCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEec
Confidence            478999999999999999999999999999998764      479999999999999999864  678999999999998


Q ss_pred             ec
Q psy7051          91 RY   92 (158)
Q Consensus        91 ~~   92 (158)
                      ..
T Consensus        76 ~~   77 (481)
T TIGR01649        76 TS   77 (481)
T ss_pred             CC
Confidence            64

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

>KOG0144|consensus

Probab=99.57  E-value=1.1e-14  Score=111.69  Aligned_cols=85  Identities=29%  Similarity=0.569  Sum_probs=76.2

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcc-cCC--ceEEE
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRM-LDG--RELRV   87 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~-i~g--~~i~v   87 (158)
                      ....++|||.+|..++|.||+++|++||.|.+|.|++|+.++..+|||||.|.+.++|.+|+..|++.. |-|  ..|.|
T Consensus        32 ~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqv  111 (510)
T KOG0144|consen   32 GSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQV  111 (510)
T ss_pred             chhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceee
Confidence            445689999999999999999999999999999999999999999999999999999999999999875 433  67899


Q ss_pred             EeeecCCC
Q psy7051          88 QMARYGRP   95 (158)
Q Consensus        88 ~~a~~~~~   95 (158)
                      .+|...+.
T Consensus       112 k~Ad~E~e  119 (510)
T KOG0144|consen  112 KYADGERE  119 (510)
T ss_pred             cccchhhh
Confidence            99875443

>KOG0109|consensus

Probab=99.55  E-value=7.7e-15  Score=107.66  Aligned_cols=72  Identities=33%  Similarity=0.541  Sum_probs=68.1

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeecC
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARYG   93 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~~   93 (158)
                      .+|||||||..+++++|+.+|++||+|.+|.|+++        |+||..++...++.||..||+..|+|..|+|+-++..
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN--------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK   74 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN--------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK   74 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc--------cceEEeecccccHHHHhhcccceecceEEEEEecccc
Confidence            57999999999999999999999999999999866        9999999999999999999999999999999988754

>PF13893 RRM_5: RNA recognition motif

Probab=99.54  E-value=5.6e-14  Score=80.82  Aligned_cols=56  Identities=43%  Similarity=0.786  Sum_probs=50.6

Q ss_pred             HHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          30 LRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        30 l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      |.++|++||+|..+.+..+.     .++|||+|.+.++|+.|++.|||..|.|+.|+|+||
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            67899999999999987653     579999999999999999999999999999999986

(a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....

>KOG0127|consensus

Probab=99.53  E-value=4.7e-14  Score=111.06  Aligned_cols=82  Identities=38%  Similarity=0.568  Sum_probs=74.4

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHh-----CC-cccCCc
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM-----DG-RMLDGR   83 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l-----~g-~~i~g~   83 (158)
                      +....||||.|||+.+++++|.+.|.+||+|.++.++.++.|++++|.|||.|.+..+|++||...     .| ..|.|+
T Consensus       289 ~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR  368 (678)
T KOG0127|consen  289 ITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGR  368 (678)
T ss_pred             ccccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEecc
Confidence            444589999999999999999999999999999999999999999999999999999999999876     23 467999


Q ss_pred             eEEEEeee
Q psy7051          84 ELRVQMAR   91 (158)
Q Consensus        84 ~i~v~~a~   91 (158)
                      .|+|..|-
T Consensus       369 ~Lkv~~Av  376 (678)
T KOG0127|consen  369 LLKVTLAV  376 (678)
T ss_pred             EEeeeecc
Confidence            99999874

>KOG0117|consensus

Probab=99.52  E-value=3.6e-14  Score=109.32  Aligned_cols=72  Identities=36%  Similarity=0.627  Sum_probs=68.1

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeec
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARY   92 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~   92 (158)
                      .+.|||.||+.++|++.|+++|.+||.|+.|+.+.|        ||||.|.+.++|.+|++.|||.+|+|..|.|.+|+.
T Consensus       259 VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD--------YaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP  330 (506)
T KOG0117|consen  259 VKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD--------YAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKP  330 (506)
T ss_pred             eeeeeeeccchhhhHHHHHHHHHhccceEEeecccc--------eeEEeecchHHHHHHHHHhcCceecCceEEEEecCC
Confidence            378999999999999999999999999999988755        999999999999999999999999999999999984

>KOG0127|consensus

Probab=99.51  E-value=7.3e-14  Score=110.02  Aligned_cols=78  Identities=40%  Similarity=0.666  Sum_probs=72.2

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ...|+|.|||+.+...+|+.+|+.||.|.+|.|+... .++..|||||+|....+|..|++.||+..|.|++|-|.||-
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 KWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKK-DGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAV  194 (678)
T ss_pred             cceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCC-CCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeec
Confidence            5689999999999999999999999999999999776 44555999999999999999999999999999999999974

>smart00361 RRM_1 RNA recognition motif

Probab=99.51  E-value=1e-13  Score=83.38  Aligned_cols=61  Identities=34%  Similarity=0.602  Sum_probs=54.4

Q ss_pred             HHHHHHHhh----hcCceEEEE-EccCCCC--CCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEE
Q psy7051          27 PDDLRRVFE----RCGEVGDIY-IPRDRFT--RESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV   87 (158)
Q Consensus        27 ~~~l~~~f~----~~G~i~~v~-~~~~~~~--~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v   87 (158)
                      +++|.++|.    +||.|..|. ++.++.+  +..+|||||+|.+.++|..|++.|||..|.|+.|.+
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            578888888    999999985 6666555  889999999999999999999999999999999986

>KOG0147|consensus

Probab=99.51  E-value=2.3e-14  Score=112.73  Aligned_cols=78  Identities=36%  Similarity=0.635  Sum_probs=74.5

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ..|||+||..++++++|..+|++||.|..|.+.++..+|.++||+||+|.+.++|..|++.|||.+|.|+.|+|..-.
T Consensus       279 ~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~  356 (549)
T KOG0147|consen  279 RRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVT  356 (549)
T ss_pred             hhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEee
Confidence            349999999999999999999999999999999999999999999999999999999999999999999999998755

>KOG4212|consensus

Probab=99.50  E-value=1.1e-13  Score=106.60  Aligned_cols=78  Identities=28%  Similarity=0.433  Sum_probs=72.9

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhh-hcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeec
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFE-RCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARY   92 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~-~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~   92 (158)
                      ..+||+|+|+++.|++|+++|. +.|+|++|.+..|. +++.+|||.|+|+++|.+++|+++||..+|.|+.|+|+....
T Consensus        45 R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~-~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~d  123 (608)
T KOG4212|consen   45 RSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDE-SGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDHD  123 (608)
T ss_pred             ceEEEecCcchhhhHhHHHHHHHhcCceEeeeeeccc-CCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccCc
Confidence            4599999999999999999996 57999999999985 899999999999999999999999999999999999998764

>KOG0144|consensus

Probab=99.50  E-value=3.3e-14  Score=109.11  Aligned_cols=85  Identities=34%  Similarity=0.515  Sum_probs=76.0

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcc-cCC--ceEEEE
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRM-LDG--RELRVQ   88 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~-i~g--~~i~v~   88 (158)
                      ...+|||+-|+..++|.+|+++|.+||.|++|.|..+. .+.++|||||.|.+.+.|..||+.|||.. +.|  .+|.|.
T Consensus       123 ~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~-~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVk  201 (510)
T KOG0144|consen  123 EERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDP-DGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVK  201 (510)
T ss_pred             cchhhhhhhccccccHHHHHHHHHhhCccchhhheecc-cccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEE
Confidence            35789999999999999999999999999999999986 77899999999999999999999999984 555  579999


Q ss_pred             eeecCCCCC
Q psy7051          89 MARYGRPPS   97 (158)
Q Consensus        89 ~a~~~~~~~   97 (158)
                      ||...+++.
T Consensus       202 FADtqkdk~  210 (510)
T KOG0144|consen  202 FADTQKDKD  210 (510)
T ss_pred             ecccCCCch
Confidence            998766543

>KOG0109|consensus

Probab=99.44  E-value=1.8e-13  Score=100.52  Aligned_cols=75  Identities=31%  Similarity=0.504  Sum_probs=69.8

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      ...++|+|+||.+.++.+||++.|++||.|.+|+|+++        |+||.|+-.++|..|++.||+.+|.|+.++|+++
T Consensus        76 k~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd--------y~fvh~d~~eda~~air~l~~~~~~gk~m~vq~s  147 (346)
T KOG0109|consen   76 KASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD--------YAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLS  147 (346)
T ss_pred             CCccccccCCCCccccCHHHhhhhcccCCceeeeeecc--------eeEEEEeeccchHHHHhcccccccccceeeeeee
Confidence            34578999999999999999999999999999999765        9999999999999999999999999999999998


Q ss_pred             ecC
Q psy7051          91 RYG   93 (158)
Q Consensus        91 ~~~   93 (158)
                      +..
T Consensus       148 tsr  150 (346)
T KOG0109|consen  148 TSR  150 (346)
T ss_pred             ccc
Confidence            743

>KOG0124|consensus

Probab=99.44  E-value=9.5e-14  Score=104.96  Aligned_cols=77  Identities=32%  Similarity=0.586  Sum_probs=74.3

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      +..||||.+.+.+.|+.|...|.+||+|+.|.+..|+.|++.+|||||+|+-+|.|+-|++.|||..++|+.|+|..
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgr  189 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGR  189 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccC
Confidence            46799999999999999999999999999999999999999999999999999999999999999999999999974

>KOG0131|consensus

Probab=99.41  E-value=9.3e-13  Score=90.86  Aligned_cols=85  Identities=25%  Similarity=0.308  Sum_probs=76.4

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEE-EEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEE
Q psy7051           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDI-YIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV   87 (158)
Q Consensus         9 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v-~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v   87 (158)
                      +......|||+||.+.+++..|.+.|+.||.|... +++.+..+|.+++|+||.|.+.+.+.+|+..|||..+++++|.|
T Consensus        92 nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv  171 (203)
T KOG0131|consen   92 NLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITV  171 (203)
T ss_pred             cccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEE
Confidence            34445789999999999999999999999988653 77888889999999999999999999999999999999999999


Q ss_pred             EeeecC
Q psy7051          88 QMARYG   93 (158)
Q Consensus        88 ~~a~~~   93 (158)
                      .++...
T Consensus       172 ~ya~k~  177 (203)
T KOG0131|consen  172 SYAFKK  177 (203)
T ss_pred             EEEEec
Confidence            999743

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

Probab=99.41  E-value=1.2e-12  Score=106.08  Aligned_cols=73  Identities=19%  Similarity=0.290  Sum_probs=60.2

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhc------------CceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcc
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERC------------GEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRM   79 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~------------G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~   79 (158)
                      ...+|||+|||+.+++++|.++|.++            +.|..+.+.      ..+|||||+|.+.++|+.|| .|+|..
T Consensus       174 ~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~~------~~kg~afVeF~~~e~A~~Al-~l~g~~  246 (509)
T TIGR01642       174 QARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNIN------KEKNFAFLEFRTVEEATFAM-ALDSII  246 (509)
T ss_pred             cccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEEC------CCCCEEEEEeCCHHHHhhhh-cCCCeE
Confidence            35789999999999999999999975            233444432      24689999999999999999 599999


Q ss_pred             cCCceEEEEeee
Q psy7051          80 LDGRELRVQMAR   91 (158)
Q Consensus        80 i~g~~i~v~~a~   91 (158)
                      |.|..|+|....
T Consensus       247 ~~g~~l~v~r~~  258 (509)
T TIGR01642       247 YSNVFLKIRRPH  258 (509)
T ss_pred             eeCceeEecCcc
Confidence            999999986543

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

>KOG0146|consensus

Probab=99.37  E-value=1e-12  Score=95.80  Aligned_cols=82  Identities=27%  Similarity=0.342  Sum_probs=77.5

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      .++...|||-.||.+..+.||..+|-+||.|+..++..|..|..++.|+||.|+++.++++||..|||..|+.+.|+|.+
T Consensus       282 GPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQL  361 (371)
T KOG0146|consen  282 GPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQL  361 (371)
T ss_pred             CCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhhh
Confidence            34568899999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ee
Q psy7051          90 AR   91 (158)
Q Consensus        90 a~   91 (158)
                      .+
T Consensus       362 KR  363 (371)
T KOG0146|consen  362 KR  363 (371)
T ss_pred             cC
Confidence            76

>KOG0153|consensus

Probab=99.34  E-value=4.3e-12  Score=95.28  Aligned_cols=80  Identities=28%  Similarity=0.475  Sum_probs=68.8

Q ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHH-hCCcccCCceE
Q psy7051           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA-MDGRMLDGREL   85 (158)
Q Consensus         7 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~-l~g~~i~g~~i   85 (158)
                      |++.....+|||++|...+++.+|.++|.+||+|..+.++..      .++|||+|.+.+.|+.|.++ ++...|+|..|
T Consensus       222 pPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl  295 (377)
T KOG0153|consen  222 PPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNKLVINGFRL  295 (377)
T ss_pred             CCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcceeeecceEE
Confidence            445556689999999999999999999999999999988765      46999999999999988775 55556899999


Q ss_pred             EEEeeec
Q psy7051          86 RVQMARY   92 (158)
Q Consensus        86 ~v~~a~~   92 (158)
                      +|.|...
T Consensus       296 ~i~Wg~~  302 (377)
T KOG0153|consen  296 KIKWGRP  302 (377)
T ss_pred             EEEeCCC
Confidence            9998775

>KOG4206|consensus

Probab=99.34  E-value=7.4e-12  Score=89.17  Aligned_cols=80  Identities=33%  Similarity=0.488  Sum_probs=71.1

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHH----HhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEE
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR   86 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~----~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~   86 (158)
                      .+..||||.||+..+..++|+.    +|++||.|..|....   +.+.+|-|||.|.+.+.|-.|+..|+|..+.|+.+.
T Consensus         7 ~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k---t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mr   83 (221)
T KOG4206|consen    7 NPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK---TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMR   83 (221)
T ss_pred             CCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC---CCCccCceEEEecChhHHHHHHHHhcCCcccCchhh
Confidence            3445999999999999999887    999999998887643   566789999999999999999999999999999999


Q ss_pred             EEeeecC
Q psy7051          87 VQMARYG   93 (158)
Q Consensus        87 v~~a~~~   93 (158)
                      |+||+..
T Consensus        84 iqyA~s~   90 (221)
T KOG4206|consen   84 IQYAKSD   90 (221)
T ss_pred             eecccCc
Confidence            9999843

>KOG4208|consensus

Probab=99.30  E-value=1.5e-11  Score=86.44  Aligned_cols=81  Identities=22%  Similarity=0.282  Sum_probs=73.6

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhc-CceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERC-GEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~-G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      ....++|..+|..+.+.+|..+|.+| |.|..+.+..++.||.++|||||+|++++.|+-|.+.||+..|.++-|.|.+-
T Consensus        48 ~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vm  127 (214)
T KOG4208|consen   48 IEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHVM  127 (214)
T ss_pred             CccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEe
Confidence            34568999999999999999999998 67888888899999999999999999999999999999999999999998886


Q ss_pred             ec
Q psy7051          91 RY   92 (158)
Q Consensus        91 ~~   92 (158)
                      ..
T Consensus       128 pp  129 (214)
T KOG4208|consen  128 PP  129 (214)
T ss_pred             Cc
Confidence            53

>KOG0132|consensus

Probab=99.30  E-value=9.4e-12  Score=101.59  Aligned_cols=77  Identities=27%  Similarity=0.458  Sum_probs=70.9

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeecC
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARYG   93 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~~   93 (158)
                      +|||||+|+..++|++|..+|+.||+|..|.++..      .+||||.+....+|++|+.+|.+..|.+..|+|.|+-..
T Consensus       422 rTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~------R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~  495 (894)
T KOG0132|consen  422 RTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP------RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGK  495 (894)
T ss_pred             eeeeeccccchhhHHHHHHHHHhcccceeEeeccC------CceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccC
Confidence            79999999999999999999999999999988654      689999999999999999999999999999999999754


Q ss_pred             CCC
Q psy7051          94 RPP   96 (158)
Q Consensus        94 ~~~   96 (158)
                      ..+
T Consensus       496 G~k  498 (894)
T KOG0132|consen  496 GPK  498 (894)
T ss_pred             Ccc
Confidence            443

>KOG4661|consensus

Probab=99.29  E-value=8.4e-12  Score=99.22  Aligned_cols=78  Identities=23%  Similarity=0.389  Sum_probs=74.2

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ..|||.+|...+...+|+.||++||+|+..+|+.+..+.-...|+||++.+.++|..||+.|+..+|.|+.|.|+-++
T Consensus       406 RNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaK  483 (940)
T KOG4661|consen  406 RNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAK  483 (940)
T ss_pred             cceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeecc
Confidence            579999999999999999999999999999999998777788999999999999999999999999999999999876

>KOG0123|consensus

Probab=99.29  E-value=1.4e-11  Score=95.79  Aligned_cols=74  Identities=23%  Similarity=0.470  Sum_probs=69.6

Q ss_pred             EEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeec
Q psy7051          16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARY   92 (158)
Q Consensus        16 l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~   92 (158)
                      |||.||++.++..+|.++|+.||+|..|++..+. .| .+|| ||+|++++.|.+|++.|||..+.+++|.|.....
T Consensus        79 ~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~-~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~  152 (369)
T KOG0123|consen   79 VFIKNLDESIDNKSLYDTFSEFGNILSCKVATDE-NG-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFER  152 (369)
T ss_pred             eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcC-CC-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccc
Confidence            9999999999999999999999999999999986 44 8899 9999999999999999999999999999987653

>KOG0116|consensus

Probab=99.23  E-value=1.5e-10  Score=90.73  Aligned_cols=78  Identities=27%  Similarity=0.396  Sum_probs=66.5

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeec
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARY   92 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~   92 (158)
                      .+|||.|||.+++..+|+++|..||.|+...|......++..+||||+|.+.++++.||++ +-..|++++|.|+.-+.
T Consensus       289 ~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~~  366 (419)
T KOG0116|consen  289 LGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKRP  366 (419)
T ss_pred             cceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEeccc
Confidence            4599999999999999999999999998876654433344458999999999999999975 57789999999998764

>KOG4212|consensus

Probab=99.23  E-value=3.6e-11  Score=92.93  Aligned_cols=76  Identities=34%  Similarity=0.463  Sum_probs=67.4

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      ....++|||.|||...||+.|++-|..||.|.++.|+.   .++.+|  .|.|.++++|+.||..|+|..|.|+.|+|.|
T Consensus       533 arKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadime---~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V~y  607 (608)
T KOG4212|consen  533 ARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIME---NGKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKVTY  607 (608)
T ss_pred             cccccEEEEecCCccccHHHHHHHHHhccceehhhhhc---cCCccc--eEEecCHHHHHHHHHHhccCcccCceeeeee
Confidence            34457899999999999999999999999999998843   455555  8999999999999999999999999999987


Q ss_pred             e
Q psy7051          90 A   90 (158)
Q Consensus        90 a   90 (158)
                      +
T Consensus       608 ~  608 (608)
T KOG4212|consen  608 F  608 (608)
T ss_pred             C
Confidence            4

>KOG0106|consensus

Probab=99.22  E-value=1.6e-11  Score=87.99  Aligned_cols=71  Identities=38%  Similarity=0.638  Sum_probs=65.7

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeec
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARY   92 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~   92 (158)
                      ..|||++||+.+.+.+|++||..||+|..|.|.        .||+||+|++..+|..|+..||+.+|++..+.|++++.
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk--------~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~   72 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMK--------NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARG   72 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceee--------cccceeccCchhhhhcccchhcCceecceeeeeecccc
Confidence            469999999999999999999999999988873        46899999999999999999999999999999999884

>KOG0533|consensus

Probab=99.22  E-value=8.7e-11  Score=85.87  Aligned_cols=79  Identities=32%  Similarity=0.516  Sum_probs=73.0

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ..++|+|.||+..|++++|+++|..||.++.+.|..++ .|.+.|.|-|.|...++|+.|++.+|+..++|..|++....
T Consensus        82 ~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~  160 (243)
T KOG0533|consen   82 RSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIIS  160 (243)
T ss_pred             CcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEec
Confidence            34789999999999999999999999999988888875 88899999999999999999999999999999999888764

>KOG4209|consensus

Probab=99.21  E-value=1.2e-10  Score=85.08  Aligned_cols=84  Identities=29%  Similarity=0.561  Sum_probs=77.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      +...+||+|+...++.++++..|+.||.|..+.++++...++++||+||+|.+.+.++.||. ||+..|.+..|.|.+.+
T Consensus       100 d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~~r  178 (231)
T KOG4209|consen  100 DAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTLKR  178 (231)
T ss_pred             CCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceeeeee
Confidence            45789999999999999999999999999999999999898999999999999999999997 99999999999999988


Q ss_pred             cCCCC
Q psy7051          92 YGRPP   96 (158)
Q Consensus        92 ~~~~~   96 (158)
                      ...+.
T Consensus       179 ~~~pg  183 (231)
T KOG4209|consen  179 TNVPG  183 (231)
T ss_pred             eecCC
Confidence            66433

>KOG0146|consensus

Probab=99.20  E-value=2.3e-11  Score=88.77  Aligned_cols=82  Identities=29%  Similarity=0.493  Sum_probs=72.6

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcc-cCC--ceEEEEe
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRM-LDG--RELRVQM   89 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~-i~g--~~i~v~~   89 (158)
                      ..+||||-|...-.|+|+..+|..||.|++|.+...+ .|..+|||||.|.+..+|+.||..|+|.. +-|  ..|.|++
T Consensus        19 drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~-dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK~   97 (371)
T KOG0146|consen   19 DRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGP-DGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVKF   97 (371)
T ss_pred             chhhhhhhhcccccHHHHHHHhcccCCcceeEEecCC-CCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEEe
Confidence            4789999999999999999999999999999998876 67799999999999999999999999985 433  5689999


Q ss_pred             eecCCC
Q psy7051          90 ARYGRP   95 (158)
Q Consensus        90 a~~~~~   95 (158)
                      +...+.
T Consensus        98 ADTdkE  103 (371)
T KOG0146|consen   98 ADTDKE  103 (371)
T ss_pred             ccchHH
Confidence            875543

>KOG0124|consensus

Probab=99.20  E-value=5.3e-11  Score=90.28  Aligned_cols=78  Identities=23%  Similarity=0.398  Sum_probs=73.5

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      ...|||..+.++.+++||+..|+.||+|..|.+-..+..+..+||+||+|.+......||..||-..|+|..|.|.-+
T Consensus       210 fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~  287 (544)
T KOG0124|consen  210 FNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKC  287 (544)
T ss_pred             hheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEecccc
Confidence            368999999999999999999999999999999999988899999999999999999999999999999999998754

>KOG0110|consensus

Probab=99.18  E-value=7.7e-11  Score=95.52  Aligned_cols=78  Identities=36%  Similarity=0.575  Sum_probs=69.1

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCC---CCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFT---RESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~---~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      ++|||.||++.++.++|..+|.++|.|..+.|...+..   -.+.|||||+|.+.++|+.|++.|+|..|+|+.|.|.++
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            34999999999999999999999999998887655422   124499999999999999999999999999999999999


Q ss_pred             e
Q psy7051          91 R   91 (158)
Q Consensus        91 ~   91 (158)
                      .
T Consensus       596 ~  596 (725)
T KOG0110|consen  596 E  596 (725)
T ss_pred             c
Confidence            8

>KOG4454|consensus

Probab=99.18  E-value=1.1e-11  Score=87.95  Aligned_cols=82  Identities=23%  Similarity=0.291  Sum_probs=72.1

Q ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEE
Q psy7051           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR   86 (158)
Q Consensus         7 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~   86 (158)
                      ++..+...||||+||...++|+.|.++|-+.|+|..|.|+.++ .+..+ ||||.|.++..+.-|++.+||..+.+..|+
T Consensus         3 aaaae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~-d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q   80 (267)
T KOG4454|consen    3 AAAAEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQ-DQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQ   80 (267)
T ss_pred             CCCcchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCc-cCCCc-eeeeecccccchhhhhhhcccchhccchhh
Confidence            3444555889999999999999999999999999999998876 44455 999999999999999999999999999988


Q ss_pred             EEee
Q psy7051          87 VQMA   90 (158)
Q Consensus        87 v~~a   90 (158)
                      |.+-
T Consensus        81 ~~~r   84 (267)
T KOG4454|consen   81 RTLR   84 (267)
T ss_pred             cccc
Confidence            8874

>KOG0123|consensus

Probab=99.18  E-value=8.7e-11  Score=91.42  Aligned_cols=72  Identities=38%  Similarity=0.482  Sum_probs=68.4

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ..||||   +.+|+..|.++|+++|+|..+.+..+. +  +.|||||.|.++++|+.|++.||...|.|+.|.|-|+.
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---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQ   73 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhc
Confidence            468998   899999999999999999999999998 6  89999999999999999999999999999999999886

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

Probab=99.16  E-value=4.6e-10  Score=71.13  Aligned_cols=78  Identities=22%  Similarity=0.381  Sum_probs=69.3

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhc--CceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccC----CceEEE
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERC--GEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLD----GRELRV   87 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~--G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~----g~~i~v   87 (158)
                      +||.|.|+|...+.++|.+++...  |....+-++.|..+..+.|||||.|.+++.|....+.++|..|.    .+.+.|
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i   81 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEI   81 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEE
Confidence            789999999999999999998663  67788899999989999999999999999999999999999875    456778


Q ss_pred             Eeee
Q psy7051          88 QMAR   91 (158)
Q Consensus        88 ~~a~   91 (158)
                      .+|+
T Consensus        82 ~yAr   85 (97)
T PF04059_consen   82 SYAR   85 (97)
T ss_pred             ehhH
Confidence            7776

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

>KOG0110|consensus

Probab=99.14  E-value=5.2e-11  Score=96.49  Aligned_cols=82  Identities=28%  Similarity=0.542  Sum_probs=75.2

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      .++.|+|.|||..++..+|+.+|..||+|..|.|+.....+...|||||+|-++.+|.+|+..|..+.|.|+.|.++||+
T Consensus       612 ~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~  691 (725)
T KOG0110|consen  612 KGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAK  691 (725)
T ss_pred             ccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhc
Confidence            36789999999999999999999999999999998875556678999999999999999999999999999999999987


Q ss_pred             cC
Q psy7051          92 YG   93 (158)
Q Consensus        92 ~~   93 (158)
                      ..
T Consensus       692 ~d  693 (725)
T KOG0110|consen  692 SD  693 (725)
T ss_pred             cc
Confidence            43

>KOG4660|consensus

Probab=99.13  E-value=5.8e-11  Score=93.98  Aligned_cols=72  Identities=36%  Similarity=0.565  Sum_probs=64.9

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEE
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR   86 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~   86 (158)
                      .....+|+|.|||..|++++|..+|+.||+|.+|.....     ..+.+||+|.+.-+|+.|++.|++.+|.|+.|+
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~-----~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPN-----KRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccc-----cCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            344578999999999999999999999999999876443     478999999999999999999999999999888

>KOG4205|consensus

Probab=99.12  E-value=8.7e-11  Score=88.97  Aligned_cols=81  Identities=33%  Similarity=0.476  Sum_probs=72.8

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ...+|||++|++.++++.|++.|.+||+|..|.++.++.++...||+||+|++.+.+.+++. ..-+.|.|+.|.+..|.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~-~~~h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLN-ARTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeec-ccccccCCccccceecc
Confidence            45789999999999999999999999999999999999999999999999999999888884 45678999999888776


Q ss_pred             cC
Q psy7051          92 YG   93 (158)
Q Consensus        92 ~~   93 (158)
                      ..
T Consensus        84 ~r   85 (311)
T KOG4205|consen   84 SR   85 (311)
T ss_pred             Cc
Confidence            43

>KOG4205|consensus

Probab=99.09  E-value=1.7e-10  Score=87.45  Aligned_cols=79  Identities=28%  Similarity=0.403  Sum_probs=73.2

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeec
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARY   92 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~   92 (158)
                      ..+|||++||..+++++|+++|++||.|..+.++.+..+...++|+||.|.+++.+..++. ..-+.|+++.|.|..|..
T Consensus        97 tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA~p  175 (311)
T KOG4205|consen   97 TKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRAIP  175 (311)
T ss_pred             eeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceeeecCceeeEeeccc
Confidence            4689999999999999999999999999999999999999999999999999999999884 578899999999998763

>KOG1457|consensus

Probab=99.08  E-value=2.2e-09  Score=76.64  Aligned_cols=83  Identities=19%  Similarity=0.319  Sum_probs=67.2

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEcc-CCCCCCcccEEEEEEcCHHHHHHHHHHhCCccc---CCceEEEE
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPR-DRFTRESRGFAFVRFFDKRDAEDALDAMDGRML---DGRELRVQ   88 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~-~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i---~g~~i~v~   88 (158)
                      ..||||.+||.++..-+|..+|..|-.-+.+.+.. ++....++-+|||+|.+..+|++|.+.|||..|   .+..|+++
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            57999999999999999999999986555554432 222233457999999999999999999999988   47889999


Q ss_pred             eeecCCC
Q psy7051          89 MARYGRP   95 (158)
Q Consensus        89 ~a~~~~~   95 (158)
                      +|+....
T Consensus       114 lAKSNtK  120 (284)
T KOG1457|consen  114 LAKSNTK  120 (284)
T ss_pred             ehhcCcc
Confidence            9986543

>KOG0106|consensus

Probab=99.05  E-value=8.8e-10  Score=79.10  Aligned_cols=67  Identities=40%  Similarity=0.648  Sum_probs=60.5

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEE
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV   87 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v   87 (158)
                      .+.|+|.+++..+.|++|.++|.++|++.+..+        ..+++||+|...++|..|+..|++..|.++.|.+
T Consensus        99 ~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--------~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~  165 (216)
T KOG0106|consen   99 HFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--------RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISV  165 (216)
T ss_pred             cceeeeccchhhhhHHHHhhhhcccCCCchhhh--------hccccceeehhhhhhhhcchhccchhhcCceeee
Confidence            467899999999999999999999999955544        2468999999999999999999999999999999

>KOG1548|consensus

Probab=99.04  E-value=1.4e-09  Score=81.98  Aligned_cols=81  Identities=26%  Similarity=0.450  Sum_probs=72.4

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceE--------EEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCce
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVG--------DIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRE   84 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~--------~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~   84 (158)
                      .+.|||.|||..+|.+++.++|+++|-|.        .|+|..+. .|+.+|-|+|.|-..++++-||+.|++..|.|+.
T Consensus       134 Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~-~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~~  212 (382)
T KOG1548|consen  134 NTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDN-QGKLKGDALCCYIKRESVELAIKILDEDELRGKK  212 (382)
T ss_pred             CceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecC-CCCccCceEEEeecccHHHHHHHHhCcccccCcE
Confidence            35699999999999999999999999774        36777775 5899999999999999999999999999999999


Q ss_pred             EEEEeeecCC
Q psy7051          85 LRVQMARYGR   94 (158)
Q Consensus        85 i~v~~a~~~~   94 (158)
                      |.|+.|+...
T Consensus       213 ~rVerAkfq~  222 (382)
T KOG1548|consen  213 LRVERAKFQM  222 (382)
T ss_pred             EEEehhhhhh
Confidence            9999997543

>KOG4211|consensus

Probab=99.00  E-value=3.4e-09  Score=83.09  Aligned_cols=78  Identities=24%  Similarity=0.431  Sum_probs=67.6

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      +...-|.+.+|||++|++||.+||+.+ .|+.+.+.+.  +|++.|-|||+|.++++++.|++ .+...+..+.|.|-.+
T Consensus         8 ~~~~~vr~rGLPwsat~~ei~~Ff~~~-~I~~~~~~r~--~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~   83 (510)
T KOG4211|consen    8 STAFEVRLRGLPWSATEKEILDFFSNC-GIENLEIPRR--NGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTA   83 (510)
T ss_pred             CcceEEEecCCCccccHHHHHHHHhcC-ceeEEEEecc--CCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEcc
Confidence            344678899999999999999999999 5877766554  79999999999999999999996 5888899999999877


Q ss_pred             ec
Q psy7051          91 RY   92 (158)
Q Consensus        91 ~~   92 (158)
                      ..
T Consensus        84 ~~   85 (510)
T KOG4211|consen   84 GG   85 (510)
T ss_pred             CC
Confidence            53

>KOG1995|consensus

Probab=98.89  E-value=2.6e-09  Score=80.85  Aligned_cols=87  Identities=22%  Similarity=0.270  Sum_probs=77.4

Q ss_pred             CCCCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceE--------EEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhC
Q psy7051           5 RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVG--------DIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD   76 (158)
Q Consensus         5 ~p~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~--------~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~   76 (158)
                      .+........+|||-+|+..+++++|.++|.++|.|.        .|+|-++++|+.+++-|.|.|.+...|++|+..++
T Consensus        58 ~~~~~~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~a  137 (351)
T KOG1995|consen   58 SSMADKSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFA  137 (351)
T ss_pred             CccccccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhc
Confidence            3444556668999999999999999999999999773        46778888999999999999999999999999999


Q ss_pred             CcccCCceEEEEeee
Q psy7051          77 GRMLDGRELRVQMAR   91 (158)
Q Consensus        77 g~~i~g~~i~v~~a~   91 (158)
                      +..+.+..|+|.+|.
T Consensus       138 gkdf~gn~ikvs~a~  152 (351)
T KOG1995|consen  138 GKDFCGNTIKVSLAE  152 (351)
T ss_pred             cccccCCCchhhhhh
Confidence            999999999998875

>KOG0120|consensus

Probab=98.86  E-value=2.8e-09  Score=84.86  Aligned_cols=83  Identities=25%  Similarity=0.418  Sum_probs=77.2

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ....|||++||..+++.++.+++..||.+..+.++.+..++-++||||.+|.+......|+..|||..+.+.+|.|+.|-
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            34689999999999999999999999999999999999889999999999999999999999999999999999999886


Q ss_pred             cCC
Q psy7051          92 YGR   94 (158)
Q Consensus        92 ~~~   94 (158)
                      .+.
T Consensus       368 ~g~  370 (500)
T KOG0120|consen  368 VGA  370 (500)
T ss_pred             ccc
Confidence            443

>KOG0151|consensus

Probab=98.83  E-value=8.8e-09  Score=83.94  Aligned_cols=79  Identities=29%  Similarity=0.437  Sum_probs=69.9

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCC---CCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDR---FTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~---~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      .+.|||+||++.++++.|...|..||+|..|+++...   +......|+||.|-+..+|++|++.|+|..|.+..+++.|
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            4789999999999999999999999999999886542   2234567999999999999999999999999999999999


Q ss_pred             ee
Q psy7051          90 AR   91 (158)
Q Consensus        90 a~   91 (158)
                      ++
T Consensus       254 gk  255 (877)
T KOG0151|consen  254 GK  255 (877)
T ss_pred             cc
Confidence            85

>KOG0226|consensus

Probab=98.83  E-value=5.1e-09  Score=76.04  Aligned_cols=81  Identities=25%  Similarity=0.422  Sum_probs=74.2

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      +....||+|.|..+++.+.|-..|.+|-.....+++.++.+++++||+||.|.+.+++..|+..|+|..++.+.|++.-+
T Consensus       188 ~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS  267 (290)
T KOG0226|consen  188 EDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKS  267 (290)
T ss_pred             cccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhh
Confidence            33478999999999999999999999988888889999999999999999999999999999999999999999987654


Q ss_pred             e
Q psy7051          91 R   91 (158)
Q Consensus        91 ~   91 (158)
                      .
T Consensus       268 ~  268 (290)
T KOG0226|consen  268 E  268 (290)
T ss_pred             h
Confidence            4

>KOG0105|consensus

Probab=98.80  E-value=2.3e-07  Score=64.69  Aligned_cols=63  Identities=22%  Similarity=0.331  Sum_probs=57.3

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccC
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLD   81 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~   81 (158)
                      ....|.|.+||++.+|++|++++.+.|+|++..+..+       |++.|+|...|+++-|+.+|+...+.
T Consensus       114 Se~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-------g~GvV~~~r~eDMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  114 SEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-------GVGVVEYLRKEDMKYAVRKLDDQKFR  176 (241)
T ss_pred             cceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-------cceeeeeeehhhHHHHHHhhcccccc
Confidence            3477999999999999999999999999999998766       58999999999999999999988764

>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=98.75  E-value=1e-07  Score=58.19  Aligned_cols=69  Identities=29%  Similarity=0.453  Sum_probs=47.2

Q ss_pred             cEEEEeCCCCCCCHHHH----HHHhhhcC-ceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEE
Q psy7051          14 VSLKVDNLTYRTTPDDL----RRVFERCG-EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ   88 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l----~~~f~~~G-~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~   88 (158)
                      ..|+|.|||...+...|    ++++..+| .|..|.          .+.|+|.|.+++.|..|.+.|+|..+.|.+|.|.
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~----------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~   72 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS----------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe----------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            46999999999887665    45556676 665551          3579999999999999999999999999999999


Q ss_pred             eeec
Q psy7051          89 MARY   92 (158)
Q Consensus        89 ~a~~   92 (158)
                      +...
T Consensus        73 ~~~~   76 (90)
T PF11608_consen   73 FSPK   76 (90)
T ss_dssp             SS--
T ss_pred             EcCC
Confidence            9853

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

>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=98.65  E-value=1.3e-07  Score=61.07  Aligned_cols=70  Identities=26%  Similarity=0.459  Sum_probs=45.5

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCc-----ccCCceEEEE
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGR-----MLDGRELRVQ   88 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~-----~i~g~~i~v~   88 (158)
                      ..|+|.+++..++.++|+++|.+||.|.+|.+....      ..|||-|.+.+.|+.|++.+...     .|.+..+.+.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~------~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGD------TEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCC------CEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            468899999999999999999999999999986652      37999999999999999876544     5677777666


Q ss_pred             e
Q psy7051          89 M   89 (158)
Q Consensus        89 ~   89 (158)
                      .
T Consensus        76 v   76 (105)
T PF08777_consen   76 V   76 (105)
T ss_dssp             -
T ss_pred             E
Confidence            5

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

>KOG0147|consensus

Probab=98.64  E-value=1.2e-08  Score=80.97  Aligned_cols=79  Identities=33%  Similarity=0.492  Sum_probs=73.9

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeec
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARY   92 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~   92 (158)
                      +.|||+-.|+..++..+|.+||+.+|.|..|.++.+..++..+|.|||+|.+.+.+..|| .|.|..+.|.+|.|.....
T Consensus       179 ~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~ai-aLsGqrllg~pv~vq~sEa  257 (549)
T KOG0147|consen  179 QRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAI-ALSGQRLLGVPVIVQLSEA  257 (549)
T ss_pred             HHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHh-hhcCCcccCceeEecccHH
Confidence            468899899999999999999999999999999999999999999999999999999999 7999999999999998653

>KOG4211|consensus

Probab=98.63  E-value=1.5e-07  Score=74.08  Aligned_cols=78  Identities=26%  Similarity=0.344  Sum_probs=64.2

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEE-EEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGD-IYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~-v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      .....|-+.+||+.|+++||.+||+..--|.. |.|+.++ .+++.|-|||+|++.+.|+.||.. |...|..+.|.|..
T Consensus       101 ~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~-rgR~tGEAfVqF~sqe~ae~Al~r-hre~iGhRYIEvF~  178 (510)
T KOG4211|consen  101 ANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQ-RGRPTGEAFVQFESQESAEIALGR-HRENIGHRYIEVFR  178 (510)
T ss_pred             CCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccC-CCCcccceEEEecCHHHHHHHHHH-HHHhhccceEEeeh
Confidence            45578999999999999999999998743333 4556665 677899999999999999999964 77788888898876


Q ss_pred             e
Q psy7051          90 A   90 (158)
Q Consensus        90 a   90 (158)
                      +
T Consensus       179 S  179 (510)
T KOG4211|consen  179 S  179 (510)
T ss_pred             h
Confidence            5

>KOG4206|consensus

Probab=98.61  E-value=2.8e-07  Score=66.04  Aligned_cols=77  Identities=23%  Similarity=0.373  Sum_probs=67.2

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccC-CceEEEE
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLD-GRELRVQ   88 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~-g~~i~v~   88 (158)
                      ..+..+||+.|||..++.+.|..+|.+|....+|.++...     .+.|||+|.+...|..|...|++..|- ...+.|.
T Consensus       143 ~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~  217 (221)
T KOG4206|consen  143 APPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQIT  217 (221)
T ss_pred             CCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhhhhccceeccCceEEec
Confidence            4456789999999999999999999999999999887653     579999999999999999999999885 7788887


Q ss_pred             eee
Q psy7051          89 MAR   91 (158)
Q Consensus        89 ~a~   91 (158)
                      +++
T Consensus       218 ~a~  220 (221)
T KOG4206|consen  218 FAK  220 (221)
T ss_pred             ccC
Confidence            764

>KOG1190|consensus

Probab=98.61  E-value=2.2e-07  Score=71.70  Aligned_cols=76  Identities=30%  Similarity=0.463  Sum_probs=68.4

Q ss_pred             CcEEEEeCCCC-CCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          13 MVSLKVDNLTY-RTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        13 ~~~l~V~nl~~-~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ...|.|.||.. .+|.+-|.-+|.-||+|..|+|..++     +..|+|+|.+...|+-|++.|+|..|.|+.|.|.+++
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nk-----kd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SK  371 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNK-----KDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSK  371 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecC-----CcceeeeecchhHHHHHHHHhhcceecCceEEEeecc
Confidence            46788999965 57999999999999999999998875     3579999999999999999999999999999999998


Q ss_pred             cC
Q psy7051          92 YG   93 (158)
Q Consensus        92 ~~   93 (158)
                      ..
T Consensus       372 H~  373 (492)
T KOG1190|consen  372 HT  373 (492)
T ss_pred             Cc
Confidence            54

>KOG2202|consensus

Probab=98.50  E-value=6e-07  Score=65.47  Aligned_cols=62  Identities=24%  Similarity=0.509  Sum_probs=51.6

Q ss_pred             HHHHHhh-hcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          29 DLRRVFE-RCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        29 ~l~~~f~-~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      +|...|+ +||+|+++.|..+ ...+..|.+||.|...++|++|++.||+.+|.|++|..++..
T Consensus        84 d~f~E~~~kygEiee~~Vc~N-l~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~p  146 (260)
T KOG2202|consen   84 DVFTELEDKYGEIEELNVCDN-LGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             HHHHHHHHHhhhhhhhhhhcc-cchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            3444444 8999999866554 356678999999999999999999999999999999999864

>KOG1457|consensus

Probab=98.44  E-value=2.3e-07  Score=66.51  Aligned_cols=64  Identities=25%  Similarity=0.353  Sum_probs=53.5

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCccc
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRML   80 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i   80 (158)
                      +.||||.||..+++|++|+.+|+.|-...-++|...  .|  ...||++|+..+.|..|+..|+|..|
T Consensus       210 cstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~--~g--~~vaf~~~~~~~~at~am~~lqg~~~  273 (284)
T KOG1457|consen  210 CSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRAR--GG--MPVAFADFEEIEQATDAMNHLQGNLL  273 (284)
T ss_pred             hhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecC--CC--cceEeecHHHHHHHHHHHHHhhccee
Confidence            578999999999999999999999977665655332  23  34799999999999999999998765

>KOG4849|consensus

Probab=98.43  E-value=2.3e-07  Score=70.47  Aligned_cols=75  Identities=20%  Similarity=0.369  Sum_probs=66.6

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcC--ceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEE
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCG--EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ   88 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G--~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~   88 (158)
                      ..+|||||-|++|.++|.+.+...|  ++.++++..+..+|.++|||+|...+....+..++.|...+|.|+.-.|.
T Consensus        81 ~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~  157 (498)
T KOG4849|consen   81 YCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVL  157 (498)
T ss_pred             EEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeee
Confidence            5799999999999999999998877  67888888899999999999999999999999999999999988764443

>KOG4210|consensus

Probab=98.41  E-value=3.5e-07  Score=69.03  Aligned_cols=80  Identities=30%  Similarity=0.498  Sum_probs=72.5

Q ss_pred             CcEEE-EeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          13 MVSLK-VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        13 ~~~l~-V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ..++| |++|+..+++++|+.+|..+|.|..+.++....++...++|||.|.+...+..++.. +...+.+..+.|.+..
T Consensus       184 s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~  262 (285)
T KOG4210|consen  184 SDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDE  262 (285)
T ss_pred             cccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccCC
Confidence            45566 999999999999999999999999999999999999999999999999999999876 7888999999998877


Q ss_pred             cC
Q psy7051          92 YG   93 (158)
Q Consensus        92 ~~   93 (158)
                      ..
T Consensus       263 ~~  264 (285)
T KOG4210|consen  263 PR  264 (285)
T ss_pred             CC
Confidence            43

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=98.36  E-value=1.5e-06  Score=65.90  Aligned_cols=78  Identities=19%  Similarity=0.417  Sum_probs=60.9

Q ss_pred             cEEEEeCCCCCCCHHH----H--HHHhhhcCceEEEEEccCCCC-CCcccE--EEEEEcCHHHHHHHHHHhCCcccCCce
Q psy7051          14 VSLKVDNLTYRTTPDD----L--RRVFERCGEVGDIYIPRDRFT-RESRGF--AFVRFFDKRDAEDALDAMDGRMLDGRE   84 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~----l--~~~f~~~G~i~~v~~~~~~~~-~~~~g~--afV~f~~~~~a~~a~~~l~g~~i~g~~   84 (158)
                      .-|||-+|++.+..++    |  .++|.+||.|..|.+-..... .-..+.  .||+|.+.++|..||...+|..++|+.
T Consensus       115 NLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr~  194 (480)
T COG5175         115 NLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGRV  194 (480)
T ss_pred             ceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCce
Confidence            4589999998876655    2  578999999998877543211 111233  499999999999999999999999999


Q ss_pred             EEEEeee
Q psy7051          85 LRVQMAR   91 (158)
Q Consensus        85 i~v~~a~   91 (158)
                      |+..|..
T Consensus       195 lkatYGT  201 (480)
T COG5175         195 LKATYGT  201 (480)
T ss_pred             EeeecCc
Confidence            9999854

>KOG0129|consensus

Probab=98.36  E-value=2.9e-06  Score=67.31  Aligned_cols=68  Identities=22%  Similarity=0.211  Sum_probs=62.1

Q ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHhh-hcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHH
Q psy7051           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFE-RCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA   74 (158)
Q Consensus         7 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~-~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~   74 (158)
                      ...+++..|||||+||--++.++|..+|+ -||.|+.+-|-.|++-..++|-|=|+|.+..+-.+||.+
T Consensus       364 sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  364 NQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             CcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            34567889999999999999999999999 699999999999988899999999999999999999864

>KOG1365|consensus

Probab=98.34  E-value=7.5e-07  Score=68.43  Aligned_cols=77  Identities=14%  Similarity=0.251  Sum_probs=67.2

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcC-ceEE--EEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCG-EVGD--IYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G-~i~~--v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      ..+|-+.+||..++.++|.+||..|. .|..  |.|+.+. .|++.|-|||+|.+.++|.+|..+.+.+..+.+.|.|-.
T Consensus       280 kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~-qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp  358 (508)
T KOG1365|consen  280 KDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNG-QGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFP  358 (508)
T ss_pred             CCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcC-CCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEee
Confidence            46799999999999999999999986 4444  7777774 788999999999999999999999998888899998876


Q ss_pred             e
Q psy7051          90 A   90 (158)
Q Consensus        90 a   90 (158)
                      +
T Consensus       359 ~  359 (508)
T KOG1365|consen  359 C  359 (508)
T ss_pred             c
Confidence            4

>KOG1456|consensus

Probab=98.33  E-value=5.4e-06  Score=63.65  Aligned_cols=77  Identities=22%  Similarity=0.219  Sum_probs=68.3

Q ss_pred             CCcEEEEeCCCCC-CCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          12 GMVSLKVDNLTYR-TTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        12 ~~~~l~V~nl~~~-~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      +...+.|-+|... ++.+.|..+|..||.|+.|++++.+     .|.|.|++.+..+.+.|+..||+..+-|.+|.|.++
T Consensus       286 ~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-----~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~S  360 (494)
T KOG1456|consen  286 PGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCVS  360 (494)
T ss_pred             CCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-----cceeEEEcCcHHHHHHHHHHhccCccccceEEEeec
Confidence            3467889999764 6788899999999999999998875     578999999999999999999999999999999998


Q ss_pred             ecC
Q psy7051          91 RYG   93 (158)
Q Consensus        91 ~~~   93 (158)
                      +..
T Consensus       361 kQ~  363 (494)
T KOG1456|consen  361 KQN  363 (494)
T ss_pred             ccc
Confidence            843

>KOG4307|consensus

Probab=98.32  E-value=2.5e-06  Score=70.01  Aligned_cols=79  Identities=19%  Similarity=0.266  Sum_probs=66.3

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      .+++.|-|.|+|..++-+||.+||..|-.+-.-.++.-...|...|-|.|.|++.++|..|...|++..|..+.|.+.+
T Consensus       865 pGp~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  865 PGPRVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             CCCeEEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            3446899999999999999999999996543332333345789999999999999999999999999999999988764

>KOG2416|consensus

Probab=98.24  E-value=1.2e-06  Score=70.61  Aligned_cols=81  Identities=22%  Similarity=0.394  Sum_probs=65.9

Q ss_pred             CCCCCCCCCcEEEEeCCCCCCCHHHHHHHhhh-cCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCccc---
Q psy7051           5 RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFER-CGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRML---   80 (158)
Q Consensus         5 ~p~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~-~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i---   80 (158)
                      .+|........|||.||---.|..+|+++|.. .|.|+.+||  |    +.+..|||.|.+.++|.+...+|||..|   
T Consensus       436 pSPsR~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~Wm--D----kIKShCyV~yss~eEA~atr~AlhnV~WP~s  509 (718)
T KOG2416|consen  436 PSPSRKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWM--D----KIKSHCYVSYSSVEEAAATREALHNVQWPPS  509 (718)
T ss_pred             CCCCCCCccceEeeecccccchHHHHHHHHhhccCchHHHHH--H----HhhcceeEecccHHHHHHHHHHHhccccCCC
Confidence            34446677889999999999999999999995 556666633  2    2467899999999999999999999987   


Q ss_pred             CCceEEEEeee
Q psy7051          81 DGRELRVQMAR   91 (158)
Q Consensus        81 ~g~~i~v~~a~   91 (158)
                      +.+.|.|.|..
T Consensus       510 NPK~L~adf~~  520 (718)
T KOG2416|consen  510 NPKHLIADFVR  520 (718)
T ss_pred             CCceeEeeecc
Confidence            56778888864

>KOG2314|consensus

Probab=98.22  E-value=1e-05  Score=65.01  Aligned_cols=76  Identities=26%  Similarity=0.508  Sum_probs=61.1

Q ss_pred             CcEEEEeCCCCCCCH------HHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccC-CceE
Q psy7051          13 MVSLKVDNLTYRTTP------DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLD-GREL   85 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~------~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~-g~~i   85 (158)
                      ...|+|.|+|.--..      .-|..+|+++|+|..+.++.+..+| .+||.|++|++..+|+.|++.|||..|+ ++..
T Consensus        58 D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~gg-tkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf  136 (698)
T KOG2314|consen   58 DSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGG-TKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTF  136 (698)
T ss_pred             ceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCC-eeeEEEEEecChhhHHHHHHhcccceecccceE
Confidence            357888888863221      3466789999999999999887555 9999999999999999999999999874 5666


Q ss_pred             EEEe
Q psy7051          86 RVQM   89 (158)
Q Consensus        86 ~v~~   89 (158)
                      .|..
T Consensus       137 ~v~~  140 (698)
T KOG2314|consen  137 FVRL  140 (698)
T ss_pred             Eeeh
Confidence            6654

>KOG1190|consensus

Probab=98.22  E-value=4.4e-06  Score=64.73  Aligned_cols=77  Identities=21%  Similarity=0.325  Sum_probs=64.0

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCc-eEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCc-eEEEE
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGE-VGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGR-ELRVQ   88 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~-i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~-~i~v~   88 (158)
                      ++..+|++.|+|.+++|++|+++|..-|. |...++..     +-..+|++++.+.|+|..|+-.++.+.+++. .|.|.
T Consensus       412 PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff~-----kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvS  486 (492)
T KOG1190|consen  412 PPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFFQ-----KDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVS  486 (492)
T ss_pred             CchhheeeccCCcccchhHHHHhhhcCCceEEeeeecC-----CCcceeecccCChhHhhhhccccccccCCCCceEEEE
Confidence            55678999999999999999999998874 45555532     2346999999999999999999999999765 89999


Q ss_pred             eeec
Q psy7051          89 MARY   92 (158)
Q Consensus        89 ~a~~   92 (158)
                      |++.
T Consensus       487 FSks  490 (492)
T KOG1190|consen  487 FSKS  490 (492)
T ss_pred             eecc
Confidence            9874

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

Probab=98.20  E-value=5.9e-06  Score=46.64  Aligned_cols=52  Identities=25%  Similarity=0.540  Sum_probs=41.8

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHH
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDAL   72 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~   72 (158)
                      +.|-|.++++...+ .|..+|..||+|+.+.+...      ..+.||.|.+..+|+.||
T Consensus         2 ~wI~V~Gf~~~~~~-~vl~~F~~fGeI~~~~~~~~------~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAE-EVLEHFASFGEIVDIYVPES------TNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHH-HHHHHHHhcCCEEEEEcCCC------CcEEEEEECCHHHHHhhC
Confidence            46889999987654 45558889999999988622      458999999999999885

>KOG1548|consensus

Probab=98.15  E-value=9.8e-06  Score=61.56  Aligned_cols=76  Identities=24%  Similarity=0.438  Sum_probs=60.7

Q ss_pred             CCcEEEEeCCCC----CCC-------HHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCccc
Q psy7051          12 GMVSLKVDNLTY----RTT-------PDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRML   80 (158)
Q Consensus        12 ~~~~l~V~nl~~----~~~-------~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i   80 (158)
                      ...+|.|.||=.    ..+       .++|.+-.++||.|..|.|...    ++.|.+-|.|.+.++|..||+.|+|.+|
T Consensus       264 ~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d~----hPdGvvtV~f~n~eeA~~ciq~m~GR~f  339 (382)
T KOG1548|consen  264 ADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYDR----HPDGVVTVSFRNNEEADQCIQTMDGRWF  339 (382)
T ss_pred             CCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEecc----CCCceeEEEeCChHHHHHHHHHhcCeee
Confidence            346788888721    223       3456667889999999987543    3678999999999999999999999999


Q ss_pred             CCceEEEEeee
Q psy7051          81 DGRELRVQMAR   91 (158)
Q Consensus        81 ~g~~i~v~~a~   91 (158)
                      .|++|...+..
T Consensus       340 dgRql~A~i~D  350 (382)
T KOG1548|consen  340 DGRQLTASIWD  350 (382)
T ss_pred             cceEEEEEEeC
Confidence            99999988754

>KOG3152|consensus

Probab=98.06  E-value=3.6e-06  Score=61.43  Aligned_cols=72  Identities=21%  Similarity=0.391  Sum_probs=59.7

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCC--------CCcc----cEEEEEEcCHHHHHHHHHHhCCccc
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFT--------RESR----GFAFVRFFDKRDAEDALDAMDGRML   80 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~--------~~~~----g~afV~f~~~~~a~~a~~~l~g~~i   80 (158)
                      .-.||++++|+.++..-|.++|..||.|-.|.|-....+        +.+.    --++|+|.+...|..+...||+..|
T Consensus        74 ~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~I  153 (278)
T KOG3152|consen   74 TGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTPI  153 (278)
T ss_pred             ceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCcc
Confidence            457999999999999999999999999988877544333        2222    2378999999999999999999999


Q ss_pred             CCce
Q psy7051          81 DGRE   84 (158)
Q Consensus        81 ~g~~   84 (158)
                      +|..
T Consensus       154 ggkk  157 (278)
T KOG3152|consen  154 GGKK  157 (278)
T ss_pred             CCCC
Confidence            9875

>KOG0120|consensus

Probab=98.01  E-value=2.5e-05  Score=62.78  Aligned_cols=62  Identities=26%  Similarity=0.426  Sum_probs=49.5

Q ss_pred             HHHHhhhcCceEEEEEccCCCC---CCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          30 LRRVFERCGEVGDIYIPRDRFT---RESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        30 l~~~f~~~G~i~~v~~~~~~~~---~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      |+..+.+||.|..|.++.+...   .--.|..||+|.+.++++.|.+.|+|..|+++.|...|-.
T Consensus       426 vr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYyd  490 (500)
T KOG0120|consen  426 VRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYD  490 (500)
T ss_pred             HHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecC
Confidence            3344568999999988766222   2235789999999999999999999999999999887743

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

Probab=97.99  E-value=5.1e-05  Score=48.46  Aligned_cols=75  Identities=13%  Similarity=0.199  Sum_probs=49.9

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCC-------CCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCce-E
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDR-------FTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRE-L   85 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~-------~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~-i   85 (158)
                      ..|.|-++|+. ....|.++|++||+|.+..-....       .......+..|+|+++.+|..||. .||..|.|.. |
T Consensus         7 ~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~mv   84 (100)
T PF05172_consen    7 TWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSLMV   84 (100)
T ss_dssp             CEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCEEE
T ss_pred             eEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcEEE
Confidence            45778899988 667788999999999776411000       001124699999999999999995 5999998864 4


Q ss_pred             EEEee
Q psy7051          86 RVQMA   90 (158)
Q Consensus        86 ~v~~a   90 (158)
                      -|.+.
T Consensus        85 GV~~~   89 (100)
T PF05172_consen   85 GVKPC   89 (100)
T ss_dssp             EEEE-
T ss_pred             EEEEc
Confidence            46655

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.

>KOG4676|consensus

Probab=97.96  E-value=5.9e-07  Score=69.08  Aligned_cols=64  Identities=20%  Similarity=0.179  Sum_probs=52.5

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccC
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLD   81 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~   81 (158)
                      ..||+|++|+..+...++.++|..+|+|.+..|...    ...-+|.|+|........|+. ++|.++.
T Consensus       151 rRt~~v~sl~~~~~l~e~~e~f~r~Gev~ya~~ask----~~s~~c~~sf~~qts~~halr-~~gre~k  214 (479)
T KOG4676|consen  151 RRTREVQSLISAAILPESGESFERKGEVSYAHTASK----SRSSSCSHSFRKQTSSKHALR-SHGRERK  214 (479)
T ss_pred             Hhhhhhhcchhhhcchhhhhhhhhcchhhhhhhhcc----CCCcchhhhHhhhhhHHHHHH-hcchhhh
Confidence            367999999999999999999999999988877433    234578899999889888985 5777665

>KOG1365|consensus

Probab=97.93  E-value=1.4e-05  Score=61.65  Aligned_cols=76  Identities=22%  Similarity=0.277  Sum_probs=57.8

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhc----CceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEE
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERC----GEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR   86 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~----G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~   86 (158)
                      +....|-+.+||.++++.++.+||.+-    |..+.|.++..+ .|+..|-|||.|..+++|+.||.+ |...|+.+.|.
T Consensus       159 ~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rp-dgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYIE  236 (508)
T KOG1365|consen  159 ENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRP-DGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYIE  236 (508)
T ss_pred             ccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECC-CCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHHH
Confidence            345667888999999999999999632    244566565554 788999999999999999999975 55556655554


Q ss_pred             EE
Q psy7051          87 VQ   88 (158)
Q Consensus        87 v~   88 (158)
                      +-
T Consensus       237 lF  238 (508)
T KOG1365|consen  237 LF  238 (508)
T ss_pred             HH
Confidence            43

>KOG1456|consensus

Probab=97.93  E-value=6.7e-05  Score=57.80  Aligned_cols=77  Identities=26%  Similarity=0.239  Sum_probs=61.5

Q ss_pred             CCcEEEEeCCC--CCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCccc-CC-ceEEE
Q psy7051          12 GMVSLKVDNLT--YRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRML-DG-RELRV   87 (158)
Q Consensus        12 ~~~~l~V~nl~--~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i-~g-~~i~v   87 (158)
                      +.+.|.++=|+  ..+|.+-|..+....|+|..|.|...  ++   --|.|||++.+.|++|...|||..| .| +.|+|
T Consensus       119 pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk--ng---VQAmVEFdsv~~AqrAk~alNGADIYsGCCTLKI  193 (494)
T KOG1456|consen  119 PNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK--NG---VQAMVEFDSVEVAQRAKAALNGADIYSGCCTLKI  193 (494)
T ss_pred             CCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec--cc---eeeEEeechhHHHHHHHhhcccccccccceeEEE
Confidence            33455555444  46899999999999999999987655  32   3599999999999999999999987 34 68999


Q ss_pred             EeeecC
Q psy7051          88 QMARYG   93 (158)
Q Consensus        88 ~~a~~~   93 (158)
                      +||+..
T Consensus       194 eyAkP~  199 (494)
T KOG1456|consen  194 EYAKPT  199 (494)
T ss_pred             EecCcc
Confidence            999844

>KOG4676|consensus

Probab=97.92  E-value=1.7e-05  Score=61.19  Aligned_cols=75  Identities=17%  Similarity=0.282  Sum_probs=60.0

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCC---CCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRF---TRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      ..|.|.||.++++.++++.||...|+|.++.|..+..   .....-.|||.|.+...+..|- +|.+..|-++.|.|-.
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQ-hLtntvfvdraliv~p   85 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQ-HLTNTVFVDRALIVRP   85 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHh-hhccceeeeeeEEEEe
Confidence            3799999999999999999999999999998765321   1234568999999999888886 6788877777666654

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

Probab=97.90  E-value=0.00012  Score=44.80  Aligned_cols=55  Identities=15%  Similarity=0.292  Sum_probs=41.8

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCC
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG   77 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g   77 (158)
                      ...+|+ +|..+...||.++|+.||.|. |.++.+.       -|||...+.+.|..|+..+.-
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~dT-------SAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWINDT-------SAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCCCCEE-EEEECTT-------EEEEEECCCHHHHHHHHHHTT
T ss_pred             eEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcCC-------cEEEEeecHHHHHHHHHHhcc
Confidence            556665 999999999999999999985 5565552       699999999999999887753

; 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=97.81  E-value=0.00015  Score=49.09  Aligned_cols=54  Identities=31%  Similarity=0.509  Sum_probs=44.9

Q ss_pred             HHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          29 DLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        29 ~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      +|.+.|..||++.-++++.+        .-+|+|.+-+.|.+|+ .|+|.+|+|+.|+|.+-.
T Consensus        52 ~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaal-s~dg~~v~g~~l~i~LKt  105 (146)
T PF08952_consen   52 ELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAAL-SLDGIQVNGRTLKIRLKT  105 (146)
T ss_dssp             HHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHH-HGCCSEETTEEEEEEE--
T ss_pred             HHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHH-ccCCcEECCEEEEEEeCC
Confidence            67778889999988888654        4899999999999999 589999999999999865

; PDB: 1UFW_A 2DNR_A.

>KOG0112|consensus

Probab=97.79  E-value=4.2e-05  Score=64.47  Aligned_cols=77  Identities=26%  Similarity=0.393  Sum_probs=67.3

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCC--ceEE
Q psy7051           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDG--RELR   86 (158)
Q Consensus         9 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g--~~i~   86 (158)
                      .....+.++|++|..++....|...|..||.|..|.+-..      .-||||.|++...+++|+..|-|..|++  +.|.
T Consensus       451 kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hg------q~yayi~yes~~~aq~a~~~~rgap~G~P~~r~r  524 (975)
T KOG0112|consen  451 KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHG------QPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLR  524 (975)
T ss_pred             ccccceeeccCCCCCCChHHHHHHHhhccCcceeeecccC------CcceeeecccCccchhhHHHHhcCcCCCCCcccc
Confidence            4456688999999999999999999999999998877332      4699999999999999999999999976  5689


Q ss_pred             EEeee
Q psy7051          87 VQMAR   91 (158)
Q Consensus        87 v~~a~   91 (158)
                      |.|+.
T Consensus       525 vdla~  529 (975)
T KOG0112|consen  525 VDLAS  529 (975)
T ss_pred             ccccc
Confidence            99876

>KOG0129|consensus

Probab=97.79  E-value=6.5e-05  Score=59.88  Aligned_cols=62  Identities=23%  Similarity=0.377  Sum_probs=48.0

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCC---CCCCccc---EEEEEEcCHHHHHHHHHHhC
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDR---FTRESRG---FAFVRFFDKRDAEDALDAMD   76 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~---~~~~~~g---~afV~f~~~~~a~~a~~~l~   76 (158)
                      .+||||+||+.++|++|...|..||.+. |.++...   .-..++|   |+|+.|+++..+...+..+.
T Consensus       260 ~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~  327 (520)
T KOG0129|consen  260 RKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACS  327 (520)
T ss_pred             cceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHh
Confidence            6899999999999999999999999874 5555211   1122456   99999999988887766543

>KOG1996|consensus

Probab=97.79  E-value=8.6e-05  Score=55.50  Aligned_cols=65  Identities=23%  Similarity=0.319  Sum_probs=51.4

Q ss_pred             HHHHHHHhhhcCceEEEEEccCCCCC-CcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          27 PDDLRRVFERCGEVGDIYIPRDRFTR-ESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        27 ~~~l~~~f~~~G~i~~v~~~~~~~~~-~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ++++++.+++||+|..|.|...+..- .-.--.||+|...+.|..|+-.|||..|+|+.+...|-+
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYN  365 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheecc
Confidence            45678889999999988775543221 123458999999999999999999999999999887754

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

Probab=97.76  E-value=0.00025  Score=41.13  Aligned_cols=54  Identities=22%  Similarity=0.228  Sum_probs=45.1

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhc---CceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHh
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERC---GEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM   75 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~---G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l   75 (158)
                      .+|+|.|+. .++.++|+.+|..|   .....|.++.|.       -|-|.|.+.+.|..||.+|
T Consensus         6 eavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            569999986 57889999999998   235678888874       5999999999999999754

>KOG1855|consensus

Probab=97.75  E-value=3.5e-05  Score=60.15  Aligned_cols=67  Identities=16%  Similarity=0.261  Sum_probs=55.3

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccC---CCCC--C--------cccEEEEEEcCHHHHHHHHHHhCCc
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRD---RFTR--E--------SRGFAFVRFFDKRDAEDALDAMDGR   78 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~---~~~~--~--------~~g~afV~f~~~~~a~~a~~~l~g~   78 (158)
                      +..+|.+.|||.+-.-+.|.++|..+|.|+.|.|+..   +...  .        .+-+|+|+|+..+.|.+|.+.|+..
T Consensus       230 ~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~e  309 (484)
T KOG1855|consen  230 PSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNPE  309 (484)
T ss_pred             ccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhchh
Confidence            5689999999999988999999999999999988655   2221  1        2458999999999999999887543

>KOG0128|consensus

Probab=97.46  E-value=6.9e-05  Score=62.90  Aligned_cols=79  Identities=18%  Similarity=0.265  Sum_probs=70.4

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeec
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARY   92 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~   92 (158)
                      ...|+|.|+|+..|.++|+.++.++|.++.+.++... .|+++|.|+|.|.++.++..++...+...+....+.|..++.
T Consensus       736 K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r-~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  736 KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVR-AGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             hhhhheeCCCCCCchHHHHhhccccCCccccchhhhh-ccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCC
Confidence            3579999999999999999999999999999887775 789999999999999999999988888888878788877654

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=97.36  E-value=0.00038  Score=49.11  Aligned_cols=83  Identities=14%  Similarity=0.181  Sum_probs=52.6

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhh-cCce---EEEE--EccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCC----
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFER-CGEV---GDIY--IPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDG----   82 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~-~G~i---~~v~--~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g----   82 (158)
                      ..+|.|.+||+.+|++++.+.+.. ++..   ..+.  ............-|||.|.+.+++...+..++|..|.+    
T Consensus         7 ~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg~   86 (176)
T PF03467_consen    7 GTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKGN   86 (176)
T ss_dssp             --EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS-
T ss_pred             CceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCCCC
Confidence            468999999999999999997777 6654   3443  22221112234579999999999999999999987633    


Q ss_pred             -ceEEEEeeecCCC
Q psy7051          83 -RELRVQMARYGRP   95 (158)
Q Consensus        83 -~~i~v~~a~~~~~   95 (158)
                       ....|++|-..+-
T Consensus        87 ~~~~~VE~Apyqk~  100 (176)
T PF03467_consen   87 EYPAVVEFAPYQKV  100 (176)
T ss_dssp             EEEEEEEE-SS---
T ss_pred             CcceeEEEcchhcc
Confidence             3467788776443

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

Probab=97.30  E-value=1.4e-05  Score=66.84  Aligned_cols=68  Identities=24%  Similarity=0.374  Sum_probs=58.4

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccC
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLD   81 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~   81 (158)
                      .++||.||+..+.+.+|...|..+|.|..+.+......++.+|+|||+|..++.+.+||.......++
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            47899999999999999999999998888777656668889999999999999999999765555444

>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=97.28  E-value=0.0044  Score=40.29  Aligned_cols=68  Identities=19%  Similarity=0.255  Sum_probs=49.0

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcC-ceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCC
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCG-EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDG   82 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G-~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g   82 (158)
                      ...+.+...|..++.++|..+.+.+- .|..+.|+.+.  ..++-.++|.|.+.++|.+.++.+||..++.
T Consensus        13 ~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~--~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   13 STLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDG--TPNRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             ceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCC--CCceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            34455545555556667776666654 67788888763  2245579999999999999999999997653

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

>KOG4307|consensus

Probab=97.26  E-value=0.00027  Score=58.50  Aligned_cols=77  Identities=25%  Similarity=0.091  Sum_probs=63.2

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEE-EEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGD-IYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~-v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      ....|||-+||..+++.++.++|...-.|+. |.|... .+++..+.|||+|..++++..|+..-+...++.+.|.|.-
T Consensus       433 ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~-P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~s  510 (944)
T KOG4307|consen  433 AGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRL-PTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDS  510 (944)
T ss_pred             ccceEEeccCCccccccchhhhhhhhhhhhheeEeccC-CcccccchhhheeccccccchhhhcccccccCceEEEeec
Confidence            3478999999999999999999998777766 555444 3777889999999998888888776677778888888875

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=97.20  E-value=0.0032  Score=42.52  Aligned_cols=74  Identities=18%  Similarity=0.161  Sum_probs=53.5

Q ss_pred             CCCCCcEEEEeCCCCCC----CHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCce
Q psy7051           9 RIEGMVSLKVDNLTYRT----TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRE   84 (158)
Q Consensus         9 ~~~~~~~l~V~nl~~~~----~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~   84 (158)
                      ..++..||.|.=|..++    +...|...++.||+|..|.+.     |  +.-|.|+|.+..+|..|+.+++. ...|..
T Consensus        82 kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c-----G--rqsavVvF~d~~SAC~Av~Af~s-~~pgtm  153 (166)
T PF15023_consen   82 KEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC-----G--RQSAVVVFKDITSACKAVSAFQS-RAPGTM  153 (166)
T ss_pred             CCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec-----C--CceEEEEehhhHHHHHHHHhhcC-CCCCce
Confidence            34567889888666555    334456677899999999763     2  34699999999999999988765 455666


Q ss_pred             EEEEee
Q psy7051          85 LRVQMA   90 (158)
Q Consensus        85 i~v~~a   90 (158)
                      +.+.|-
T Consensus       154 ~qCsWq  159 (166)
T PF15023_consen  154 FQCSWQ  159 (166)
T ss_pred             EEeecc
Confidence            666553

>KOG4660|consensus

Probab=97.18  E-value=0.0007  Score=54.58  Aligned_cols=55  Identities=20%  Similarity=0.340  Sum_probs=44.5

Q ss_pred             cCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCccc---C-CceEEEEeee
Q psy7051          37 CGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRML---D-GRELRVQMAR   91 (158)
Q Consensus        37 ~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i---~-g~~i~v~~a~   91 (158)
                      .|.-..+.++.|..+.++.|||||.|.+++++..+.+++||+.|   + .+.+.+.||+
T Consensus       413 ~gtYDFlYLPiDF~nkcNvGYAFINm~sp~ai~~F~kAFnGk~W~~FnS~Kia~itYAr  471 (549)
T KOG4660|consen  413 KGTYDFLYLPIDFKNKCNVGYAFINMTSPEAIIRFYKAFNGKKWEKFNSEKIASITYAR  471 (549)
T ss_pred             cCccceEEeccccccccccceeEEeecCHHHHHHHHHHHcCCchhhhcceeeeeeehhh
Confidence            45556777888888888999999999999999999999999965   3 3445777765

>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=97.15  E-value=0.0056  Score=36.82  Aligned_cols=66  Identities=30%  Similarity=0.505  Sum_probs=39.3

Q ss_pred             EEEEeCC--CCCCCHHHHHHHhhhcC-----ceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEE
Q psy7051          15 SLKVDNL--TYRTTPDDLRRVFERCG-----EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV   87 (158)
Q Consensus        15 ~l~V~nl--~~~~~~~~l~~~f~~~G-----~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v   87 (158)
                      +||| |+  -..++..+|..+|...+     .|-.|.+..+        |+||+... +.|+.+++.|++..+.|+.|.|
T Consensus         2 rl~i-n~Gr~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~~--------~S~vev~~-~~a~~v~~~l~~~~~~gk~v~v   71 (74)
T PF03880_consen    2 RLFI-NVGRKDGLTPRDIVGAICNEAGIPGRDIGRIDIFDN--------FSFVEVPE-EVAEKVLEALNGKKIKGKKVRV   71 (74)
T ss_dssp             EEEE-S-SGGGT--HHHHHHHHHTCTTB-GGGEEEEEE-SS---------EEEEE-T-T-HHHHHHHHTT--SSS----E
T ss_pred             EEEE-EcccccCCCHHHHHHHHHhccCCCHHhEEEEEEeee--------EEEEEECH-HHHHHHHHHhcCCCCCCeeEEE
Confidence            4555 33  34678899999988764     4567777443        89999865 4788889999999999999999


Q ss_pred             Eee
Q psy7051          88 QMA   90 (158)
Q Consensus        88 ~~a   90 (158)
                      +.|
T Consensus        72 e~A   74 (74)
T PF03880_consen   72 ERA   74 (74)
T ss_dssp             EE-
T ss_pred             EEC
Confidence            865

; PDB: 2G0C_A 3MOJ_B.

>KOG0115|consensus

Probab=97.09  E-value=0.0008  Score=49.46  Aligned_cols=75  Identities=24%  Similarity=0.255  Sum_probs=58.8

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCc----ccCCceEEEEe
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGR----MLDGRELRVQM   89 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~----~i~g~~i~v~~   89 (158)
                      ..|+|.||+..+..+.|...|+.||+|....++.|. .++..+-++|+|...-.+.+|+..+.-.    ...+..+-|..
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~-r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~VeP  110 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDD-RGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGVEP  110 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecc-cccccccchhhhhcchhHHHHHHHhccCccccCCCCCccCCCh
Confidence            569999999999999999999999999766555553 6778889999999999999998876422    33455555543

>KOG2193|consensus

Probab=97.03  E-value=0.0008  Score=52.81  Aligned_cols=69  Identities=30%  Similarity=0.529  Sum_probs=55.7

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhc--CceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCc-ccCCceEEEEee
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERC--GEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGR-MLDGRELRVQMA   90 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~--G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~-~i~g~~i~v~~a   90 (158)
                      ..||++||.+.++..+|+.+|...  +.-..+ |+       ..||+||.+.+..-|..|++.++|. ++.|..+.|+++
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~f-l~-------k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~s   73 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQF-LV-------KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHS   73 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcce-ee-------ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccch
Confidence            468999999999999999999754  111122 22       2479999999999999999999987 689999999875

>KOG2135|consensus

Probab=96.97  E-value=0.00054  Score=54.31  Aligned_cols=72  Identities=24%  Similarity=0.341  Sum_probs=57.9

Q ss_pred             cEEEEeCCCCCC-CHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeec
Q psy7051          14 VSLKVDNLTYRT-TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARY   92 (158)
Q Consensus        14 ~~l~V~nl~~~~-~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~   92 (158)
                      ..|-+.-.+... +-++|...|.+||.|..|.+-..      ...|.|+|.+..+|..|. ..++..|+++.|+|.|-+.
T Consensus       373 s~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~------~~~a~vTF~t~aeag~a~-~s~~avlnnr~iKl~whnp  445 (526)
T KOG2135|consen  373 SPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS------SLHAVVTFKTRAEAGEAY-ASHGAVLNNRFIKLFWHNP  445 (526)
T ss_pred             chhhhhccCCCCchHhhhhhhhhhcCccccccccCc------hhhheeeeeccccccchh-ccccceecCceeEEEEecC
Confidence            445555555555 56889999999999999987543      347999999999998887 4799999999999999764

>KOG2253|consensus

Probab=96.92  E-value=0.00083  Score=55.23  Aligned_cols=70  Identities=16%  Similarity=0.214  Sum_probs=59.7

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      ++..+|||+|+...+..+-+..++..+|.|..+...         -|+|++|..+.....|+..|+...++|..+.+..
T Consensus        38 ~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~---------~fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~~  107 (668)
T KOG2253|consen   38 PPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRD---------KFGFCEFLKHIGDLRASRLLTELNIDDQKLIENV  107 (668)
T ss_pred             CCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhh---------hhcccchhhHHHHHHHHHHhcccCCCcchhhccc
Confidence            445789999999999999999999999988766543         2899999999999999988998889888776665

>KOG0112|consensus

Probab=96.82  E-value=0.00027  Score=59.78  Aligned_cols=77  Identities=19%  Similarity=0.367  Sum_probs=61.9

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      ..|||++||...+++.+|...|..+|.|..|.|-..+ -+.-.-|+||.|.+...+..|+..+.+..|..-.+++.+.
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 TRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPH-IKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLG  448 (975)
T ss_pred             hhhhhhcCcccchhhhhhhhhhhhhccccccccccCC-CCcccchhhhhhhccccCcccchhhcCCccccCccccccc
Confidence            4689999999999999999999999999999885543 2223459999999999999998888888775544444443

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

Probab=96.72  E-value=0.0068  Score=43.04  Aligned_cols=60  Identities=18%  Similarity=0.225  Sum_probs=45.3

Q ss_pred             CHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhC--CcccCCceEEEEeee
Q psy7051          26 TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD--GRMLDGRELRVQMAR   91 (158)
Q Consensus        26 ~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~--g~~i~g~~i~v~~a~   91 (158)
                      ..+.|+++|..|+.+..+.+...      .+-..|.|.+.++|..|...|+  +..+.|..|+|.++.
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s------FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~   69 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS------FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQ   69 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT------TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE---
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC------CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcc
Confidence            45789999999998887766554      3568999999999999999999  889999999999885

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.

>KOG4285|consensus

Probab=96.61  E-value=0.016  Score=43.84  Aligned_cols=61  Identities=25%  Similarity=0.456  Sum_probs=47.3

Q ss_pred             EEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCce
Q psy7051          16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRE   84 (158)
Q Consensus        16 l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~   84 (158)
                      |-|-++++. ....|..+|++||+|.......      +-.|-+|.|.+.-+|++||. .||..|+|..
T Consensus       200 VTVfGFppg-~~s~vL~~F~~cG~Vvkhv~~~------ngNwMhirYssr~~A~KALs-kng~ii~g~v  260 (350)
T KOG4285|consen  200 VTVFGFPPG-QVSIVLNLFSRCGEVVKHVTPS------NGNWMHIRYSSRTHAQKALS-KNGTIIDGDV  260 (350)
T ss_pred             EEEeccCcc-chhHHHHHHHhhCeeeeeecCC------CCceEEEEecchhHHHHhhh-hcCeeeccce
Confidence            445578876 4566888999999997765531      23589999999999999996 5999998764

>KOG2591|consensus

Probab=96.61  E-value=0.005  Score=49.99  Aligned_cols=71  Identities=13%  Similarity=0.258  Sum_probs=55.8

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhh--cCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCc--ccCCceEEE
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFER--CGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGR--MLDGRELRV   87 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~--~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~--~i~g~~i~v   87 (158)
                      ..+.|+|.-||..+-.++|+.||..  +-.++.|.+-.+.       .=||+|++..||+.|++.|...  +|.|+.|..
T Consensus       174 kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~-------nWyITfesd~DAQqAykylreevk~fqgKpImA  246 (684)
T KOG2591|consen  174 KRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND-------NWYITFESDTDAQQAYKYLREEVKTFQGKPIMA  246 (684)
T ss_pred             ceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC-------ceEEEeecchhHHHHHHHHHHHHHhhcCcchhh
Confidence            3467889999999999999999976  5677888775542       3599999999999999877643  577777654


Q ss_pred             Ee
Q psy7051          88 QM   89 (158)
Q Consensus        88 ~~   89 (158)
                      .+
T Consensus       247 RI  248 (684)
T KOG2591|consen  247 RI  248 (684)
T ss_pred             hh
Confidence            43

>KOG2068|consensus

Probab=96.58  E-value=0.00078  Score=51.28  Aligned_cols=78  Identities=21%  Similarity=0.368  Sum_probs=57.6

Q ss_pred             cEEEEeCCCCCCCHH-HHH--HHhhhcCceEEEEEccCCC--CCC-cccEEEEEEcCHHHHHHHHHHhCCcccCCceEEE
Q psy7051          14 VSLKVDNLTYRTTPD-DLR--RVFERCGEVGDIYIPRDRF--TRE-SRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV   87 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~-~l~--~~f~~~G~i~~v~~~~~~~--~~~-~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v   87 (158)
                      .-+||-+|+..+..+ .|+  +.|.+||.|..|.+..+..  ... ...-+||+|...++|..||...+|..+.|+.|+.
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lka  157 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALKA  157 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhHH
Confidence            347788888776444 443  5788999999888766541  111 1224899999999999999999999999988777


Q ss_pred             Eeee
Q psy7051          88 QMAR   91 (158)
Q Consensus        88 ~~a~   91 (158)
                      .+..
T Consensus       158 ~~gt  161 (327)
T KOG2068|consen  158 SLGT  161 (327)
T ss_pred             hhCC
Confidence            7643

>KOG0804|consensus

Probab=96.30  E-value=0.023  Score=45.20  Aligned_cols=68  Identities=24%  Similarity=0.348  Sum_probs=57.3

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcC-ceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCC
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCG-EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDG   82 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G-~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g   82 (158)
                      .+.|+|-.+|..++..||..|+..+- .|..+.++.+.  -.+.-.++|.|.+.++|...++.+||..|+.
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~--~pnrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDG--MPNRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecC--CCceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            67899999999999999999998764 68888888863  2234568999999999999999999998754

>KOG4574|consensus

Probab=95.96  E-value=0.0054  Score=52.01  Aligned_cols=70  Identities=29%  Similarity=0.393  Sum_probs=57.8

Q ss_pred             EEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCccc--CCceEEEEeeec
Q psy7051          17 KVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRML--DGRELRVQMARY   92 (158)
Q Consensus        17 ~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i--~g~~i~v~~a~~   92 (158)
                      ++-|.+-..+-.-|..+|.+||.|..++...+      ...|.|+|...+.|..|++.|+|.++  .|-+.+|.+|+.
T Consensus       302 ~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~------~N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~  373 (1007)
T KOG4574|consen  302 SLENNAVNLTSSSLATLCSDYGSVASAWTLRD------LNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKT  373 (1007)
T ss_pred             hhhcccccchHHHHHHHHHhhcchhhheeccc------ccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccc
Confidence            34444555667788999999999999988666      35899999999999999999999974  678899999873

>KOG4210|consensus

Probab=95.76  E-value=0.008  Score=45.63  Aligned_cols=80  Identities=18%  Similarity=0.118  Sum_probs=63.3

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ...++|++++...+.+.++..++..+|.+..+.+.........+++++|.|...+.+..|+.......+.+..+...+.+
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~~  166 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLNT  166 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCcccc
Confidence            46789999999999999999999999988777666655677789999999999999999996433345555555555444

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=95.51  E-value=0.11  Score=30.49  Aligned_cols=55  Identities=24%  Similarity=0.404  Sum_probs=43.2

Q ss_pred             CCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEE
Q psy7051          24 RTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV   87 (158)
Q Consensus        24 ~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v   87 (158)
                      .++.++|+..|..|+- ..|  ..++ +|     -||.|.+..+|+.|+...++..+.+..|.+
T Consensus        11 ~~~v~d~K~~Lr~y~~-~~I--~~d~-tG-----fYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRW-DRI--RDDR-TG-----FYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCc-ceE--EecC-CE-----EEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            5688999999999963 233  3332 33     589999999999999999999888877765

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

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=94.99  E-value=1.7  Score=36.88  Aligned_cols=70  Identities=9%  Similarity=0.156  Sum_probs=50.7

Q ss_pred             CcEEEEeCC--CCCCCHHHHHHHhhhcCce-----EEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceE
Q psy7051          13 MVSLKVDNL--TYRTTPDDLRRVFERCGEV-----GDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGREL   85 (158)
Q Consensus        13 ~~~l~V~nl--~~~~~~~~l~~~f~~~G~i-----~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i   85 (158)
                      +.++|| |+  ...++..+|..++..-+.|     -.|.|..        .|.||+... +.+...+..|++..+.|+.|
T Consensus       486 ~~~~~~-~~g~~~~~~~~~~~~~i~~~~~~~~~~ig~i~i~~--------~~s~v~~~~-~~~~~~~~~~~~~~~~~~~~  555 (629)
T PRK11634        486 MQLYRI-EVGRDDGVEVRHIVGAIANEGDISSRYIGNIKLFA--------SHSTIELPK-GMPGEVLQHFTRTRILNKPM  555 (629)
T ss_pred             CEEEEE-ecccccCCCHHHHHHHHHhhcCCChhhCCcEEEeC--------CceEEEcCh-hhHHHHHHHhccccccCCce
Confidence            455655 44  4568888888888766544     4455533        378998864 55778888999999999999


Q ss_pred             EEEeeec
Q psy7051          86 RVQMARY   92 (158)
Q Consensus        86 ~v~~a~~   92 (158)
                      .|+.++.
T Consensus       556 ~~~~~~~  562 (629)
T PRK11634        556 NMQLLGD  562 (629)
T ss_pred             EEEECCC
Confidence            9998753

>KOG2318|consensus

Probab=94.40  E-value=0.4  Score=39.57  Aligned_cols=79  Identities=18%  Similarity=0.205  Sum_probs=57.8

Q ss_pred             CCCCcEEEEeCCCCC-CCHHHHHHHhhhc----CceEEEEEccCC----------CCCC---------------------
Q psy7051          10 IEGMVSLKVDNLTYR-TTPDDLRRVFERC----GEVGDIYIPRDR----------FTRE---------------------   53 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~-~~~~~l~~~f~~~----G~i~~v~~~~~~----------~~~~---------------------   53 (158)
                      ...+..|-|.||.|. +...+|.-+|..|    |.|..|.|...-          ..|.                     
T Consensus       171 ~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~ee~  250 (650)
T KOG2318|consen  171 GEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDDEEE  250 (650)
T ss_pred             ccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccchhhh
Confidence            456788999999985 6888999998876    477777653210          0111                     


Q ss_pred             ----------------cccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEE
Q psy7051          54 ----------------SRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ   88 (158)
Q Consensus        54 ----------------~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~   88 (158)
                                      .--||.|+|.+.+.|.++++.|+|.+|...-..+.
T Consensus       251 ~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~D  301 (650)
T KOG2318|consen  251 EDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLD  301 (650)
T ss_pred             hhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceee
Confidence                            12489999999999999999999999865444433

>KOG2193|consensus

Probab=94.37  E-value=0.0039  Score=49.11  Aligned_cols=74  Identities=15%  Similarity=0.265  Sum_probs=62.0

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEc-cCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIP-RDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~-~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ..+.|.|+|+...|+.|..++..||.++.|..+ ++.    ..-..-|+|.+.+.+..||.+|+|..|....++|.|-.
T Consensus        81 rk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~----etavvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~YiP  155 (584)
T KOG2193|consen   81 RKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDS----ETAVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGYIP  155 (584)
T ss_pred             hhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccch----HHHHHHHHHHHHHHHHHHHHhhcchHhhhhhhhcccCc
Confidence            458899999999999999999999999888653 232    23345678999999999999999999999999998854

>KOG4207|consensus

Probab=94.29  E-value=0.41  Score=34.61  Aligned_cols=55  Identities=29%  Similarity=0.235  Sum_probs=29.5

Q ss_pred             CHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHH--HhCCccc
Q psy7051          26 TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD--AMDGRML   80 (158)
Q Consensus        26 ~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~--~l~g~~i   80 (158)
                      +---|.+-+...|+|---.-....+.....-.-|-.=.+.++|.+|+.  .|+|.+|
T Consensus        29 ~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRel   85 (256)
T KOG4207|consen   29 DLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGREL   85 (256)
T ss_pred             HHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeecccee
Confidence            444455666666654221111111111122245666677888888887  4888877

>KOG4483|consensus

Probab=94.21  E-value=0.16  Score=39.99  Aligned_cols=58  Identities=22%  Similarity=0.199  Sum_probs=48.8

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhhcCc-eEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHH
Q psy7051           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGE-VGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD   73 (158)
Q Consensus         9 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~-i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~   73 (158)
                      +.+-.+.|-|-++|.....+||...|+.|++ -..|.|+.+.       +||-.|.+...|..||.
T Consensus       387 e~dlpHVlEIydfp~efkteDll~~f~~yq~kgfdIkWvDdt-------halaVFss~~~AaeaLt  445 (528)
T KOG4483|consen  387 ESDLPHVLEIYDFPDEFKTEDLLKAFETYQNKGFDIKWVDDT-------HALAVFSSVNRAAEALT  445 (528)
T ss_pred             cccccceeEeccCchhhccHHHHHHHHHhhcCCceeEEeecc-------eeEEeecchHHHHHHhh
Confidence            3445678999999999999999999999974 4667787774       79999999999999985

>KOG0835|consensus

Probab=93.58  E-value=0.092  Score=40.30  Aligned_cols=10  Identities=20%  Similarity=0.418  Sum_probs=4.8

Q ss_pred             CCCHHHHHHH
Q psy7051          24 RTTPDDLRRV   33 (158)
Q Consensus        24 ~~~~~~l~~~   33 (158)
                      .+++.+|.++
T Consensus       212 d~~k~eid~i  221 (367)
T KOG0835|consen  212 DTTKREIDEI  221 (367)
T ss_pred             CCcHHHHHHH
Confidence            3455555444

>smart00596 PRE_C2HC PRE_C2HC domain

Probab=92.92  E-value=0.25  Score=29.18  Aligned_cols=61  Identities=15%  Similarity=0.216  Sum_probs=46.3

Q ss_pred             HHHHHHhhhcC-ceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          28 DDLRRVFERCG-EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        28 ~~l~~~f~~~G-~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      .+|++.|...| ++.++..+....+..+...-||+.....+...   .|+=..|++..|.|+-..
T Consensus         2 ~~I~~~L~~~G~~v~~i~~m~~~~~r~P~nmf~vel~~~~~~~~---Il~ik~Lg~~~V~VEr~~   63 (69)
T smart00596        2 SQIEEALKDIGFPVLFIHNMLNRDTKNPQNMFEVELVPAANGKE---ILNIKTLGGQRVTVERPH   63 (69)
T ss_pred             HHHHHHHHHcCCceeEEEcccccCCCCcceeEEEEeeecCCCcc---eEeehhhCCeeEEEecCc
Confidence            46888899998 88888888877777777888999887655444   345567889998887543

>KOG4019|consensus

Probab=92.49  E-value=0.18  Score=35.55  Aligned_cols=73  Identities=15%  Similarity=0.193  Sum_probs=53.9

Q ss_pred             cEEEEeCCCCCCCH-----HHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCc-eEEE
Q psy7051          14 VSLKVDNLTYRTTP-----DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGR-ELRV   87 (158)
Q Consensus        14 ~~l~V~nl~~~~~~-----~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~-~i~v   87 (158)
                      +++++.+++..+..     ...+.+|.+|-+...+.+...      .+..-|.|.+++.|..|...++...|.|. .++.
T Consensus        11 ~~~~~c~i~~~VF~~~~~k~~~~~lFrq~n~~~~fq~lrs------frrvRi~f~~p~~a~~a~i~~~~~~f~~~~~~k~   84 (193)
T KOG4019|consen   11 TAIIACDIHEEVFVNREDKALFENLFRQINEDATFQLLRS------FRRVRINFSNPEAAADARIKLHSTSFNGKNELKL   84 (193)
T ss_pred             ceeeeecccHHhhccHHHHHHHHhHHhhhCcchHHHHHHh------hceeEEeccChhHHHHHHHHhhhcccCCCceEEE
Confidence            55888888776532     234566777766665555443      45677899999999999999999999988 7887


Q ss_pred             Eeeec
Q psy7051          88 QMARY   92 (158)
Q Consensus        88 ~~a~~   92 (158)
                      -++..
T Consensus        85 yfaQ~   89 (193)
T KOG4019|consen   85 YFAQP   89 (193)
T ss_pred             EEccC
Confidence            77763

>PF07530 PRE_C2HC: Associated with zinc fingers; InterPro: IPR006579 This domain is present in proteins found exclusively in the arthropods, including a number of Drosophila species, the silk moth and the gypsy moth

Probab=92.14  E-value=0.55  Score=27.72  Aligned_cols=61  Identities=20%  Similarity=0.328  Sum_probs=45.9

Q ss_pred             HHHHHHhhhcC-ceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          28 DDLRRVFERCG-EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        28 ~~l~~~f~~~G-~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ++|.+.|...| +|.+|.-+....+..+....||+.+...+...+   ++=..|++..|+|+...
T Consensus         2 ~~I~~~L~~~G~~v~~i~~~~~~~~k~pl~mf~veL~p~~~~k~i---~~Ik~l~~~~V~vE~~~   63 (68)
T PF07530_consen    2 EEIKEELKDQGHPVRNIHNMHSRNTKKPLNMFFVELEPKPNNKEI---YKIKTLCGQRVKVERPR   63 (68)
T ss_pred             HHHHHHHHHcCCceEEEEccccCCCCCCceEEEEeeccCccccce---eehHhhCCeEEEEecCC
Confidence            46888888888 788888777776777888999999876664433   44567888889988654

These proteins are possibly involved in RNA binding or single strand DNA binding.

>KOG4410|consensus

Probab=90.49  E-value=0.87  Score=34.53  Aligned_cols=46  Identities=20%  Similarity=0.248  Sum_probs=35.8

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCce-EEEEEccCCCCCCcccEEEEEEcCH
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEV-GDIYIPRDRFTRESRGFAFVRFFDK   65 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i-~~v~~~~~~~~~~~~g~afV~f~~~   65 (158)
                      +-|+|+||+..+...+|+..+.+.+.+ ..+.|.     | +.+-||+.|.+.
T Consensus       331 ~di~~~nl~rd~rv~dlk~~lr~~~~~pm~iswk-----g-~~~k~flh~~~~  377 (396)
T KOG4410|consen  331 TDIKLTNLSRDIRVKDLKSELRKRECTPMSISWK-----G-HFGKCFLHFGNR  377 (396)
T ss_pred             cceeeccCccccchHHHHHHHHhcCCCceeEeee-----c-CCcceeEecCCc
Confidence            569999999999999999999998744 444442     2 357899999754

>KOG0107|consensus

Probab=88.22  E-value=1.8  Score=30.58  Aligned_cols=12  Identities=17%  Similarity=-0.061  Sum_probs=7.4

Q ss_pred             CcEEEEeCCCCC
Q psy7051          13 MVSLKVDNLTYR   24 (158)
Q Consensus        13 ~~~l~V~nl~~~   24 (158)
                      ...|||.-.|+.
T Consensus        37 lrsvWvArnPPG   48 (195)
T KOG0107|consen   37 LRSVWVARNPPG   48 (195)
T ss_pred             ceeEEEeecCCC
Confidence            456777665554

>KOG1295|consensus

Probab=86.88  E-value=0.97  Score=35.50  Aligned_cols=69  Identities=19%  Similarity=0.258  Sum_probs=48.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCc-eEEEEEccCCCC--CCcccEEEEEEcCHHHHHHHHHHhCCccc
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGE-VGDIYIPRDRFT--RESRGFAFVRFFDKRDAEDALDAMDGRML   80 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~-i~~v~~~~~~~~--~~~~g~afV~f~~~~~a~~a~~~l~g~~i   80 (158)
                      ....|.|.+||+..++.+|.+.+.+|-. +....+......  ....+.|||.|..+++.......++|..|
T Consensus         6 ~~~Kvv~rrlpp~l~~~~~~eqi~p~~~~v~~~~F~~a~~s~~~~~ysrayinFk~~~dv~ef~~~f~g~if   77 (376)
T KOG1295|consen    6 AKVKVVVRRLPPKLTEEQLLEQINPFPEHVNWEFFAKADESLRNHKYSRAYINFKNPEDVEEFRRRFDGYIF   77 (376)
T ss_pred             cceeeeeecCCCcccHHHHhhhcCCCccccchheeccccccchhhhhhhhhhccccHHHHHHHHhhCCceEE
Confidence            3467889999999999999988887642 222223211111  12356799999999999988888898865

>KOG2295|consensus

Probab=85.94  E-value=0.12  Score=42.35  Aligned_cols=73  Identities=15%  Similarity=0.102  Sum_probs=54.8

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceE
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGREL   85 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i   85 (158)
                      ..+|||.|++++++-.+|+.++..+--+..+.+..........-+.+|+|.---....|+.+||+..+....+
T Consensus       231 e~sll~rni~Pnis~aeIe~~ck~i~~~lrfals~~~aek~~~r~lwv~fk~~~ni~~a~~aLn~irl~s~~~  303 (648)
T KOG2295|consen  231 ECSLLVRNILPNISVAEIENLCKGIPGFLRFALSTINAEKNFERRLWVTFKRGTNIKEACWALNGIRLRSNFL  303 (648)
T ss_pred             HHHHHHhccCCcccHHHHHHHhccCchheeeeccCchHHHHHHHHhhHhhccccchHHHHHHhhhcccccccc
Confidence            3578999999999999999999998766666554443333345678999997777888888888876654443

>PRK14548 50S ribosomal protein L23P; Provisional

Probab=85.32  E-value=6.1  Score=24.34  Aligned_cols=57  Identities=19%  Similarity=0.223  Sum_probs=40.4

Q ss_pred             EEEeCCCCCCCHHHHHHHhhh-cC-ceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHh
Q psy7051          16 LKVDNLTYRTTPDDLRRVFER-CG-EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM   75 (158)
Q Consensus        16 l~V~nl~~~~~~~~l~~~f~~-~G-~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l   75 (158)
                      .|+--++..++..+|++.++. || .|..|....-+ .+  .-=|||.+...++|......+
T Consensus        23 ~y~F~V~~~anK~eIK~AvE~lf~VkV~~VnT~~~~-~~--~KKA~V~L~~g~~A~~va~ki   81 (84)
T PRK14548         23 KLTFIVDRRATKPDIKRAVEELFDVKVEKVNTLITP-KG--EKKAYVKLAEEYDAEEIASRL   81 (84)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHhCCceEEEEeEEcC-CC--cEEEEEEeCCCCcHHHHHHhh
Confidence            344456888999999999988 66 67777554433 11  235999999888888776543

>PF03468 XS: XS domain; InterPro: IPR005380 The XS (rice gene X and SGS3) domain is found in a family of plant proteins including gene X Q9SBW2 from SWISSPROT and SGS3 Q9LDX1 from SWISSPROT

Probab=84.51  E-value=3.4  Score=27.11  Aligned_cols=55  Identities=15%  Similarity=0.184  Sum_probs=28.1

Q ss_pred             EEEEeCCCCC---------CCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCH-HHHHHHH
Q psy7051          15 SLKVDNLTYR---------TTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK-RDAEDAL   72 (158)
Q Consensus        15 ~l~V~nl~~~---------~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~-~~a~~a~   72 (158)
                      ++.|-|++..         ++.++|.+.|..|..++ +..+.+..  ...|+++|+|..- .-...|+
T Consensus        10 mgIi~N~~~~~~~~g~~~g~~~~~l~~~l~~f~p~k-v~~l~~~~--gh~g~aiv~F~~~w~Gf~~A~   74 (116)
T PF03468_consen   10 MGIIVNIPTEKDDDGRWVGMSNEELLDKLAEFNPLK-VKPLYGKQ--GHTGFAIVEFNKDWSGFKNAM   74 (116)
T ss_dssp             EEEEE----EE-TTS-EE---SHHHHHHHHH---SE-EEEEEETT--EEEEEEEEE--SSHHHHHHHH
T ss_pred             EEEEEcCccccCCCCceeccCHHHHHHHHHhcCCce-eEECcCCC--CCcEEEEEEECCChHHHHHHH
Confidence            4667788553         35678999999998775 33334432  3678999999854 3344444

SGS3 is thought to be involved in post-transcriptional gene silencing (PTGS). This domain contains a conserved aspartate residue that may be functionally important. The XS domain containing proteins contain coiled-coils, which suggests that they will oligomerise. Most coiled-coil proteins form either a dimeric or a trimeric structure. It is possible that different members of the XS domain family could oligomerise via their coiled-coils forming a variety of complexes [].; PDB: 4E8U_C.

>KOG4365|consensus

Probab=84.23  E-value=0.17  Score=40.36  Aligned_cols=78  Identities=5%  Similarity=-0.125  Sum_probs=58.7

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeec
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARY   92 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~   92 (158)
                      +..|+..|+..+++.++.-+|..||-|..+.+...-..+.....+||+..+ .++..+|.-+....+.|.++.|.++..
T Consensus         4 ~~~~l~d~~~~~~~~~~~~~~~d~~~i~~~d~~~~~~~~~~~v~~f~~~~~-~~~~~~i~~~k~q~~~~~~~r~~~~~~   81 (572)
T KOG4365|consen    4 MKKSLKDSVASNNKDQNSMKHEDPSIISMEDGSPYVNGSLGEVTPFQHAKK-ANGPNYIQPQKRQTTFESQDRKAVSPS   81 (572)
T ss_pred             hhhhHhhcccccccchhhhhccCCcceeeccCCccccCCcceeeeeeeeec-cCcccccCHHHHhhhhhhhhhhhcCch
Confidence            456778899999999999999999999888775544444445567776654 566777777777778888888888763

>PF10567 Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IPR018885 This conserved domain is found in fungal proteins and appears to be involved in RNA-processing

Probab=83.95  E-value=3  Score=31.77  Aligned_cols=78  Identities=14%  Similarity=0.255  Sum_probs=56.3

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCC-------CCCCcccEEEEEEcCHHHHHHHHHH----hCC--ccc
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDR-------FTRESRGFAFVRFFDKRDAEDALDA----MDG--RML   80 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~-------~~~~~~g~afV~f~~~~~a~~a~~~----l~g--~~i   80 (158)
                      ..|.+.||..+++-..+...|.+||+|+.|.++.+.       ..........+-|-+.+.|...+..    |..  ..+
T Consensus        16 RSLLfeNv~~sidLh~Fl~~fv~~~pIESiYL~~~~~~~~d~~~~d~~~~SilLSFlsr~~CLdFYNnvLQrLsEfK~~L   95 (309)
T PF10567_consen   16 RSLLFENVNNSIDLHSFLTKFVKFGPIESIYLIKSNDKPSDDYNDDKNNQSILLSFLSREICLDFYNNVLQRLSEFKTKL   95 (309)
T ss_pred             HHHHHhhccccccHHHHHHHhhccCceeEEEEecCCCcccccccccccceEEEEeeechHHHHHHHHHHHHHHHHHHHhc
Confidence            457788999999988899999999999999988764       1223345788899988887665432    221  246


Q ss_pred             CCceEEEEeee
Q psy7051          81 DGRELRVQMAR   91 (158)
Q Consensus        81 ~g~~i~v~~a~   91 (158)
                      ....|.|.+..
T Consensus        96 ~S~~L~lsFV~  106 (309)
T PF10567_consen   96 KSESLTLSFVS  106 (309)
T ss_pred             CCcceeEEEEE
Confidence            66777777754

It binds to poly-adenylated RNA, interacts genetically with mRNA 3'-end processing factors, co-purifies with the nuclear cap-binding protein Cbp20p, and is found in complexes containing other translation factors, such as EIF4G as in P39935 from SWISSPROT and P39936 from SWISSPROT.

>TIGR03636 L23_arch archaeal ribosomal protein L23

Probab=81.44  E-value=9.5  Score=23.08  Aligned_cols=57  Identities=16%  Similarity=0.207  Sum_probs=39.9

Q ss_pred             EEEeCCCCCCCHHHHHHHhhh-cC-ceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHh
Q psy7051          16 LKVDNLTYRTTPDDLRRVFER-CG-EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM   75 (158)
Q Consensus        16 l~V~nl~~~~~~~~l~~~f~~-~G-~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l   75 (158)
                      -|+-.++..++..+|+..++. |+ .|..|....-+ .  ..-=|||.+..-+.|......+
T Consensus        16 ~y~F~V~~~anK~eIK~avE~lf~VkV~~Vnt~~~~-~--~~KKA~VtL~~g~~a~~va~k~   74 (77)
T TIGR03636        16 KLTFIVDRKATKGDIKRAVEKLFDVKVEKVNTLITP-R--GEKKAYVKLAEEYAAEEIASRL   74 (77)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHhCCceEEEEeEEcC-C--CceEEEEEECCCCcHHHHHHhh
Confidence            455567889999999999988 66 66666544332 1  1235999998888877765543

This model describes the archaeal ribosomal protein L23P and rigorously excludes the bacterial counterpart L23. In order to capture every known instance of archaeal L23P, the trusted cutoff is set lower than a few of the highest scoring eukaryotic cytosolic ribosomal counterparts.

>KOG4454|consensus

Probab=80.78  E-value=0.43  Score=34.78  Aligned_cols=76  Identities=29%  Similarity=0.423  Sum_probs=58.7

Q ss_pred             CCCcEEEEeC----CCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEE
Q psy7051          11 EGMVSLKVDN----LTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR   86 (158)
Q Consensus        11 ~~~~~l~V~n----l~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~   86 (158)
                      +...+++.|+    |...++++.+...|+..|.+..+.+..+. .+.+..++|+.+.-....-.++...++..+.-+++.
T Consensus        78 e~q~~~r~G~shapld~r~~~ei~~~v~s~a~p~~~~R~~~~~-d~rnrn~~~~~~qr~~~~P~~~~~y~~l~~~~~~~~  156 (267)
T KOG4454|consen   78 EEQRTLRCGNSHAPLDERVTEEILYEVFSQAGPIEGVRIPTDN-DGRNRNFGFVTYQRLCAVPFALDLYQGLELFQKKVT  156 (267)
T ss_pred             hhhcccccCCCcchhhhhcchhhheeeecccCCCCCccccccc-cCCccCccchhhhhhhcCcHHhhhhcccCcCCCCcc
Confidence            4446777888    77788999999999999999999888775 477888999999877777777777677665555444


Q ss_pred             E
Q psy7051          87 V   87 (158)
Q Consensus        87 v   87 (158)
                      +
T Consensus       157 ~  157 (267)
T KOG4454|consen  157 I  157 (267)
T ss_pred             c
Confidence            4

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

Probab=80.12  E-value=3.1  Score=30.01  Aligned_cols=62  Identities=23%  Similarity=0.315  Sum_probs=42.3

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHH
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDAL   72 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~   72 (158)
                      .....+++.+++..++..++..+|..+|.+..+.+.............++.+.....+..++
T Consensus       223 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  284 (306)
T COG0724         223 EKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNEASKDALESN  284 (306)
T ss_pred             cccceeeccccccccchhHHHHhccccccceeeeccCCCCCcccccccccchhHHHhhhhhh
Confidence            44578999999999999999999999999977776555433333334444444444444333

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	158
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		1e-39
2kn4_A	158	The Structure Of The Rrm Domain Of Sc35 Length = 15		6e-35
2dnm_A	103	Solution Structure Of Rna Binding Domain In Srp46 S		5e-29
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		3e-12
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		1e-10
2e5h_A	94	Solution Structure Of Rna Binding Domain In Zinc Fi		3e-10
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		3e-10
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		1e-09
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		1e-09
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		1e-09
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		2e-09
1whw_A	99	Solution Structure Of The N-Terminal Rna Binding Do		2e-09
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		3e-08
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		4e-08
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		5e-08
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		5e-08
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		6e-08
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		7e-08
2jwn_A	124	Solution Nmr Structure Of The Protease-Resistent Do		8e-08
2fc9_A	101	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		9e-08
2cq0_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		1e-07
1h2t_Z	156	Structure Of The Human Nuclear Cap-Binding-Complex		1e-07
3bs9_A	87	X-Ray Structure Of Human Tia-1 Rrm2 Length = 87		1e-07
3ucg_A	89	Crystal Structure Of A Rna Binding Domain Of Hypoth		1e-07
3b4d_A	96	Crystal Structure Of Human Pabpn1 Rrm Length = 96		1e-07
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		2e-07
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		2e-07
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		3e-07
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		4e-07
1sxl_A	97	Resonance Assignments And Solution Structure Of The		5e-07
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		5e-07
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		7e-07
1x5u_A	105	Solution Structure Of Rrm Domain In Splicing Factor		8e-07
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		8e-07
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		8e-07
2hvz_A	101	Solution Structure Of The Rrm Domain Of Sr Rich Fac		1e-06
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		1e-06
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		1e-06
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		2e-06
1h6k_Z	98	Nuclear Cap Binding Complex Length = 98		2e-06
2cpf_A	98	Solution Structure Of The Penultimate Rna Recogniti		2e-06
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		2e-06
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		2e-06
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		2e-06
3lpy_A	79	Crystal Structure Of The Rrm Domain Of Cyp33 Length		2e-06
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		2e-06
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		2e-06
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		2e-06
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		2e-06
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		3e-06
4a8x_A	88	Structure Of The Core Asap Complex Length = 88		3e-06
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		3e-06
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		4e-06
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		4e-06
3cw1_K	216	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		4e-06
2rs2_A	109	1h, 13c, And 15n Chemical Shift Assignments For Mus		4e-06
3md1_A	83	Crystal Structure Of The Second Rrm Domain Of Yeast		4e-06
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		5e-06
2cpj_A	99	Solution Structure Of The N-Terminal Rna Recognitio		5e-06
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		5e-06
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		6e-06
2err_A	109	Nmr Structure Of The Rna Binding Domain Of Human Fo		7e-06
3pgw_S	437	Crystal Structure Of Human U1 Snrnp Length = 437		7e-06
2cq3_A	103	Solution Structure Of Rna Binding Domain In Rna Bin		7e-06
1x4b_A	116	Solution Structure Of Rrm Domain In Heterogeneous N		7e-06
3s7r_A	87	Crystal Structure Of A Heterogeneous Nuclear Ribonu		8e-06
1uaw_A	77	Solution Structure Of The N-Terminal Rna-Binding Do		8e-06
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		1e-05
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		1e-05
2i2y_A	150	Solution Structure Of The Rrm Of Srp20 Bound To The		1e-05
2cqg_A	103	Solution Structure Of The Rna Binding Domain Of Tar		2e-05
2i38_A	150	Solution Structure Of The Rrm Of Srp20 Length = 150		2e-05
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		3e-05
1fje_B	175	Solution Structure Of Nucleolin Rbd12 In Complex Wi		4e-05
2cph_A	107	Solution Structure Of The C-Terminal Rna Recognitio		5e-05
2krr_A	180	Solution Structure Of The Rbd1,2 Domains From Human		7e-05
2j0q_D	109	The Crystal Structure Of The Exon Junction Complex		1e-04
1hd0_A	75	Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D		2e-04
2j0s_D	89	The Crystal Structure Of The Exon Junction Complex		2e-04
2hyi_B	91	Structure Of The Human Exon Junction Complex With A		2e-04
3ex7_B	126	The Crystal Structure Of Ejc In Its Transition Stat		2e-04
2xb2_D	90	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		2e-04
1oo0_B	110	Crystal Structure Of The Drosophila Mago Nashi-Y14		2e-04
3lqv_A	115	Branch Recognition By Sf3b14 Length = 115		2e-04
1p27_B	106	Crystal Structure Of The Human Y14MAGOH COMPLEX Len		2e-04
3bo2_A	95	A Relaxed Active Site Following Exon Ligation By A		3e-04
1u6b_A	98	Crystal Structure Of A Self-Splicing Group I Intron		3e-04
3k0j_A	96	Crystal Structure Of The E. Coli Thim Riboswitch In		3e-04
3l3c_A	90	Crystal Structure Of The Bacillus Anthracis Glms Ri		3e-04
1m5k_C	100	Crystal Structure Of A Hairpin Ribozyme In The Cata		3e-04
1urn_A	97	U1a MutantRNA COMPLEX + GLYCEROL Length = 97		3e-04
3nnh_A	88	Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuug		3e-04
3iwn_C	91	Co-Crystal Structure Of A Bacterial C-Di-Gmp Ribosw		3e-04
2nz4_A	94	Structural Investigation Of The Glms Ribozyme Bound		3e-04
1aud_A	101	U1a-Utrrna, Nmr, 31 Structures Length = 101		3e-04
1hl6_A	165	A Novel Mode Of Rbd-Protein Recognition In The Y14-		3e-04
1fjc_A	96	Solution Structure Of Nucleolin Rbd2 Length = 96		4e-04
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		4e-04
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		4e-04
1x4a_A	109	Solution Structure Of Rrm Domain In Splicing Factor		4e-04
3nnc_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		5e-04
2dhs_A	187	Solution Structure Of Nucleic Acid Binding Protein		5e-04
2dnq_A	90	Solution Structure Of Rna Binding Domain 1 In Rna-B		6e-04
1wf2_A	98	Solution Structure Of Rrm Domain In Hnrpc Protein L		6e-04
2fho_B	87	Nmr Solution Structure Of The Human Spliceosomal Pr		6e-04
1oia_A	95	U1a Rnp Domain 1-95 Length = 95		7e-04
2cpe_A	113	Solution Structure Of The Rna Recognition Motif Of		7e-04
2f9d_A	125	2.5 Angstrom Resolution Structure Of The Spliceosom		8e-04
2f9j_A	125	3.0 Angstrom Resolution Structure Of A Y22m Mutant		8e-04
3pgw_A	282	Crystal Structure Of Human U1 Snrnp Length = 282		8e-04
1fht_A	116	Rna-Binding Domain Of The U1a Spliceosomal Protein		9e-04

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score =  158 bits (399), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 75/90 (83%), Positives = 83/90 (92%)
Query: 1   MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
           MSYGRPPP +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFV
Sbjct: 35  MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 94
Query: 61  RFFDKRDAEDALDAMDGRMLDGRELRVQMA 90
           RF DKRDAEDA+DAMDG +LDGRELRVQMA
Sbjct: 95  RFHDKRDAEDAMDAMDGAVLDGRELRVQMA 124

>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35 Length = 158

Iteration: 1
 Score =  142 bits (359), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 67/81 (82%), Positives = 75/81 (92%)
Query: 10  IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAE 69
           +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFVRF DKRDAE
Sbjct: 67  VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAE 126
Query: 70  DALDAMDGRMLDGRELRVQMA 90
           DA+DAMDG +LDGRELRVQMA
Sbjct: 127 DAMDAMDGAVLDGRELRVQMA 147

>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing Factor Length = 103

Iteration: 1
 Score =  123 bits (308), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 60/89 (67%), Positives = 72/89 (80%)
Query: 2  SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          S G   P ++GM++LKVDNLTYRT+PD LRRVFE+ G VGD+YIPR+  T+  RGFAFVR
Sbjct: 2  SSGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVR 61
Query: 62 FFDKRDAEDALDAMDGRMLDGRELRVQMA 90
          F D+RDA+DA  AMDG  LDGRELRVQ+A
Sbjct: 62 FHDRRDAQDAEAAMDGAELDGRELRVQVA 90

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 67.4 bits (163), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 31/75 (41%), Positives = 50/75 (66%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V  L++ T    L +VF + G++ ++ + +DR T+ SRGF FV F +  DA+DA+ AM
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 76 DGRMLDGRELRVQMA 90
          +G+ +DGR++RV  A
Sbjct: 75 NGKSVDGRQIRVDQA 89

>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic Granule-Associated Rna Binding Protein 1 Length = 115

Iteration: 1
 Score = 62.4 bits (150), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 27/73 (36%), Positives = 44/73 (60%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V +L+   T +D++  F   G + D  + +D  T +S+G+ FV FF+K DAE+A+  M G
Sbjct: 20 VGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGG 79
Query: 78 RMLDGRELRVQMA 90
          + L GR++R   A
Sbjct: 80 QWLGGRQIRTNWA 92

>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger Cchc-Type And Rna Binding Motif 1 Length = 94

Iteration: 1
 Score = 60.8 bits (146), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 27/76 (35%), Positives = 48/76 (63%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          ++ V NL +  T +DL R+F + G+V  + I +D+ TR+S+G AF+ F DK  A++   A
Sbjct: 18 TVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRA 77
Query: 75 MDGRMLDGRELRVQMA 90
          ++ + L GR ++  +A
Sbjct: 78 INNKQLFGRVIKASIA 93

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 60.8 bits (146), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 26/73 (35%), Positives = 45/73 (61%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V +L+   T +D++  F   G++ D  + +D  T +S+G+ FV F++K DAE+A+  M G
Sbjct: 20 VGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHMGG 79
Query: 78 RMLDGRELRVQMA 90
          + L GR++R   A
Sbjct: 80 QWLGGRQIRTNWA 92

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 58.9 bits (141), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 33/74 (44%), Positives = 45/74 (60%)
Query: 14  VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
             L V  L+  TT  DLR VF + G + D+ I  D+ +R SRGFAFV F +  DA++A +
Sbjct: 47  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 106
Query: 74  AMDGRMLDGRELRV 87
             +G  LDGR +RV
Sbjct: 107 RANGMELDGRRIRV 120

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 58.5 bits (140), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 33/75 (44%), Positives = 45/75 (60%)
Query: 14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
            L V  L+  TT  DLR VF + G + D+ I  D+ +R SRGFAFV F +  DA++A +
Sbjct: 16 CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 75
Query: 74 AMDGRMLDGRELRVQ 88
            +G  LDGR +RV 
Sbjct: 76 RANGMELDGRRIRVS 90

>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2 Beta Protein In Complex With Rna (Gaagaa) Length = 99

Iteration: 1
 Score = 58.5 bits (140), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 33/77 (42%), Positives = 46/77 (59%)
Query: 14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
            L V  L+  TT  DLR VF + G + D+ I  D+ +R SRGFAFV F +  DA++A +
Sbjct: 16 CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 75
Query: 74 AMDGRMLDGRELRVQMA 90
            +G  LDGR +RV  +
Sbjct: 76 RANGMELDGRRIRVDFS 92

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 58.5 bits (140), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 33/77 (42%), Positives = 46/77 (59%)
Query: 14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
            L V  L+  TT  DLR VF + G + D+ I  D+ +R SRGFAFV F +  DA++A +
Sbjct: 13 CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 72
Query: 74 AMDGRMLDGRELRVQMA 90
            +G  LDGR +RV  +
Sbjct: 73 RANGMELDGRRIRVDFS 89

>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain From Hypothetical Protein Bab23448 Length = 99

Iteration: 1
 Score = 58.2 bits (139), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 26/72 (36%), Positives = 42/72 (58%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V NL+Y ++ +DL ++F   G + +++ P D  T++ +GFAFV F     A  A   +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 76 DGRMLDGRELRV 87
          DG++  GR L V
Sbjct: 71 DGQVFQGRMLHV 82

>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition Motif (Rrm1) Of The Au-Rich Element (Are) Binding Protein Hur At 2.0 Angstrom Resolution Length = 84

Iteration: 1
 Score = 54.3 bits (129), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 26/79 (32%), Positives = 42/79 (53%)
Query: 12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDA 71
          G  +L V+ L    T D+LR +F   GEV    + RD+    S G+ FV +   +DAE A
Sbjct: 3  GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 62
Query: 72 LDAMDGRMLDGRELRVQMA 90
          ++ ++G  L  + ++V  A
Sbjct: 63 INTLNGLRLQSKTIKVSYA 81

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 53.5 bits (127), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 24/76 (31%), Positives = 43/76 (56%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          +L V+ L    T ++ R +F   GE+    + RD+ T +S G+ FV + D +DAE A++ 
Sbjct: 4  NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 75 MDGRMLDGRELRVQMA 90
          ++G  L  + ++V  A
Sbjct: 64 LNGLRLQTKTIKVSYA 79

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

Iteration: 1
 Score = 53.5 bits (127), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 26/79 (32%), Positives = 42/79 (53%)
Query: 12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDA 71
          G  +L V+ L    T D+LR +F   GEV    + RD+    S G+ FV +   +DAE A
Sbjct: 1  GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 72 LDAMDGRMLDGRELRVQMA 90
          ++ ++G  L  + ++V  A
Sbjct: 61 INTLNGLRLQSKTIKVSYA 79

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

Iteration: 1
 Score = 53.5 bits (127), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 26/79 (32%), Positives = 42/79 (53%)
Query: 12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDA 71
          G  +L V+ L    T D+LR +F   GEV    + RD+    S G+ FV +   +DAE A
Sbjct: 1  GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 72 LDAMDGRMLDGRELRVQMA 90
          ++ ++G  L  + ++V  A
Sbjct: 61 INTLNGLRLQSKTIKVSYA 79

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 53.1 bits (126), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 26/75 (34%), Positives = 45/75 (60%), Gaps = 1/75 (1%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L +  L   T    L+ VF + G + ++ + +DR T +SRGFAF+ F +  DA++A   M
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDM 68
Query: 76 DGRMLDGRELRVQMA 90
          +G+ L G+ ++V+ A
Sbjct: 69 NGKSLHGKAIKVEQA 83

>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From Homo Sapiens At 1.90 A Resolution Length = 99

Iteration: 1
 Score = 52.8 bits (125), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 25/76 (32%), Positives = 41/76 (53%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          +L V+ L    T D+LR +F   GEV    + RD+    S G+ FV +   +DAE A++ 
Sbjct: 21 NLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 80
Query: 75 MDGRMLDGRELRVQMA 90
          ++G  L  + ++V  A
Sbjct: 81 LNGLRLQSKTIKVSYA 96

>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of Xenopus Laevis Epabp2 Length = 124

Iteration: 1
 Score = 52.8 bits (125), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 26/73 (35%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 15  SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
           S+ V N+ Y +T  DL   F  CG +  I I  D+F+   +G+A++ F + R++ DA  A
Sbjct: 38  SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAE-RNSVDAAVA 96
Query: 75  MDGRMLDGRELRV 87
           MD  +  GR ++V
Sbjct: 97  MDETVFRGRTIKV 109

>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 101

Iteration: 1
 Score = 52.4 bits (124), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 49/75 (65%), Gaps = 4/75 (5%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          +L + NL+Y  T + L+ VFE+      I +P+++   +S+G+AF+ F    DA++AL++
Sbjct: 17 TLVLSNLSYSATEETLQEVFEK---ATFIKVPQNQ-NGKSKGYAFIEFASFEDAKEALNS 72
Query: 75 MDGRMLDGRELRVQM 89
           + R ++GR +R+++
Sbjct: 73 CNKREIEGRAIRLEL 87

>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 3 Subunit 4 Length = 103

Iteration: 1
 Score = 52.4 bits (124), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 28/85 (32%), Positives = 46/85 (54%)
Query: 6  PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
          P  R +   +++V NL+  T   DL+ +F   G +  IY+ +D+ T +S+GFAF+ F  +
Sbjct: 8  PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRR 67
Query: 66 RDAEDALDAMDGRMLDGRELRVQMA 90
           DA  A+  + G   D   L V+ A
Sbjct: 68 EDAARAIAGVSGFGYDHLILNVEWA 92

>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc) In Complex With A Cap Analogue M7gpppg Length = 156

Iteration: 1
 Score = 52.4 bits (124), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 23/74 (31%), Positives = 44/74 (59%)
Query: 14  VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
            +L V NL++ TT + +  +F + G++  I +  D+  + + GF FV ++ + DAE+A+ 
Sbjct: 40  CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 99
Query: 74  AMDGRMLDGRELRV 87
            ++G  LD R +R 
Sbjct: 100 YINGTRLDDRIIRT 113

>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2 Length = 87

Iteration: 1
 Score = 52.0 bits (123), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 22/53 (41%), Positives = 34/53 (64%)
Query: 38 GEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA 90
          G + D  + +D  T +S+G+ FV FF+K DAE+A+  M G+ L GR++R   A
Sbjct: 31 GRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA 83

>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of Hypothetical Polyadenylate-Binding Protein (Pabpn1) From Homo Sapiens At 1.95 A Resolution Length = 89

Iteration: 1
 Score = 52.0 bits (123), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          S+ V N+ Y  T ++L   F  CG V  + I  D+F+   +GFA++ F DK     +L A
Sbjct: 8  SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-A 66
Query: 75 MDGRMLDGRELRV 87
          +D  +  GR+++V
Sbjct: 67 LDESLFRGRQIKV 79

>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm Length = 96

Iteration: 1
 Score = 52.0 bits (123), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          S+ V N+ Y  T ++L   F  CG V  + I  D+F+   +GFA++ F DK     +L A
Sbjct: 7  SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-A 65
Query: 75 MDGRMLDGRELRV 87
          +D  +  GR+++V
Sbjct: 66 LDESLFRGRQIKV 78

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 51.6 bits (122), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 28/77 (36%), Positives = 43/77 (55%)
Query: 11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
           G   L V +L +  T D LR +FE  G++ +I + +D  T  S+G+ F+ F D   A  
Sbjct: 3  SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARR 62
Query: 71 ALDAMDGRMLDGRELRV 87
          AL+ ++G  L GR +RV
Sbjct: 63 ALEQLNGFELAGRPMRV 79

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 51.6 bits (122), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 30/75 (40%), Positives = 42/75 (56%), Gaps = 6/75 (8%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V NL    T +D +R+FER GE  +++I RDR      GF F+R   +  AE A   +
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRLESRTLAEIAKAEL 78
Query: 76 DGRMLDGRELRVQMA 90
          DG +L  R LR++ A
Sbjct: 79 DGTILKSRPLRIRFA 93

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 50.8 bits (120), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 26/68 (38%), Positives = 42/68 (61%), Gaps = 2/68 (2%)
Query: 25  TTPDD--LRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDG 82
           TT D+  LR++FER G +  + I  DR TR+SRG+ FV+F     A+ A+  ++G  +  
Sbjct: 52  TTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILN 111
Query: 83  RELRVQMA 90
           + L+V +A
Sbjct: 112 KRLKVALA 119

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 50.4 bits (119), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 28/85 (32%), Positives = 46/85 (54%), Gaps = 4/85 (4%)
Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          MS    P   E +  L +  L++ TT + LR  FE+ G + D  + RD  T+ SRGF FV
Sbjct: 1  MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFV 60
Query: 61 RFFDKRDAEDALDA----MDGRMLD 81
           +    + + A++A    +DGR+++
Sbjct: 61 TYATVEEVDAAMNARPHKVDGRVVE 85

>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second Rna-Binding Domain Of Sex-Lethal Determined By Multidimensional Heteronuclear Magnetic Resonance Spectroscopy Length = 97

Iteration: 1
 Score = 50.4 bits (119), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 31/92 (33%), Positives = 49/92 (53%), Gaps = 2/92 (2%)
Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          MSY RP        +L V NL    T D L  +F + G +    I RD+ T   RG AFV
Sbjct: 1  MSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFV 60
Query: 61 RFFDKRDAEDALDAMDGRMLDG--RELRVQMA 90
          R+  + +A++A+ A++  + +G  + L V++A
Sbjct: 61 RYNKREEAQEAISALNNVIPEGGSQPLSVRLA 92

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 50.1 bits (118), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 28/85 (32%), Positives = 46/85 (54%), Gaps = 4/85 (4%)
Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          MS    P   E +  L +  L++ TT + LR  FE+ G + D  + RD  T+ SRGF FV
Sbjct: 1  MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFV 60
Query: 61 RFFDKRDAEDALDA----MDGRMLD 81
           +    + + A++A    +DGR+++
Sbjct: 61 TYATVEEVDAAMNARPHKVDGRVVE 85

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 49.7 bits (117), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 22/77 (28%), Positives = 42/77 (54%)
Query: 14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
           +L V+ L    T D+ + +F   G++    + RD+ T +S G+ FV + D  DA+ A++
Sbjct: 5  TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 74 AMDGRMLDGRELRVQMA 90
           ++G  L  + ++V  A
Sbjct: 65 TLNGLKLQTKTIKVSYA 81

>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b Length = 105

Iteration: 1
 Score = 49.7 bits (117), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 24/76 (31%), Positives = 42/76 (55%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          ++ V  L  + +   L  +F + G V + ++P+DR T + +G+ FV F  + DA+ A+  
Sbjct: 17 TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI 76
Query: 75 MDGRMLDGRELRVQMA 90
          MD   L G+ +RV  A
Sbjct: 77 MDMIKLYGKPIRVNKA 92

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 49.7 bits (117), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 22/77 (28%), Positives = 42/77 (54%)
Query: 14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
           +L V+ L    T D+ + +F   G++    + RD+ T +S G+ FV + D  DA+ A++
Sbjct: 5  TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 74 AMDGRMLDGRELRVQMA 90
           ++G  L  + ++V  A
Sbjct: 65 TLNGLKLQTKTIKVSYA 81

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 49.7 bits (117), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 27/76 (35%), Positives = 42/76 (55%)
Query: 12  GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDA 71
           G + L V +L +  T D LR +FE  G +  I +  D  T  S+G+ F+ F D   A+ A
Sbjct: 25  GPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKA 84
Query: 72  LDAMDGRMLDGRELRV 87
           L+ ++G  L GR ++V
Sbjct: 85  LEQLNGFELAGRPMKV 100

>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8 Length = 101

Iteration: 1
 Score = 49.3 bits (116), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 27/77 (35%), Positives = 42/77 (54%), Gaps = 5/77 (6%)
Query: 14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
          + + V NL       +L R F   G +  ++I      R   GFAFV F D RDAEDA+ 
Sbjct: 1  MKVYVGNLGTGAGKGELERAFSYYGPLRTVWI-----ARNPPGFAFVEFEDPRDAEDAVR 55
Query: 74 AMDGRMLDGRELRVQMA 90
           +DG+++ G  +RV+++
Sbjct: 56 GLDGKVICGSRVRVELS 72

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 48.9 bits (115), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 30/75 (40%), Positives = 37/75 (49%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V  L        L   F   G++ DI IP D  T + RGFAFV F    DA  A+D M
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 76 DGRMLDGRELRVQMA 90
          +   L GR +RV +A
Sbjct: 75 NESELFGRTIRVNLA 89

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 48.5 bits (114), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 28/70 (40%), Positives = 38/70 (54%), Gaps = 4/70 (5%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA- 74
          L V  L + TT + LR  F + GEV D  I +D+ T +SRGF FV+F D       L + 
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASR 78
Query: 75 ---MDGRMLD 81
             +DGR +D
Sbjct: 79 PHTLDGRNID 88

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 27/61 (44%), Positives = 34/61 (55%)
Query: 30  LRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM 89
           L   F   G++ DI IP D  T + RGFAFV F    DA  A+D M+   L GR +RV +
Sbjct: 80  LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 139
Query: 90  A 90
           A
Sbjct: 140 A 140

>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex Length = 98

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/74 (31%), Positives = 44/74 (59%), Gaps = 1/74 (1%)
Query: 14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
           +L V NL++ TT + +  +F + G++  I +  D+  + + GF FV ++ + DAE+A+ 
Sbjct: 19 CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKM-KTACGFCFVEYYSRADAENAMR 77
Query: 74 AMDGRMLDGRELRV 87
           ++G  LD R +R 
Sbjct: 78 YINGTRLDDRIIRT 91

>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition Motif Of Hypothetical Rna-Binding Protein Rbm19 Length = 98

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/82 (29%), Positives = 40/82 (48%), Gaps = 3/82 (3%)
Query: 12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRE---SRGFAFVRFFDKRDA 68
          G   L + NL + TT + L+ VF + G +    I + +       S GF FV +     A
Sbjct: 4  GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQA 63
Query: 69 EDALDAMDGRMLDGRELRVQMA 90
          + AL  + G  +DG +L V+++
Sbjct: 64 QKALKQLQGHTVDGHKLEVRIS 85

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 30/92 (32%), Positives = 49/92 (53%), Gaps = 2/92 (2%)
Query: 1   MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
           +SY RP        +L V NL    T D L  +F + G +    I RD+ T   RG AFV
Sbjct: 88  VSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFV 147
Query: 61  RFFDKRDAEDALDAMDGRMLDG--RELRVQMA 90
           R+  + +A++A+ A++  + +G  + L V++A
Sbjct: 148 RYNKREEAQEAISALNNVIPEGGSQPLSVRLA 179

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 27/61 (44%), Positives = 34/61 (55%)
Query: 30 LRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM 89
          L   F   G++ DI IP D  T + RGFAFV F    DA  A+D M+   L GR +RV +
Sbjct: 22 LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 81
Query: 90 A 90
          A
Sbjct: 82 A 82

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 27/61 (44%), Positives = 34/61 (55%)
Query: 30 LRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM 89
          L   F   G++ DI IP D  T + RGFAFV F    DA  A+D M+   L GR +RV +
Sbjct: 24 LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 83
Query: 90 A 90
          A
Sbjct: 84 A 84

>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33 Length = 79

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 30/75 (40%), Positives = 37/75 (49%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V  L        L   F   G++ DI IP D  T + RGFAFV F    DA  A+D M
Sbjct: 5  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 76 DGRMLDGRELRVQMA 90
          +   L GR +RV +A
Sbjct: 65 NESELFGRTIRVNLA 79

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 30/92 (32%), Positives = 49/92 (53%), Gaps = 2/92 (2%)
Query: 1   MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
           +SY RP        +L V NL    T D L  +F + G +    I RD+ T   RG AFV
Sbjct: 77  VSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFV 136
Query: 61  RFFDKRDAEDALDAMDGRMLDG--RELRVQMA 90
           R+  + +A++A+ A++  + +G  + L V++A
Sbjct: 137 RYNKREEAQEAISALNNVIPEGGSQPLSVRLA 168

>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1 (up1) Using Segmental Isotope Labeling Length = 197

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 27/84 (32%), Positives = 45/84 (53%), Gaps = 4/84 (4%)
Query: 2  SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          S    P   E +  L +  L++ TT + LR  FE+ G + D  + RD  T+ SRGF FV 
Sbjct: 3  SKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVT 62
Query: 62 FFDKRDAEDALDA----MDGRMLD 81
          +    + + A++A    +DGR+++
Sbjct: 63 YATVEEVDAAMNARPHKVDGRVVE 86

>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi) G); A Human Telomeric Repeat Containing 6-Methyl-8-(2- Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi) Length = 195

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 27/84 (32%), Positives = 45/84 (53%), Gaps = 4/84 (4%)
Query: 2  SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          S    P   E +  L +  L++ TT + LR  FE+ G + D  + RD  T+ SRGF FV 
Sbjct: 1  SKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVT 60
Query: 62 FFDKRDAEDALDA----MDGRMLD 81
          +    + + A++A    +DGR+++
Sbjct: 61 YATVEEVDAAMNARPHKVDGRVVE 84

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 28/78 (35%), Positives = 40/78 (51%)
Query: 13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDAL 72
          M SL V +L    T   L   F   G +  I + RD  TR S G+A+V F    DAE AL
Sbjct: 15 MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERAL 74
Query: 73 DAMDGRMLDGRELRVQMA 90
          D M+  ++ G+ +R+  +
Sbjct: 75 DTMNFDVIKGKPVRIMWS 92

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score = 47.8 bits (112), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 28/78 (35%), Positives = 40/78 (51%)
Query: 13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDAL 72
          M SL V +L    T   L   F   G +  I + RD  TR S G+A+V F    DAE AL
Sbjct: 10 MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERAL 69
Query: 73 DAMDGRMLDGRELRVQMA 90
          D M+  ++ G+ +R+  +
Sbjct: 70 DTMNFDVIKGKPVRIMWS 87

>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex Length = 88

Iteration: 1
 Score = 47.8 bits (112), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 1/71 (1%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRE-SRGFAFVRFFDKRDAEDALDA 74
          + +  LT   T D +  +F   G++  I +P +R     S+G+A+V F +  +AE AL  
Sbjct: 7  VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 75 MDGRMLDGREL 85
          MDG  +DG+E+
Sbjct: 67 MDGGQIDGQEI 77

>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage Stimulation Factor 64 Kda Subunit Length = 104

Iteration: 1
 Score = 47.4 bits (111), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 25/76 (32%), Positives = 39/76 (51%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          S+ V N+ Y  T + L+ +F   G V    +  DR T + +G+ F  + D+  A  A+  
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 75 MDGRMLDGRELRVQMA 90
          ++GR   GR LRV  A
Sbjct: 70 LNGREFSGRALRVDNA 85

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 47.4 bits (111), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 26/76 (34%), Positives = 41/76 (53%)
Query: 15  SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
           +L V +L      + LR  F+        ++  D  T  SRG+ FV F  + DA++A+D+
Sbjct: 89  NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 148
Query: 75  MDGRMLDGRELRVQMA 90
           M G+ L+GR LR+  A
Sbjct: 149 MQGQDLNGRPLRINWA 164

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 47.4 bits (111), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 26/79 (32%), Positives = 44/79 (55%), Gaps = 4/79 (5%)
Query: 7  PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKR 66
          P   E +  L +  L++ TT + LR  FE+ G + D  + RD  T+ SRGF FV +    
Sbjct: 5  PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 64
Query: 67 DAEDALDA----MDGRMLD 81
          + + A++A    +DGR+++
Sbjct: 65 EVDAAMNARPHKVDGRVVE 83

>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 216

Iteration: 1
 Score = 47.4 bits (111), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 25/73 (34%), Positives = 40/73 (54%)
Query: 15  SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
           +L V  + Y TT   LRR FE  G +  I++   + + + RG+AF+ +  +RD   A   
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 75  MDGRMLDGRELRV 87
            DG+ +DGR + V
Sbjct: 164 ADGKKIDGRRVLV 176

>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1 Rbd1:r(Guagu) Complex Length = 109

Iteration: 1
 Score = 47.0 bits (110), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 21/55 (38%), Positives = 32/55 (58%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDAL 72
          +  L+++TT + LR  F + GEV +  + RD  T+ SRGF FV F D+   +  L
Sbjct: 30 IGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 84

>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast Poly(U)-Binding Protein (Pub1) Length = 83

Iteration: 1
 Score = 47.0 bits (110), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 26/76 (34%), Positives = 41/76 (53%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          +L V +L      + LR  F+        ++  D  T  SRG+ FV F  + DA++A+D+
Sbjct: 3  NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 75 MDGRMLDGRELRVQMA 90
          M G+ L+GR LR+  A
Sbjct: 63 MQGQDLNGRPLRINWA 78

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 47.0 bits (110), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 39/75 (52%)
Query: 13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDAL 72
          M  + V ++ Y    D +R+ F   G +  I +  D  T + +GFAFV +     A+ AL
Sbjct: 13 MCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLAL 72
Query: 73 DAMDGRMLDGRELRV 87
          + M+  ML GR ++V
Sbjct: 73 EQMNSVMLGGRNIKV 87

>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif Of Nono Length = 99

Iteration: 1
 Score = 46.6 bits (109), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 26/75 (34%), Positives = 44/75 (58%), Gaps = 6/75 (8%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V NL    T +++R++FE+ G+ G+++I +D      +GF F+R   +  AE A   +
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVEL 71
Query: 76 DGRMLDGRELRVQMA 90
          D   L G++LRV+ A
Sbjct: 72 DNMPLRGKQLRVRFA 86

>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To Ssdna From A Portion Of Fuse Length = 216

Iteration: 1
 Score = 46.6 bits (109), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 39/75 (52%)
Query: 13  MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDAL 72
           M  + V ++ Y    D +R+ F   G +  I +  D  T + +GFAFV +     A+ AL
Sbjct: 28  MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLAL 87
Query: 73  DAMDGRMLDGRELRV 87
           + M+  ML GR ++V
Sbjct: 88  EQMNSVMLGGRNIKV 102

>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 46.6 bits (109), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 26/75 (34%), Positives = 44/75 (58%), Gaps = 6/75 (8%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V NL    T +++R++FE+ G+ G+++I +D      +GF F+R   +  AE A   +
Sbjct: 25 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVEL 78
Query: 76 DGRMLDGRELRVQMA 90
          D   L G++LRV+ A
Sbjct: 79 DNMPLRGKQLRVRFA 93

>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In Complex With Ugcaugu Length = 109

Iteration: 1
 Score = 46.2 bits (108), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 26/75 (34%), Positives = 45/75 (60%), Gaps = 2/75 (2%)
Query: 16  LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
           L V N+ +R    DLR++F + G++ D+ I  +   R S+GF FV F +  DA+ A + +
Sbjct: 32  LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKL 89
Query: 76  DGRMLDGRELRVQMA 90
            G +++GR++ V  A
Sbjct: 90  HGTVVEGRKIEVNNA 104

>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp Length = 437

Iteration: 1
 Score = 46.2 bits (108), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 41/75 (54%)
Query: 15  SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
           +L V  + Y TT   LRR FE  G +  I++   + + + RG+AF+ +  +RD   A   
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 75  MDGRMLDGRELRVQM 89
            DG+ +DGR + V +
Sbjct: 164 ADGKKIDGRRVLVDV 178

>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding Motif Protein 9 Length = 103

Iteration: 1
 Score = 46.2 bits (108), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 26/75 (34%), Positives = 45/75 (60%), Gaps = 2/75 (2%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V N+ +R    DLR++F + G++ D+ I  +   R S+GF FV F +  DA+ A + +
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKL 75
Query: 76 DGRMLDGRELRVQMA 90
           G +++GR++ V  A
Sbjct: 76 HGTVVEGRKIEVNNA 90

>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear Ribonucleaoproteins A2B1 Length = 116

Iteration: 1
 Score = 46.2 bits (108), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 23/70 (32%), Positives = 41/70 (58%), Gaps = 4/70 (5%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA- 74
          L +  L++ TT + LR  +E+ G++ D  + RD  ++ SRGF FV F    + + A+ A 
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAAR 89
Query: 75 ---MDGRMLD 81
             +DGR+++
Sbjct: 90 PHSIDGRVVE 99

>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15 A Resolution Length = 87

Iteration: 1
 Score = 46.2 bits (108), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 27/68 (39%), Positives = 36/68 (52%), Gaps = 4/68 (5%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA--- 74
          V  L++ T+  DL+  F + GEV D  I  D  T  SRGF F+ F D    E  LD    
Sbjct: 16 VGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQKEH 75
Query: 75 -MDGRMLD 81
           +DGR++D
Sbjct: 76 RLDGRVID 83

>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of Mouse Musashi1 Length = 77

Iteration: 1
 Score = 46.2 bits (108), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 21/55 (38%), Positives = 32/55 (58%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDAL 72
          +  L+++TT + LR  F + GEV +  + RD  T+ SRGF FV F D+   +  L
Sbjct: 5  IGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 59

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 45.8 bits (107), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 43/75 (57%), Gaps = 4/75 (5%)
Query: 11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
          E +  L +  L++ TT + LR  FE+ G + D  + RD  T+ SRGF FV +    + + 
Sbjct: 4  EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 63
Query: 71 ALDA----MDGRMLD 81
          A++A    +DGR+++
Sbjct: 64 AMNARPHKVDGRVVE 78

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 27/73 (36%), Positives = 40/73 (54%), Gaps = 1/73 (1%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V  L Y TT   LR+ FE  G++ +  +  DR T +SRG+ FV   D+  AE A    + 
Sbjct: 22 VGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPN- 80
Query: 78 RMLDGRELRVQMA 90
           ++DGR+  V +A
Sbjct: 81 PIIDGRKANVNLA 93

>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna Cauc Length = 150

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 27/73 (36%), Positives = 39/73 (53%), Gaps = 5/73 (6%)
Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
           V NL       +L R F   G +  +++ R+       GFAFV F D RDA DA+  +DG
Sbjct: 78  VGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDG 132
Query: 78  RMLDGRELRVQMA 90
           R L G  +RV+++
Sbjct: 133 RTLCGCRVRVELS 145

>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna- Binding Protein-43 Length = 103

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 27/69 (39%), Positives = 37/69 (53%), Gaps = 4/69 (5%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V  L ++TT  DL+  F   GEV  + + +D  T  S+GF FVRF    + E  +  M
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRF---TEYETQVKVM 74
Query: 76 DGR-MLDGR 83
            R M+DGR
Sbjct: 75 SQRHMIDGR 83

>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20 Length = 150

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 27/73 (36%), Positives = 39/73 (53%), Gaps = 5/73 (6%)
Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
           V NL       +L R F   G +  +++ R+       GFAFV F D RDA DA+  +DG
Sbjct: 78  VGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRDLDG 132
Query: 78  RMLDGRELRVQMA 90
           R L G  +RV+++
Sbjct: 133 RTLCGCRVRVELS 145

>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2 Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori Length = 90

Iteration: 1
 Score = 44.3 bits (103), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 23/78 (29%), Positives = 42/78 (53%), Gaps = 1/78 (1%)
Query: 13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDAL 72
          M ++ V NL Y  T + ++ +F + G+V ++ +  DR T++ +GF FV    +    +A+
Sbjct: 1  MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVE-MQEESVSEAI 59
Query: 73 DAMDGRMLDGRELRVQMA 90
            +D     GR +RV  A
Sbjct: 60 AKLDNTDFMGRTIRVTEA 77

>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre Rna Length = 175

Iteration: 1
 Score = 43.9 bits (102), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 25/84 (29%), Positives = 44/84 (52%), Gaps = 5/84 (5%)
Query: 4   GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFF 63
           GR   ++    +L   NL++  T D+L+ VFE   E+    + +D    +S+G A++ F 
Sbjct: 90  GRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIR--LVSQDG---KSKGIAYIEFK 144
Query: 64  DKRDAEDALDAMDGRMLDGRELRV 87
            + DAE  L+   G  +DGR + +
Sbjct: 145 SEADAEKNLEEKQGAEIDGRSVSL 168

>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif Of Hypothetical Rna-Binding Protein Rbm19 Length = 107

Iteration: 1
 Score = 43.5 bits (101), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 25/85 (29%), Positives = 44/85 (51%), Gaps = 2/85 (2%)
Query: 8  PRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRF-TRESRGFAFVRFFDKR 66
          P+ +    + V N+ ++    ++R +F   GE+  + +P+    T   RGF FV F  K+
Sbjct: 10 PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQ 69
Query: 67 DAEDALDAM-DGRMLDGRELRVQMA 90
          DA+ A +A+     L GR L ++ A
Sbjct: 70 DAKKAFNALCHSTHLYGRRLVLEWA 94

>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human Nucleoli Length = 180

Iteration: 1
 Score = 42.7 bits (99), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 5/73 (6%)
Query: 15  SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
           +L   NL Y+ T D+L+ VFE   E+    + +D    +S+G A++ F  + DAE   + 
Sbjct: 95  TLLAKNLPYKVTQDELKEVFEDAAEIR--LVSKDG---KSKGIAYIEFKTEADAEKTFEE 149
Query: 75  MDGRMLDGRELRV 87
             G  +DGR + +
Sbjct: 150 KQGTEIDGRSISL 162

>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 109

Iteration: 1
 Score = 42.0 bits (97), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 22/82 (26%), Positives = 44/82 (53%), Gaps = 1/82 (1%)
Query: 6  PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
          P   +EG + L V  +    T +D+   F   GE+ +I++  DR T   +G+  V +   
Sbjct: 1  PQRSVEGWI-LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 59
Query: 66 RDAEDALDAMDGRMLDGRELRV 87
          ++A+ A++ ++G+ L G+ + V
Sbjct: 60 KEAQAAMEGLNGQDLMGQPISV 81

>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0 Rbd1), Nmr Length = 75

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/68 (32%), Positives = 36/68 (52%), Gaps = 4/68 (5%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA--- 74
          +  L++ TT  DL+  F + GEV D  +  D  T  SRGF FV F +    +  +D    
Sbjct: 4  IGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEH 63
Query: 75 -MDGRMLD 81
           ++G+++D
Sbjct: 64 KLNGKVID 71

>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2 A Resolution Length = 89

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/82 (26%), Positives = 44/82 (53%), Gaps = 1/82 (1%)
Query: 6  PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
          P   +EG + L V  +    T +D+   F   GE+ +I++  DR T   +G+  V +   
Sbjct: 1  PQRSVEGWI-LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 59
Query: 66 RDAEDALDAMDGRMLDGRELRV 87
          ++A+ A++ ++G+ L G+ + V
Sbjct: 60 KEAQAAMEGLNGQDLMGQPISV 81

>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A Trapped Dead-Box Helicase Bound To Rna Length = 91

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/82 (26%), Positives = 44/82 (53%), Gaps = 1/82 (1%)
Query: 6  PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
          P   +EG + L V  +    T +D+   F   GE+ +I++  DR T   +G+  V +   
Sbjct: 3  PQRSVEGWI-LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 61
Query: 66 RDAEDALDAMDGRMLDGRELRV 87
          ++A+ A++ ++G+ L G+ + V
Sbjct: 62 KEAQAAMEGLNGQDLMGQPISV 83

>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State Length = 126

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/82 (26%), Positives = 44/82 (53%), Gaps = 1/82 (1%)
Query: 6  PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
          P   +EG + L V  +    T +D+   F   GE+ +I++  DR T   +G+  V +   
Sbjct: 16 PQRSVEGWI-LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 74
Query: 66 RDAEDALDAMDGRMLDGRELRV 87
          ++A+ A++ ++G+ L G+ + V
Sbjct: 75 KEAQAAMEGLNGQDLMGQPISV 96

>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd Machinery Length = 90

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/82 (26%), Positives = 44/82 (53%), Gaps = 1/82 (1%)
Query: 6  PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
          P   +EG + L V  +    T +D+   F   GE+ +I++  DR T   +G+  V +   
Sbjct: 1  PQRSVEGWI-LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 59
Query: 66 RDAEDALDAMDGRMLDGRELRV 87
          ++A+ A++ ++G+ L G+ + V
Sbjct: 60 KEAQAAMEGLNGQDLMGQPISV 81

>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex Length = 110

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/82 (28%), Positives = 45/82 (54%), Gaps = 1/82 (1%)
Query: 6   PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
           P   +EG + L V ++      D+++  F   GE+ +I++  DR T  S+G+A V +   
Sbjct: 20  PQRSVEGWI-LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETH 78
Query: 66  RDAEDALDAMDGRMLDGRELRV 87
           + A  A +A++G  + G+ ++V
Sbjct: 79  KQALAAKEALNGAEIMGQTIQV 100

>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14 Length = 115

Iteration: 1
 Score = 41.2 bits (95), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 27/83 (32%), Positives = 45/83 (54%), Gaps = 5/83 (6%)
Query: 5  RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
          R PP +  +  L + NL Y+ T +++  +F + G +  I   R   T E+RG A+V + D
Sbjct: 2  RLPPEVNRI--LYIRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRGTAYVVYED 56
Query: 65 KRDAEDALDAMDGRMLDGRELRV 87
            DA++A+D + G  +  R L V
Sbjct: 57 IFDAKNAVDHLSGFNVSNRYLVV 79

>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX Length = 106

Iteration: 1
 Score = 41.2 bits (95), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/82 (26%), Positives = 44/82 (53%), Gaps = 1/82 (1%)
Query: 6  PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
          P   +EG + L V  +    T +D+   F   GE+ +I++  DR T   +G+  V +   
Sbjct: 17 PQRSVEGWI-LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 75
Query: 66 RDAEDALDAMDGRMLDGRELRV 87
          ++A+ A++ ++G+ L G+ + V
Sbjct: 76 KEAQAAMEGLNGQDLMGQPISV 97

>pdb|3BO2|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I Intron Length = 95

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/80 (30%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 15 SLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
          ++ ++NL  +   D+L++    +F R G++ DI + R   + + RG AFV F +   A +
Sbjct: 8  TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 64
Query: 71 ALDAMDGRMLDGRELRVQMA 90
          AL +M G     + +R+Q A
Sbjct: 65 ALRSMQGFPFYDKPMRIQYA 84

>pdb|1U6B|A Chain A, Crystal Structure Of A Self-Splicing Group I Intron With Both Exons Length = 98

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/80 (30%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 15 SLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
          ++ ++NL  +   D+L++    +F R G++ DI + R   + + RG AFV F +   A +
Sbjct: 11 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 67
Query: 71 ALDAMDGRMLDGRELRVQMA 90
          AL +M G     + +R+Q A
Sbjct: 68 ALRSMQGFPFYDKPMRIQYA 87

>pdb|3K0J|A Chain A, Crystal Structure Of The E. Coli Thim Riboswitch In Complex With Thiamine Pyrophosphate And The U1a Crystallization Module Length = 96

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/80 (30%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 15 SLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
          ++ ++NL  +   D+L++    +F R G++ DI + R   + + RG AFV F +   A +
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 66
Query: 71 ALDAMDGRMLDGRELRVQMA 90
          AL +M G     + +R+Q A
Sbjct: 67 ALRSMQGFPFYDKPMRIQYA 86

>pdb|3L3C|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme Bound To Glc6p Length = 90

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/80 (30%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 15 SLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
          ++ ++NL  +   D+L++    +F R G++ DI + R   + + RG AFV F +   A +
Sbjct: 5  TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 61
Query: 71 ALDAMDGRMLDGRELRVQMA 90
          AL +M G     + +R+Q A
Sbjct: 62 ALRSMQGFPFYDKPMRIQYA 81

>pdb|1M5K|C Chain C, Crystal Structure Of A Hairpin Ribozyme In The Catalytically-Active Conformation Length = 100

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/80 (30%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 15 SLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
          ++ ++NL  +   D+L++    +F R G++ DI + R   + + RG AFV F +   A +
Sbjct: 11 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 67
Query: 71 ALDAMDGRMLDGRELRVQMA 90
          AL +M G     + +R+Q A
Sbjct: 68 ALRSMQGFPFYDKPMRIQYA 87

>pdb|1URN|A Chain A, U1a MutantRNA COMPLEX + GLYCEROL Length = 97

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/80 (30%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 15 SLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
          ++ ++NL  +   D+L++    +F R G++ DI + R   + + RG AFV F +   A +
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 66
Query: 71 ALDAMDGRMLDGRELRVQMA 90
          AL +M G     + +R+Q A
Sbjct: 67 ALRSMQGFPFYDKPMRIQYA 86

>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna Length = 88

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 23/64 (35%), Positives = 38/64 (59%), Gaps = 3/64 (4%)
Query: 29 DLRRVFERCGEVGDIYIPRDRFTR--ESRGFAFVRFFDKRDAEDALDAMDG-RMLDGREL 85
          DLR +FE+ G V +I + RDR     +S+G  FV F+ ++ A +A +A+   ++L G   
Sbjct: 19 DLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHH 78
Query: 86 RVQM 89
           +QM
Sbjct: 79 PIQM 82

>pdb|3IWN|C Chain C, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch Length = 91

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/80 (30%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 15 SLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
          ++ ++NL  +   D+L++    +F R G++ DI + R   + + RG AFV F +   A +
Sbjct: 6  TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 62
Query: 71 ALDAMDGRMLDGRELRVQMA 90
          AL +M G     + +R+Q A
Sbjct: 63 ALRSMQGFPFYDKPMRIQYA 82

>pdb|2NZ4|A Chain A, Structural Investigation Of The Glms Ribozyme Bound To Its Catalytic Cofactor Length = 94

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/80 (30%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 15 SLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
          ++ ++NL  +   D+L++    +F R G++ DI + R   + + RG AFV F +   A +
Sbjct: 7  TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 63
Query: 71 ALDAMDGRMLDGRELRVQMA 90
          AL +M G     + +R+Q A
Sbjct: 64 ALRSMQGFPFYDKPMRIQYA 83

>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures Length = 101

Iteration: 1
 Score = 40.8 bits (94), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/80 (30%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 15 SLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
          ++ ++NL  +   D+L++    +F R G++ DI + R   + + RG AFV F +   A +
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 66
Query: 71 ALDAMDGRMLDGRELRVQMA 90
          AL +M G     + +R+Q A
Sbjct: 67 ALRSMQGFPFYDKPMRIQYA 86

>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago Complex Length = 165

Iteration: 1
 Score = 40.8 bits (94), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 23/82 (28%), Positives = 45/82 (54%), Gaps = 1/82 (1%)
Query: 6   PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
           P   +EG + L V ++      D+++  F   GE+ +I++  DR T  S+G+A V +   
Sbjct: 66  PQRSVEGWI-LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETH 124
Query: 66  RDAEDALDAMDGRMLDGRELRV 87
           + A  A +A++G  + G+ ++V
Sbjct: 125 KQALAAKEALNGAEIMGQTIQV 146

>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2 Length = 96

Iteration: 1
 Score = 40.8 bits (94), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 5/73 (6%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          +L   NL++  T D+L+ VFE   E+    + +D    +S+G A++ F  + DAE  L+ 
Sbjct: 18 TLLAKNLSFNITEDELKEVFEDALEIR--LVSQDG---KSKGIAYIEFKSEADAEKNLEE 72
Query: 75 MDGRMLDGRELRV 87
            G  +DGR + +
Sbjct: 73 KQGAEIDGRSVSL 85

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 40.4 bits (93), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 22/67 (32%), Positives = 36/67 (53%), Gaps = 3/67 (4%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA--- 74
          +  L + TT D+LR  F + G V D+ I +D  T  SRGF F+ F      ++ +     
Sbjct: 8  IGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHI 67
Query: 75 MDGRMLD 81
          +DG+++D
Sbjct: 68 LDGKVID 74

>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U Binding Splicing Factor 60kda (Puf60) From Homo Sapiens At 2.50 A Resolution Length = 200

Iteration: 1
 Score = 40.4 bits (93), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 19/63 (30%), Positives = 36/63 (57%)
Query: 28  DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV 87
           DD++ VFE  G++    + RD  T + +G+ F+ +   + ++DA+ + +   L G+ LRV
Sbjct: 124 DDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRV 183
Query: 88  QMA 90
             A
Sbjct: 184 GKA 186

>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2 Length = 109

Iteration: 1
 Score = 40.4 bits (93), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 37/74 (50%), Gaps = 3/74 (4%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          + V NL       D+  VF + G + DI +   +  R    FAFV F D RDAEDA+   
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDL---KNRRGGPPFAFVEFEDPRDAEDAVYGR 81
Query: 76 DGRMLDGRELRVQM 89
          DG   DG  LRV+ 
Sbjct: 82 DGYDYDGYRLRVEF 95

>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 40.0 bits (92), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 23/64 (35%), Positives = 38/64 (59%), Gaps = 3/64 (4%)
Query: 29 DLRRVFERCGEVGDIYIPRDRFTR--ESRGFAFVRFFDKRDAEDALDAMDG-RMLDGREL 85
          DLR +FE+ G V +I + RDR     +S+G  FV F+ ++ A +A +A+   ++L G   
Sbjct: 19 DLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHH 78
Query: 86 RVQM 89
           +QM
Sbjct: 79 PIQM 82

>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein Cugbp1ab And Its Binding Study With Dna And Rna Length = 187

Iteration: 1
 Score = 40.0 bits (92), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 23/64 (35%), Positives = 38/64 (59%), Gaps = 3/64 (4%)
Query: 29 DLRRVFERCGEVGDIYIPRDRFTR--ESRGFAFVRFFDKRDAEDALDAMDG-RMLDGREL 85
          DLR +FE+ G V +I + RDR     +S+G  FV F+ ++ A +A +A+   ++L G   
Sbjct: 31 DLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHH 90
Query: 86 RVQM 89
           +QM
Sbjct: 91 PIQM 94

>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding Protein 30 Length = 90

Iteration: 1
 Score = 40.0 bits (92), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 8/79 (10%)
Query: 12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDA 71
          GMV L + NL    T  ++R +FE+ G+V +  I ++        + FV   DK  AEDA
Sbjct: 7  GMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKN--------YGFVHIEDKTAAEDA 58
Query: 72 LDAMDGRMLDGRELRVQMA 90
          +  +    L G  + V+ +
Sbjct: 59 IRNLHHYKLHGVNINVEAS 77

>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein Length = 98

Iteration: 1
 Score = 40.0 bits (92), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 9/74 (12%)
Query: 18 VDNL-TYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD 76
          + NL T      D+  +F + G++    +         +GFAFV++ ++R+A  A+   D
Sbjct: 20 IGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGED 71
Query: 77 GRMLDGRELRVQMA 90
          GRM+ G+ L + +A
Sbjct: 72 GRMIAGQVLDINLA 85

>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein Complex P14-Sf3b155 Length = 87

Iteration: 1
 Score = 40.0 bits (92), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 27/83 (32%), Positives = 44/83 (53%), Gaps = 5/83 (6%)
Query: 5  RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
          R PP +  +  L + NL Y+ T +++  +F + G +  I   R   T E+RG A+V + D
Sbjct: 6  RLPPEVNRI--LYIRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRGTAYVVYED 60
Query: 65 KRDAEDALDAMDGRMLDGRELRV 87
            DA++A D + G  +  R L V
Sbjct: 61 IFDAKNACDHLSGFNVCNRYLVV 83

>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95 Length = 95

Iteration: 1
 Score = 39.7 bits (91), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 23/80 (28%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 15 SLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
          ++ ++NL  +   D+L++    +F + G++ DI + R   + + RG AFV F +   A +
Sbjct: 11 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 67
Query: 71 ALDAMDGRMLDGRELRVQMA 90
          AL +M G     + +R+Q A
Sbjct: 68 ALRSMQGFPFYDKPMRIQYA 87

>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing Sarcoma(Ews) Protein Length = 113

Iteration: 1
 Score = 39.7 bits (91), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 27/84 (32%), Positives = 43/84 (51%), Gaps = 8/84 (9%)
Query: 15  SLKVDNLTYRTTPDDLRRVFERCGEV------GD--IYIPRDRFTRESRGFAFVRFFDKR 66
           ++ V  L    T DDL   F++CG V      G   I+I  D+ T + +G A V + D  
Sbjct: 17  AIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPP 76
Query: 67  DAEDALDAMDGRMLDGRELRVQMA 90
            A+ A++  DG+   G +L+V +A
Sbjct: 77  TAKAAVEWFDGKDFQGSKLKVSLA 100

>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal Protein P14 Bound To Region Of Sf3b155 Length = 125

Iteration: 1
 Score = 39.7 bits (91), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 27/83 (32%), Positives = 44/83 (53%), Gaps = 5/83 (6%)
Query: 5  RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
          R PP +  +  L + NL Y+ T +++  +F + G +  I   R   T E+RG A+V + D
Sbjct: 12 RLPPEVNRI--LYIRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRGTAYVVYED 66
Query: 65 KRDAEDALDAMDGRMLDGRELRV 87
            DA++A D + G  +  R L V
Sbjct: 67 IFDAKNACDHLSGFNVCNRYLVV 89

>pdb|2F9J|A Chain A, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The Spliceosomal Protein P14 Bound To A Region Of Sf3b155 Length = 125

Iteration: 1
 Score = 39.7 bits (91), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 27/83 (32%), Positives = 44/83 (53%), Gaps = 5/83 (6%)
Query: 5  RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
          R PP +  +  L + NL Y+ T +++  +F + G +  I   R   T E+RG A+V + D
Sbjct: 12 RLPPEVNRI--LMIRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRGTAYVVYED 66
Query: 65 KRDAEDALDAMDGRMLDGRELRV 87
            DA++A D + G  +  R L V
Sbjct: 67 IFDAKNACDHLSGFNVCNRYLVV 89

>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp Length = 282

Iteration: 1
 Score = 39.7 bits (91), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 23/80 (28%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 15 SLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
          ++ ++NL  +   D+L++    +F + G++ DI + R   + + RG AFV F +   A +
Sbjct: 11 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 67
Query: 71 ALDAMDGRMLDGRELRVQMA 90
          AL +M G     + +R+Q A
Sbjct: 68 ALRSMQGFPFYDKPMRIQYA 87

>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117, Nmr, 43 Structures Length = 116

Iteration: 1
 Score = 39.3 bits (90), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 23/80 (28%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 15 SLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
          ++ ++NL  +   D+L++    +F + G++ DI + R   + + RG AFV F +   A +
Sbjct: 10 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 66
Query: 71 ALDAMDGRMLDGRELRVQMA 90
          AL +M G     + +R+Q A
Sbjct: 67 ALRSMQGFPFYDKPMRIQYA 86

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	158
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	2e-36
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	6e-33
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	6e-32
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	2e-31
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	5e-31
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	5e-31
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	1e-28
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	3e-28
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	5e-27
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	1e-26
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	1e-26
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	2e-26
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	3e-26
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	3e-26
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	2e-25
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	2e-25
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	3e-25
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	2e-14
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	3e-25
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	5e-25
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	7e-25
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	7e-25
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	1e-24
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-24
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	2e-24
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	5e-24
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	8e-24
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	8e-24
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	7e-18
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	1e-23
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	2e-23
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-19
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	3e-23
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	3e-23
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-23
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	7e-23
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	7e-23
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	8e-23
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	8e-23
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	2e-22
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	2e-22
1x4e_A	85	RNA binding motif, single-stranded interacting pro	3e-22
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	3e-22
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-22
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	5e-22
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	6e-22
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	8e-22
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	1e-21
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	1e-21
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-21
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	3e-18
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	2e-21
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	2e-21
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	2e-21
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	2e-21
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	2e-21
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	4e-21
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	4e-21
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	4e-21
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	6e-21
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	6e-21
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	7e-21
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	7e-21
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-20
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-18
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	1e-20
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	1e-20
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-20
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	6e-16
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-15
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	2e-20
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	3e-20
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	4e-20
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	7e-20
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	7e-20
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	8e-20
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	1e-19
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	1e-19
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	4e-19
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	4e-19
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	5e-19
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	5e-19
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	6e-19
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	7e-19
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	1e-15
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	9e-19
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	9e-19
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	4e-11
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	9e-19
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	1e-18
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	1e-18
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	2e-18
2div_A	99	TRNA selenocysteine associated protein; structural	2e-18
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	3e-18
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-18
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	3e-18
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	7e-15
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	4e-18
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-15
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	5e-18
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	5e-18
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	6e-18
1x5p_A	97	Negative elongation factor E; structure genomics,	1e-17
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	1e-17
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-17
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-15
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	4e-15
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	2e-17
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	3e-17
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	7e-17
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	3e-17
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	4e-17
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	4e-17
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-12
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	5e-17
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	9e-17
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	1e-16
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-16
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	9e-12
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-16
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-15
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-16
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-16
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-14
1x5o_A	114	RNA binding motif, single-stranded interacting pro	2e-16
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	3e-16
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	3e-16
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	4e-16
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	4e-16
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	4e-16
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	5e-16
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	5e-16
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	5e-16
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	6e-16
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	6e-16
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-09
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	1e-15
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	2e-15
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-15
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-14
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	3e-15
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	3e-15
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	5e-15
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	7e-15
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	8e-15
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	1e-14
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	1e-14
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	2e-14
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	3e-14
2dis_A	109	Unnamed protein product; structural genomics, RRM	4e-14
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	6e-14
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	8e-14
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	2e-13
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	2e-13
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	2e-13
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	2e-13
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	6e-13
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	7e-13
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	1e-12
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	2e-12
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	6e-12
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	6e-12
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	6e-12
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	2e-11
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	2e-11
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	3e-11
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	4e-11
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	8e-11
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	1e-10
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	1e-10
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	4e-10
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	4e-10
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	8e-10
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	9e-10
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	1e-09
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-09
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	1e-09
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	1e-09
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	3e-09
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	4e-09
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	6e-09
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	7e-09
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	7e-09
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	7e-09
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	9e-09
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	2e-08
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	2e-08
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	1e-07
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	1e-07
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-07
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	3e-07
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	6e-07
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	1e-06
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	8e-06
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	5e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-05
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	2e-04
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	8e-04

>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 =  120 bits (304), Expect = 2e-36
 Identities = 67/102 (65%), Positives = 79/102 (77%)

Query: 2   SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
           S G   P ++GM++LKVDNLTYRT+PD LRRVFE+ G VGD+YIPR+  T+  RGFAFVR
Sbjct: 2   SSGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVR 61

Query: 62  FFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRG 103
           F D+RDA+DA  AMDG  LDGRELRVQ+ARYGR   S  S G
Sbjct: 62  FHDRRDAQDAEAAMDGAELDGRELRVQVARYGRRDLSGPSSG 103

>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 =  113 bits (284), Expect = 6e-33
 Identities = 75/100 (75%), Positives = 84/100 (84%)

Query: 2   SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
            +      +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFVR
Sbjct: 59  HHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVR 118

Query: 62  FFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRS 101
           F DKRDAEDA+DAMDG +LDGRELRVQMARYGRPP S  S
Sbjct: 119 FHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPDSHHS 158

>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 =  109 bits (274), Expect = 6e-32
 Identities = 30/98 (30%), Positives = 49/98 (50%), Gaps = 1/98 (1%)

Query: 4   GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFF 63
             P  R +   +++V NL+  T   DL+ +F   G +  IY+ +D+ T +S+GFAF+ F 
Sbjct: 6   SGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFH 65

Query: 64  DKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRS 101
            + DA  A+  + G   D   L V+ A+     S   S
Sbjct: 66  RREDAARAIAGVSGFGYDHLILNVEWAKP-STNSGPSS 102

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score =  108 bits (272), Expect = 2e-31
 Identities = 83/101 (82%), Positives = 91/101 (90%)

Query: 1   MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
           MSYGRPPP +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFV
Sbjct: 35  MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 94

Query: 61  RFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRS 101
           RF DKRDAEDA+DAMDG +LDGRELRVQMARYGRPP S  S
Sbjct: 95  RFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPDSHHS 135

>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 =  106 bits (267), Expect = 5e-31
 Identities = 34/90 (37%), Positives = 47/90 (52%)

Query: 4  GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFF 63
                 +    L V  L+  TT  DLR VF + G + D+ I  D+ +R SRGFAFV F 
Sbjct: 6  SGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFE 65

Query: 64 DKRDAEDALDAMDGRMLDGRELRVQMARYG 93
          +  DA++A +  +G  LDGR +RV     G
Sbjct: 66 NVDDAKEAKERANGMELDGRRIRVSGPSSG 95

>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 =  106 bits (267), Expect = 5e-31
 Identities = 30/98 (30%), Positives = 48/98 (48%)

Query: 7   PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKR 66
                G   L V NL+Y ++ +DL ++F   G + +++ P D  T++ +GFAFV F    
Sbjct: 2   SSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPE 61

Query: 67  DAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGG 104
            A  A   +DG++  GR L V  +   +  S S    G
Sbjct: 62  HAVKAYAEVDGQVFQGRMLHVLPSTIKKEASQSGPSSG 99

>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 =  100 bits (251), Expect = 1e-28
 Identities = 31/90 (34%), Positives = 53/90 (58%), Gaps = 4/90 (4%)

Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          MS G  P +     ++ V NL +  T +DL R+F + G+V  + I +D+ TR+S+G AF+
Sbjct: 8  MSGGLAPSK----STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFI 63

Query: 61 RFFDKRDAEDALDAMDGRMLDGRELRVQMA 90
           F DK  A++   A++ + L GR ++  +A
Sbjct: 64 LFLDKDSAQNCTRAINNKQLFGRVIKASIA 93

>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 =  100 bits (251), Expect = 3e-28
 Identities = 32/115 (27%), Positives = 54/115 (46%), Gaps = 1/115 (0%)

Query: 4   GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFF 63
              P R      L V  +    T +D+   F   GE+ +I++  DR T   +G+  V + 
Sbjct: 13  EPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYE 72

Query: 64  DKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRD 118
             ++A+ A++ ++G+ L G+ + V      R P   + RGGR R R  DR R  +
Sbjct: 73  TYKEAQAAMEGLNGQDLMGQPISVDWCFV-RGPPKGKRRGGRRRSRSPDRRRRLE 126

>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 = 97.5 bits (243), Expect = 5e-27
 Identities = 35/95 (36%), Positives = 50/95 (52%)

Query: 1   MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
             +       +    L V  L+  TT  DLR VF + G + D+ I  D+ +R SRGFAFV
Sbjct: 34  SRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFV 93

Query: 61  RFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRP 95
            F +  DA++A +  +G  LDGR +RV  +   RP
Sbjct: 94  YFENVDDAKEAKERANGMELDGRRIRVDFSITKRP 128

>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 = 95.4 bits (238), Expect = 1e-26
 Identities = 29/99 (29%), Positives = 49/99 (49%), Gaps = 6/99 (6%)

Query: 5   RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
                      L V NL    T +++R++FE+ G+ G+++I +D+      GF F+R   
Sbjct: 7   GGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFIRLET 60

Query: 65  KRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRG 103
           +  AE A   +D   L G++LRV+ A +    +S  S G
Sbjct: 61  RTLAEIAKVELDNMPLRGKQLRVRFACHSASLTSGPSSG 99

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 95.5 bits (238), Expect = 1e-26
 Identities = 19/92 (20%), Positives = 36/92 (39%), Gaps = 5/92 (5%)

Query: 4  GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFF 63
          G+ P +      +    L        L+ +  + GEV ++ I     TR+  G A V F 
Sbjct: 2  GQIPLK-----EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFT 56

Query: 64 DKRDAEDALDAMDGRMLDGRELRVQMARYGRP 95
            R A++ +  +    + G  +  Q+   G+ 
Sbjct: 57 STRGAKETVKNLHLTSVMGNIIHAQLDIKGQQ 88

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 96.4 bits (240), Expect = 2e-26
 Identities = 31/89 (34%), Positives = 38/89 (42%)

Query: 2   SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
             G           L V  L        L   F   G++ DI IP D  T + RGFAFV 
Sbjct: 52  GSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 111

Query: 62  FFDKRDAEDALDAMDGRMLDGRELRVQMA 90
           F    DA  A+D M+   L GR +RV +A
Sbjct: 112 FELAEDAAAAIDNMNESELFGRTIRVNLA 140

>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 = 94.1 bits (235), Expect = 3e-26
 Identities = 29/74 (39%), Positives = 37/74 (50%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V  L        L   F   G++ DI IP D  T + RGFAFV F    DA  A+D M+ 
Sbjct: 12 VGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNE 71

Query: 78 RMLDGRELRVQMAR 91
            L GR +RV +A+
Sbjct: 72 SELFGRTIRVNLAK 85

>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 = 94.6 bits (236), Expect = 3e-26
 Identities = 27/99 (27%), Positives = 46/99 (46%), Gaps = 1/99 (1%)

Query: 6   PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
           P        ++ V  L  + +   L  +F + G V + ++P+DR T + +G+ FV F  +
Sbjct: 8   PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSE 67

Query: 66  RDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGG 104
            DA+ A+  MD   L G+ +RV  A      + S    G
Sbjct: 68  EDADYAIKIMDMIKLYGKPIRVNKAS-AHNKNLSGPSSG 105

>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 = 92.7 bits (231), Expect = 2e-25
 Identities = 33/86 (38%), Positives = 41/86 (47%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
           V  L        L   F   G++ DI IP D  T + RGFAFV F    DA  A+D M+ 
Sbjct: 17  VGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNE 76

Query: 78  RMLDGRELRVQMARYGRPPSSSRSRG 103
             L GR +RV +A+  R   S  S G
Sbjct: 77  SELFGRTIRVNLAKPMRIKESGPSSG 102

>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 = 92.2 bits (230), Expect = 2e-25
 Identities = 25/79 (31%), Positives = 40/79 (50%), Gaps = 1/79 (1%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRF-TRESRGFAFVRFFDKRDAEDALDAMD 76
          +  LT   T D +  +F   G++  I +P +R     S+G+A+V F +  +AE AL  MD
Sbjct: 9  IGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMD 68

Query: 77 GRMLDGRELRVQMARYGRP 95
          G  +DG+E+         P
Sbjct: 69 GGQIDGQEITATAVLAPWP 87

>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 = 95.0 bits (237), Expect = 3e-25
 Identities = 34/105 (32%), Positives = 49/105 (46%), Gaps = 2/105 (1%)

Query: 1   MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
           +    P      M SL V +L    T   L   F   G +  I + RD  TR S G+A+V
Sbjct: 3   LGSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYV 62

Query: 61  RFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGR 105
            F    DAE ALD M+  ++ G+ +R+  ++  R PS  +S  G 
Sbjct: 63  NFQQPADAERALDTMNFDVIKGKPVRIMWSQ--RDPSLRKSGVGN 105

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 66.5 bits (163), Expect = 2e-14
 Identities = 26/105 (24%), Positives = 43/105 (40%), Gaps = 4/105 (3%)

Query: 1   MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
            S   P  R  G+ ++ + NL        L   F   G +    +  D     S+G+ FV
Sbjct: 91  WSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFV 148

Query: 61  RFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGR 105
            F  +  AE A++ M+G +L+ R++ V   R+          G R
Sbjct: 149 HFETQEAAERAIEKMNGMLLNDRKVFV--GRFKSRKEREAELGAR 191

>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 = 92.4 bits (230), Expect = 3e-25
 Identities = 30/106 (28%), Positives = 51/106 (48%), Gaps = 1/106 (0%)

Query: 16  LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
           L +  L   T    L+ VF + G + ++ + +DR T +SRGFAF+ F +  DA++A   M
Sbjct: 10  LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDM 68

Query: 76  DGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRDRRY 121
           +G+ L G+ ++V+ A+     S  R R       R          +
Sbjct: 69  NGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRNRSPSGSLEHHHH 114

>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 = 91.0 bits (227), Expect = 5e-25
 Identities = 28/81 (34%), Positives = 44/81 (54%), Gaps = 1/81 (1%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          S+ V N+ Y  T ++L   F  CG V  + I  D+F+   +GFA++ F DK     +L A
Sbjct: 8  SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-A 66

Query: 75 MDGRMLDGRELRVQMARYGRP 95
          +D  +  GR+++V   R  RP
Sbjct: 67 LDESLFRGRQIKVIPKRTNRP 87

>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 = 90.7 bits (226), Expect = 7e-25
 Identities = 29/87 (33%), Positives = 44/87 (50%), Gaps = 1/87 (1%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
           V +L +  T D LR +FE  G++ +I + +D  T  S+G+ F+ F D   A  AL+ ++G
Sbjct: 10  VGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNG 69

Query: 78  RMLDGRELRVQMARYGRPPSSSRSRGG 104
             L GR +RV      R    S    G
Sbjct: 70  FELAGRPMRVGHVT-ERLDGGSGPSSG 95

>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 = 90.8 bits (226), Expect = 7e-25
 Identities = 25/92 (27%), Positives = 40/92 (43%), Gaps = 1/92 (1%)

Query: 2  SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          S G  P + E   ++ V NL  R   + L  +F + G +  + I +DR  +  + F FV 
Sbjct: 5  SSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGK-PKSFGFVC 63

Query: 62 FFDKRDAEDALDAMDGRMLDGRELRVQMARYG 93
          F        A+  ++G  L GR + V     G
Sbjct: 64 FKHPESVSYAIALLNGIRLYGRPINVSGPSSG 95

>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 = 91.7 bits (228), Expect = 1e-24
 Identities = 27/103 (26%), Positives = 49/103 (47%), Gaps = 1/103 (0%)

Query: 5   RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
           +  P  + + +L V+ +        LR++FER G +  + I  DR TR+SRG+ FV+F  
Sbjct: 34  QMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQS 93

Query: 65  KRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDR 107
              A+ A+  ++G  +  + L+V +A          +    D 
Sbjct: 94  GSSAQQAIAGLNGFNILNKRLKVALAA-SGHQRPGIAGAVGDG 135

>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 = 89.6 bits (223), Expect = 2e-24
 Identities = 32/87 (36%), Positives = 52/87 (59%), Gaps = 1/87 (1%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
           V  L++ T    L +VF + G++ ++ + +DR T+ SRGF FV F +  DA+DA+ AM+G
Sbjct: 17  VGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNG 76

Query: 78  RMLDGRELRVQMARYGRPPSSSRSRGG 104
           + +DGR++RV  A      + S    G
Sbjct: 77  KSVDGRQIRVDQAG-KSSDNRSGPSSG 102

>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 = 90.1 bits (224), Expect = 2e-24
 Identities = 27/87 (31%), Positives = 42/87 (48%)

Query: 5   RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
                  G + L V +L +  T D LR +FE  G +  I +  D  T  S+G+ F+ F D
Sbjct: 18  NLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSD 77

Query: 65  KRDAEDALDAMDGRMLDGRELRVQMAR 91
              A+ AL+ ++G  L GR ++V    
Sbjct: 78  SECAKKALEQLNGFELAGRPMKVGHVT 104

>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 = 89.3 bits (222), Expect = 5e-24
 Identities = 28/86 (32%), Positives = 40/86 (46%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
           + NL+ R T  DL  +F R  E     I     T   RG AF+ F +K  A  AL  ++G
Sbjct: 30  LKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNG 89

Query: 78  RMLDGRELRVQMARYGRPPSSSRSRG 103
             L G+ L ++  +  +  SS  S G
Sbjct: 90  YKLYGKILVIEFGKNKKQRSSGPSSG 115

>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 = 88.1 bits (219), Expect = 8e-24
 Identities = 18/88 (20%), Positives = 36/88 (40%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
           + ++ Y  T + +  +    G V ++ +  D  T  S+G+AF+ F D   +  A+  ++G
Sbjct: 7   LGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNG 66

Query: 78  RMLDGRELRVQMARYGRPPSSSRSRGGR 105
             L  R L+   +        S      
Sbjct: 67  YQLGSRFLKCGYSSNSDISGVSLEHHHH 94

>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 = 89.9 bits (224), Expect = 8e-24
 Identities = 29/91 (31%), Positives = 49/91 (53%), Gaps = 4/91 (4%)

Query: 15  SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
           +L V+ L    T ++ R +F   GE+    + RD+ T +S G+ FV + D +DAE A++ 
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 75  MDGRMLDGRELRVQMARYGRPPSSSRSRGGR 105
           ++G  L  + ++V  AR    PSS+  R   
Sbjct: 64  LNGLRLQTKTIKVSYAR----PSSASIRDAN 90

>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 = 74.9 bits (185), Expect = 7e-18
 Identities = 27/91 (29%), Positives = 44/91 (48%), Gaps = 2/91 (2%)

Query: 2   SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
           SY RP        +L V  L    T  +L ++F + G +    I  D+ T  SRG  F+R
Sbjct: 77  SYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIR 136

Query: 62  FFDKRDAEDALDAMDGRMLDG--RELRVQMA 90
           F  + +AE+A+  ++G+   G    + V+ A
Sbjct: 137 FDKRIEAEEAIKGLNGQKPSGATEPITVKFA 167

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 87.7 bits (218), Expect = 1e-23
 Identities = 28/98 (28%), Positives = 45/98 (45%)

Query: 7   PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKR 66
           P     + S+ V N+ Y  T + L+ +F   G V    +  DR T + +G+ F  + D+ 
Sbjct: 2   PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61

Query: 67  DAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGG 104
            A  A+  ++GR   GR LRV  A   +     +S G 
Sbjct: 62  TALSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGT 99

>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 = 88.8 bits (221), Expect = 2e-23
 Identities = 25/90 (27%), Positives = 41/90 (45%), Gaps = 4/90 (4%)

Query: 15  SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
           +L V+ L    T  +L  +F   G +    I RD  T  S G+AFV F  + D++ A+  
Sbjct: 5   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64

Query: 75  MDGRMLDGRELRVQMARYGRPPSSSRSRGG 104
           ++G  +  + L+V  AR    P     +  
Sbjct: 65  LNGITVRNKRLKVSYAR----PGGESIKDT 90

>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 = 79.2 bits (196), Expect = 1e-19
 Identities = 30/91 (32%), Positives = 48/91 (52%), Gaps = 2/91 (2%)

Query: 2   SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
           SY RP        +L V NL    T D L  +F + G +    I RD+ T   RG AFVR
Sbjct: 78  SYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVR 137

Query: 62  FFDKRDAEDALDAMDGRMLDG--RELRVQMA 90
           +  + +A++A+ A++  + +G  + L V++A
Sbjct: 138 YNKREEAQEAISALNNVIPEGGSQPLSVRLA 168

>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 = 86.5 bits (215), Expect = 3e-23
 Identities = 28/95 (29%), Positives = 45/95 (47%), Gaps = 3/95 (3%)

Query: 12  GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRE---SRGFAFVRFFDKRDA 68
           G   L + NL + TT + L+ VF + G +    I + +       S GF FV +     A
Sbjct: 4   GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQA 63

Query: 69  EDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRG 103
           + AL  + G  +DG +L V+++     P+S  S G
Sbjct: 64  QKALKQLQGHTVDGHKLEVRISERATKPASGPSSG 98

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 86.9 bits (216), Expect = 3e-23
 Identities = 20/79 (25%), Positives = 40/79 (50%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
           V  +    T +D+   F   GE+ +I++  DR T   +G+  V +   ++A+ A++ ++G
Sbjct: 28  VTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNG 87

Query: 78  RMLDGRELRVQMARYGRPP 96
           + L G+ + V       PP
Sbjct: 88  QDLMGQPISVDWCFVRGPP 106

>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 = 85.6 bits (213), Expect = 5e-23
 Identities = 25/74 (33%), Positives = 39/74 (52%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V +L      + LR  F+        ++  D  T  SRG+ FV F  + DA++A+D+M G
Sbjct: 6  VGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQG 65

Query: 78 RMLDGRELRVQMAR 91
          + L+GR LR+  A 
Sbjct: 66 QDLNGRPLRINWAA 79

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 86.7 bits (215), Expect = 7e-23
 Identities = 29/88 (32%), Positives = 46/88 (52%), Gaps = 1/88 (1%)

Query: 15  SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
           S+ V N+ Y +T  DL   F  CG +  I I  D+F+   +G+A++ F ++   + A+ A
Sbjct: 38  SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-A 96

Query: 75  MDGRMLDGRELRVQMARYGRPPSSSRSR 102
           MD  +  GR ++V   R   P  SS  R
Sbjct: 97  MDETVFRGRTIKVLPKRTNMPGISSTDR 124

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 86.2 bits (214), Expect = 7e-23
 Identities = 24/91 (26%), Positives = 45/91 (49%), Gaps = 1/91 (1%)

Query: 6   PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
           P   +EG   L V ++      D+++  F   GE+ +I++  DR T  S+G+A V +   
Sbjct: 20  PQRSVEGW-ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETH 78

Query: 66  RDAEDALDAMDGRMLDGRELRVQMARYGRPP 96
           + A  A +A++G  + G+ ++V       P 
Sbjct: 79  KQALAAKEALNGAEIMGQTIQVDWCFVKGPK 109

>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 = 85.4 bits (212), Expect = 8e-23
 Identities = 27/94 (28%), Positives = 44/94 (46%), Gaps = 7/94 (7%)

Query: 11  EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
            GM  L + NL+   T DDLR++F          +P         G+AFV + D+  A  
Sbjct: 6   SGMNKLYIGNLSPAVTADDLRQLFGDRK------LPLAGQVLLKSGYAFVDYPDQNWAIR 59

Query: 71  ALDAMDGRM-LDGRELRVQMARYGRPPSSSRSRG 103
           A++ + G++ L G+ + V  +   +  SS  S G
Sbjct: 60  AIETLSGKVELHGKIMEVDYSVSKKLRSSGPSSG 93

>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 = 86.2 bits (214), Expect = 8e-23
 Identities = 29/104 (27%), Positives = 51/104 (49%), Gaps = 1/104 (0%)

Query: 4   GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFF 63
                       + V +L+   T +D++  F   G + D  + +D  T +S+G+ FV FF
Sbjct: 6   SGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFF 65

Query: 64  DKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDR 107
           +K DAE+A+  M G+ L GR++R   A   +PP+   +     +
Sbjct: 66  NKWDAENAIQQMGGQWLGGRQIRTNWAT-RKPPAPKSTYESNTK 108

>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 = 85.1 bits (211), Expect = 2e-22
 Identities = 36/99 (36%), Positives = 43/99 (43%), Gaps = 3/99 (3%)

Query: 5   RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
              P       + V NL       D+  VF + G + DI +   R       FAFV F D
Sbjct: 14  IRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR---GGPPFAFVEFED 70

Query: 65  KRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRG 103
            RDAEDA+   DG   DG  LRV+  R GR   S  S G
Sbjct: 71  PRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGTGSGPSSG 109

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 84.3 bits (209), Expect = 2e-22
 Identities = 20/83 (24%), Positives = 38/83 (45%), Gaps = 6/83 (7%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCG--EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDAL 72
          ++ + N+   T  D +           V +I + +D+ T+++RGFAFV+     DA   L
Sbjct: 11 TIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLL 70

Query: 73 DAMDGR----MLDGRELRVQMAR 91
            +        +DG+ + V  A+
Sbjct: 71 QILQSLHPPLKIDGKTIGVDFAK 93

>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 = 83.7 bits (208), Expect = 3e-22
 Identities = 16/76 (21%), Positives = 32/76 (42%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          +  L   TT  DL ++ +  G++       D+ T + +G+ FV F     A+ A+ A+  
Sbjct: 10 IRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKA 69

Query: 78 RMLDGRELRVQMARYG 93
            +  +  +      G
Sbjct: 70 SGVQAQMAKQSGPSSG 85

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 85.6 bits (212), Expect = 3e-22
 Identities = 28/120 (23%), Positives = 53/120 (44%), Gaps = 1/120 (0%)

Query: 2   SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
                   ++   +L V NL++ TT + +  +F + G++  I +  D+  + + GF FV 
Sbjct: 28  DNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVE 87

Query: 62  FFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRDRRY 121
           ++ + DAE+A+  ++G  LD R +R      G        RG      R +  +  D   
Sbjct: 88  YYSRADAENAMRYINGTRLDDRIIRTDWDA-GFKEGRQYGRGRSGGQVRDEYRQDYDAGR 146

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 83.9 bits (208), Expect = 5e-22
 Identities = 15/74 (20%), Positives = 29/74 (39%), Gaps = 6/74 (8%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          + N+ +  T  DL  +F+  G + D     ++      G  F+++     A   + A+  
Sbjct: 32 IGNIPHFATEADLIPLFQNFGFILDFKHYPEK------GCCFIKYDTHEQAAVCIVALAN 85

Query: 78 RMLDGRELRVQMAR 91
              GR LR    +
Sbjct: 86 FPFQGRNLRTGWGK 99

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 83.0 bits (206), Expect = 5e-22
 Identities = 26/74 (35%), Positives = 41/74 (55%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V +L+   T   +   F   G + D  + +D  T +S+G+ FV FF+K DAE+A+  M G
Sbjct: 11 VGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGG 70

Query: 78 RMLDGRELRVQMAR 91
          + L GR++R   A 
Sbjct: 71 QWLGGRQIRTNWAT 84

>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 = 83.5 bits (207), Expect = 6e-22
 Identities = 27/90 (30%), Positives = 45/90 (50%), Gaps = 5/90 (5%)

Query: 15  SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
           +L V NL+   T   + ++F + G      +  +  +     + FV F++ RDA  AL A
Sbjct: 17  TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAA 74

Query: 75  MDGRMLDGRELRVQMARYGRPPSSSRSRGG 104
           M+GR + G+E++V  A     PSS +S   
Sbjct: 75  MNGRKILGKEVKVNWA---TTPSSQKSGPS 101

>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 = 83.1 bits (206), Expect = 8e-22
 Identities = 28/99 (28%), Positives = 47/99 (47%), Gaps = 2/99 (2%)

Query: 7   PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDR-FTRESRGFAFVRFFDK 65
            P+ +    + V N+ ++    ++R +F   GE+  + +P+    T   RGF FV F  K
Sbjct: 9   VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITK 68

Query: 66  RDAEDALDAM-DGRMLDGRELRVQMARYGRPPSSSRSRG 103
           +DA+ A +A+     L GR L ++ A       S  S G
Sbjct: 69  QDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQSGPSSG 107

>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 = 83.1 bits (206), Expect = 1e-21
 Identities = 27/86 (31%), Positives = 41/86 (47%), Gaps = 1/86 (1%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
              L  R  P DL   F   G+V D+ I  DR +R S+G A+V F + +    A+  + G
Sbjct: 30  CMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTG 88

Query: 78  RMLDGRELRVQMARYGRPPSSSRSRG 103
           + L G  + VQ ++  +   S  S G
Sbjct: 89  QRLLGVPIIVQASQAEKNRLSGPSSG 114

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 82.9 bits (205), Expect = 1e-21
 Identities = 19/84 (22%), Positives = 36/84 (42%), Gaps = 5/84 (5%)

Query: 17 KVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD 76
           + +         L  +F + G+V ++  P D  T +++GF FV      DA+  + +  
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 77 GRMLDGRE-LRV----QMARYGRP 95
          G+ LD +  L +     + RY   
Sbjct: 76 GKRLDLKHRLFLYTMKDVERYNSD 99

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 85.4 bits (212), Expect = 2e-21
 Identities = 26/108 (24%), Positives = 44/108 (40%), Gaps = 2/108 (1%)

Query: 5   RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
           +    +  M  + V ++ Y    D +R+ F   G +  I +  D  T + +GFAFV +  
Sbjct: 20  QRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEV 79

Query: 65  KRDAEDALDAMDGRMLDGRELRVQMA--RYGRPPSSSRSRGGRDRDRR 110
              A+ AL+ M+  ML GR ++V          P   +         R
Sbjct: 80  PEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNR 127

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 77.0 bits (190), Expect = 3e-18
 Identities = 22/82 (26%), Positives = 43/82 (52%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
           V ++    + DD++ VFE  G++    + RD  T + +G+ F+ +   + ++DA+ +M+ 
Sbjct: 130 VASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNL 189

Query: 78  RMLDGRELRVQMARYGRPPSSS 99
             L G+ LRV  A     P  +
Sbjct: 190 FDLGGQYLRVGKAVTPPMPLLT 211

>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 = 82.4 bits (204), Expect = 2e-21
 Identities = 16/87 (18%), Positives = 37/87 (42%), Gaps = 9/87 (10%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
              +    T   +R+ F   G++ +I +  ++      G++FVRF     A  A+ +++G
Sbjct: 30  CGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK------GYSFVRFSTHESAAHAIVSVNG 83

Query: 78  RMLDGRELRVQMARYGRPPSSSRSRGG 104
             ++G  ++     +G+      S   
Sbjct: 84  TTIEGHVVKC---YWGKESPDMTSGPS 107

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 82.0 bits (203), Expect = 2e-21
 Identities = 29/98 (29%), Positives = 46/98 (46%), Gaps = 5/98 (5%)

Query: 14  VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
           + + V NL       +L R F   G +  ++I R+       GFAFV F D RDAEDA+ 
Sbjct: 1   MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVR 55

Query: 74  AMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRR 111
            +DG+++ G  +RV+++      S       R +    
Sbjct: 56  GLDGKVICGSRVRVELSTGMPRRSRFDRPPARRKLLEV 93

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 82.4 bits (204), Expect = 2e-21
 Identities = 26/100 (26%), Positives = 40/100 (40%), Gaps = 10/100 (10%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEV--------GDIYIPRDRFTRESRGFAFVRFFDKRDAE 69
           V  L    T + +   F++ G +          I +  DR T + +G A V F D   A+
Sbjct: 12  VQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAK 71

Query: 70  DALDAMDGRMLDGRELRVQMA--RYGRPPSSSRSRGGRDR 107
            A+D  DG+   G  ++V  A  R          RGG + 
Sbjct: 72  AAIDWFDGKEFSGNPIKVSFATRRADFNRGGGNGRGGLEH 111

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 81.9 bits (203), Expect = 2e-21
 Identities = 30/105 (28%), Positives = 44/105 (41%), Gaps = 6/105 (5%)

Query: 2   SYGRPPPRIEGMVSLK--VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAF 59
           S G   P      S    V  L+  TT + L+  F          I  DR T  S+GF F
Sbjct: 2   SSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGF 58

Query: 60  VRFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGG 104
           V F  + DA+ A +AM+   +DG ++ +  A+  +    S    G
Sbjct: 59  VDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAK-PKGEGGSGPSSG 102

>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 = 81.4 bits (202), Expect = 2e-21
 Identities = 23/90 (25%), Positives = 44/90 (48%), Gaps = 1/90 (1%)

Query: 13  MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDAL 72
           M ++ V NL Y  T + ++ +F + G+V ++ +  DR T++ +GF FV   ++    +A+
Sbjct: 1   MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEE-SVSEAI 59

Query: 73  DAMDGRMLDGRELRVQMARYGRPPSSSRSR 102
             +D     GR +RV  A   +        
Sbjct: 60  AKLDNTDFMGRTIRVTEANPKKSLEHHHHH 89

>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 = 81.6 bits (202), Expect = 4e-21
 Identities = 23/106 (21%), Positives = 45/106 (42%), Gaps = 4/106 (3%)

Query: 2   SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
           S G    +    + L +  +       DL+ +FE  G++ ++ + +DRFT   +G AF+ 
Sbjct: 2   SSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLT 61

Query: 62  FFDKRDAEDALDAMDGRML---DGRELRVQMARYGRPPSSSRSRGG 104
           + ++  A  A  A+  +       R ++V+ A        S    G
Sbjct: 62  YCERESALKAQSALHEQKTLPGMNRPIQVKPAD-SESRGGSGPSSG 106

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 81.1 bits (201), Expect = 4e-21
 Identities = 25/89 (28%), Positives = 46/89 (51%), Gaps = 7/89 (7%)

Query: 7  PPRIEGMVSLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRF 62
           P      ++ ++NL  +   D+L++    +F R G++ DI + R   + + RG AFV F
Sbjct: 2  VPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIF 58

Query: 63 FDKRDAEDALDAMDGRMLDGRELRVQMAR 91
           +   A +AL +M G     + +R+Q A+
Sbjct: 59 KEVSSATNALRSMQGFPFYDKPMRIQYAK 87

>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 = 81.2 bits (201), Expect = 4e-21
 Identities = 31/104 (29%), Positives = 53/104 (50%), Gaps = 4/104 (3%)

Query: 1   MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
            S G    +      L V N+ +R    DLR++F + G++ D+ I  +   R S+GF FV
Sbjct: 4   GSSGNSESKSTPK-RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFV 60

Query: 61  RFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGG 104
            F +  DA+ A + + G +++GR++ V  A   R  ++S    G
Sbjct: 61  TFENSADADRAREKLHGTVVEGRKIEVNNAT-ARVMTNSGPSSG 103

>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 = 80.7 bits (200), Expect = 6e-21
 Identities = 21/80 (26%), Positives = 39/80 (48%), Gaps = 2/80 (2%)

Query: 14 VSLKVDNLTYRTTPDDLRRVFERCG--EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDA 71
          ++L + NLT+ TT +DL       G  ++ +I    +R   +S+GFA V    +  ++  
Sbjct: 2  IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKL 61

Query: 72 LDAMDGRMLDGRELRVQMAR 91
          +D +  R L G+   V  + 
Sbjct: 62 MDLLPKRELHGQNPVVTPSN 81

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 80.8 bits (200), Expect = 6e-21
 Identities = 19/87 (21%), Positives = 41/87 (47%), Gaps = 2/87 (2%)

Query: 5  RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
          R    +E    L +  L +  T ++L  + +  G V D+ +  +R   + +G A+V + +
Sbjct: 10 RYSTSLEKH-KLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYEN 67

Query: 65 KRDAEDALDAMDGRMLDGRELRVQMAR 91
          +  A  A+  MDG  +    ++V ++ 
Sbjct: 68 ESQASQAVMKMDGMTIKENIIKVAISN 94

>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 = 80.8 bits (200), Expect = 7e-21
 Identities = 22/81 (27%), Positives = 35/81 (43%), Gaps = 8/81 (9%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGD--------IYIPRDRFTRESRGFAFVRFFDKRDAE 69
          V  L    T + +   F++ G +          I +  DR T + +G A V F D   A+
Sbjct: 18 VQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAK 77

Query: 70 DALDAMDGRMLDGRELRVQMA 90
           A+D  DG+   G  ++V  A
Sbjct: 78 AAIDWFDGKEFSGNPIKVSFA 98

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

 Score = 81.3 bits (201), Expect = 7e-21
 Identities = 22/74 (29%), Positives = 36/74 (48%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
           + +L    T  DL   F   G V    +  D+ T  S+ F FV F +   A+ A+ AM+G
Sbjct: 45  IYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNG 104

Query: 78  RMLDGRELRVQMAR 91
             +  + L+VQ+ +
Sbjct: 105 FQVGTKRLKVQLKK 118

>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 = 82.2 bits (204), Expect = 1e-20
 Identities = 23/91 (25%), Positives = 42/91 (46%), Gaps = 3/91 (3%)

Query: 15  SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
            L V NL    T D L++ F+  G + +I I  D+   ++  +AFV +    DA  AL  
Sbjct: 2   VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQT 60

Query: 75  MDGRMLDGRELRVQMARYGRPPSSSRSRGGR 105
           ++G+ ++   +++  A   +   SS      
Sbjct: 61  LNGKQIENNIVKINWAF--QSQQSSSDDTFN 89

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 76.0 bits (188), Expect = 3e-18
 Identities = 26/90 (28%), Positives = 44/90 (48%)

Query: 1   MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
            ++       +   +L V +L      + LR  F+        ++  D  T  SRG+ FV
Sbjct: 75  WAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFV 134

Query: 61  RFFDKRDAEDALDAMDGRMLDGRELRVQMA 90
            F  + DA++A+D+M G+ L+GR LR+  A
Sbjct: 135 SFTSQDDAQNAMDSMQGQDLNGRPLRINWA 164

>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 = 80.5 bits (199), Expect = 1e-20
 Identities = 31/94 (32%), Positives = 46/94 (48%), Gaps = 8/94 (8%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEV--------GDIYIPRDRFTRESRGFAFVRFFDKRDAE 69
           V  L    T DDL   F++CG V          I+I  D+ T + +G A V + D   A+
Sbjct: 20  VQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAK 79

Query: 70  DALDAMDGRMLDGRELRVQMARYGRPPSSSRSRG 103
            A++  DG+   G +L+V +AR   P +S  S G
Sbjct: 80  AAVEWFDGKDFQGSKLKVSLARKKPPMNSGPSSG 113

>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 = 79.6 bits (197), Expect = 1e-20
 Identities = 22/87 (25%), Positives = 39/87 (44%), Gaps = 5/87 (5%)

Query: 5  RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
              ++    +L   NL++  T D+L+ VFE   E+            +S+G A++ F  
Sbjct: 8  CTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEI-----RLVSQDGKSKGIAYIEFKS 62

Query: 65 KRDAEDALDAMDGRMLDGRELRVQMAR 91
          + DAE  L+   G  +DGR + +    
Sbjct: 63 EADAEKNLEEKQGAEIDGRSVSLYYTG 89

>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 = 83.9 bits (208), Expect = 2e-20
 Identities = 19/85 (22%), Positives = 31/85 (36%)

Query: 16  LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
           L V NL    T      +    G +   ++     T +S+G+ F  +  K  A  A   +
Sbjct: 98  LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157

Query: 76  DGRMLDGRELRVQMARYGRPPSSSR 100
            G+ L  R L V     G+   +  
Sbjct: 158 LGKPLGPRTLYVHWTDAGQLTPALL 182

>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 = 71.9 bits (177), Expect = 6e-16
 Identities = 24/103 (23%), Positives = 35/103 (33%), Gaps = 6/103 (5%)

Query: 16  LKVDNLTYRTT-PDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
           L VD L       D L R            +   +  +  +GFA + +     AE+A   
Sbjct: 187 LCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQ-LKGFAVLEYETAEMAEEAQQQ 245

Query: 75  MDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSR 117
            DG  L G  LRV    +  P    RS        +   + +R
Sbjct: 246 ADGLSLGGSHLRV---SFCAPGPPGRSMLAALIAAQA-TALNR 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 = 69.2 bits (170), Expect = 4e-15
 Identities = 17/74 (22%), Positives = 28/74 (37%), Gaps = 7/74 (9%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          +  L    T  ++  +             +  F  + +G AFV   +   AE A++A   
Sbjct: 27 IRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKYKGTAFVTLLNGEQAEAAINAFHQ 79

Query: 78 RMLDGRELRVQMAR 91
            L  REL VQ+  
Sbjct: 80 SRLRERELSVQLQP 93

>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 = 79.7 bits (197), Expect = 2e-20
 Identities = 27/109 (24%), Positives = 50/109 (45%), Gaps = 5/109 (4%)

Query: 5   RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
           R PP +     L + NL Y+ T +++  +F + G +  I +     T E+RG A+V + D
Sbjct: 2   RLPPEVNR--ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYED 56

Query: 65  KRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDR 113
             DA++A+D + G  +  R L V      R      ++   ++ +    
Sbjct: 57  IFDAKNAVDHLSGFNVSNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKE 105

>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 = 79.3 bits (196), Expect = 3e-20
 Identities = 26/106 (24%), Positives = 49/106 (46%), Gaps = 7/106 (6%)

Query: 5   RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
             P  +    ++ + NL++ +  + L  V ++ G++  + +     T  S+G AF +F  
Sbjct: 7   GLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMT 66

Query: 65  KRDAEDALDAMD------GRMLDGRELRVQMARYGRPPSSSRSRGG 104
           +  A+  L A        G  LDGR+L+V +A   R  ++S    G
Sbjct: 67  QEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAV-TRDEAASGPSSG 111

>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 = 79.3 bits (196), Expect = 4e-20
 Identities = 23/87 (26%), Positives = 41/87 (47%), Gaps = 1/87 (1%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
           + +L       DL ++F   G V    +  D+ T  S+ F FV + +   A+ A+ +M+G
Sbjct: 30  IYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNG 89

Query: 78  RMLDGRELRVQMARYGRPPSSSRSRGG 104
             +  + L+VQ+ R  +  S S    G
Sbjct: 90  FQIGMKRLKVQLKR-SKNDSKSGPSSG 115

>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 = 78.1 bits (193), Expect = 7e-20
 Identities = 24/86 (27%), Positives = 42/86 (48%), Gaps = 6/86 (6%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
           V NL   T+ + + + F          + +       R +AFV F ++ DA +A+ A++G
Sbjct: 20  VRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMKALNG 73

Query: 78  RMLDGRELRVQMARYGRPPSSSRSRG 103
           ++LDG  + V +A+     SS  S G
Sbjct: 74  KVLDGSPIEVTLAKPVDKDSSGPSSG 99

>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 = 81.7 bits (201), Expect = 7e-20
 Identities = 23/137 (16%), Positives = 47/137 (34%), Gaps = 3/137 (2%)

Query: 4   GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCG--EVGDIYIPRDRFTRESRGFAFVR 61
                     ++L + NLT+ TT +DL       G  ++ +I    +R   +S+GFA V 
Sbjct: 59  NVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVG 118

Query: 62  FFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRDRRY 121
              +  ++  +D +  R L G+   V      +  S    +  +     +     +    
Sbjct: 119 VGSEASSKKLMDLLPKRELHGQNPVVTPVN-KQFLSQFEMQSRKTTQSGQMSGEGKAGPP 177

Query: 122 TRSRSFSSRSRSGSKSP 138
             S   +       +  
Sbjct: 178 GGSSRAAFPQGGRGRGR 194

>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 = 79.9 bits (197), Expect = 8e-20
 Identities = 25/102 (24%), Positives = 46/102 (45%)

Query: 4   GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFF 63
              P R      L V ++      D+++  F   GE+ +I++  DR T  S+G+A V + 
Sbjct: 63  EPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYE 122

Query: 64  DKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGR 105
             + A  A +A++G  + G+ ++V       P    +S   R
Sbjct: 123 THKQALAAKEALNGAEIMGQTIQVDWCFVKGPKRVKKSEKRR 164

>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 = 77.2 bits (191), Expect = 1e-19
 Identities = 28/92 (30%), Positives = 43/92 (46%), Gaps = 8/92 (8%)

Query: 12  GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDA 71
           GMV L + NL    T  ++R +FE+ G+V +  I +         + FV   DK  AEDA
Sbjct: 7   GMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIK--------NYGFVHIEDKTAAEDA 58

Query: 72  LDAMDGRMLDGRELRVQMARYGRPPSSSRSRG 103
           +  +    L G  + V+ ++     SS  S G
Sbjct: 59  IRNLHHYKLHGVNINVEASKNKSKASSGPSSG 90

>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 = 77.3 bits (191), Expect = 1e-19
 Identities = 25/90 (27%), Positives = 49/90 (54%), Gaps = 5/90 (5%)

Query: 15  SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
           +L + NL+Y  T + L+ VFE+   +  +         +S+G+AF+ F    DA++AL++
Sbjct: 17  TLVLSNLSYSATEETLQEVFEKATFI-KVP---QNQNGKSKGYAFIEFASFEDAKEALNS 72

Query: 75  MDGRMLDGRELRVQMARYGRPPSSSRSRGG 104
            + R ++GR +R+++    R   +S    G
Sbjct: 73  CNKREIEGRAIRLELQG-PRGSPNSGPSSG 101

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 76.1 bits (188), Expect = 4e-19
 Identities = 18/86 (20%), Positives = 35/86 (40%), Gaps = 2/86 (2%)

Query: 6  PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
                   +L + NL    +  +L+          D+ +  D  T  +R F +V F   
Sbjct: 10 EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAV-VDVRTGTNRKFGYVDFESA 68

Query: 66 RDAEDALDAMDGRMLDGRELRVQMAR 91
           D E AL+ + G  + G E++++  +
Sbjct: 69 EDLEKALE-LTGLKVFGNEIKLEKPK 93

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 77.7 bits (191), Expect = 4e-19
 Identities = 21/98 (21%), Positives = 45/98 (45%), Gaps = 3/98 (3%)

Query: 18  VDNLTYRTTPDDLRRVFERCG--EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
           V + ++ TT   L +V    G  +V ++    +R   +S+G+A V    +      L+ +
Sbjct: 60  VGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELL 119

Query: 76  DGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDR 113
            G++L+G ++ V+ A   +  S   ++  +    R  R
Sbjct: 120 PGKVLNGEKVDVRPAT-RQNLSQFEAQARKRECVRVPR 156

>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 = 76.2 bits (188), Expect = 5e-19
 Identities = 26/86 (30%), Positives = 39/86 (45%), Gaps = 1/86 (1%)

Query: 5   RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
                +E    L V NL +  +  D++ +F   G +    +  DR  R S G A V F  
Sbjct: 21  GGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGR-SLGTADVHFER 79

Query: 65  KRDAEDALDAMDGRMLDGRELRVQMA 90
           K DA  A+   +G  LDGR + +Q+ 
Sbjct: 80  KADALKAMKQYNGVPLDGRPMNIQLV 105

>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 = 76.2 bits (188), Expect = 5e-19
 Identities = 23/97 (23%), Positives = 42/97 (43%), Gaps = 11/97 (11%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
           V NL    T + L + F + G++  +   +D        +AF+ F ++  A  A++ M+G
Sbjct: 16  VRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEEMNG 67

Query: 78  RMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRS 114
           + L+G  + +  A   +PP   R      R      S
Sbjct: 68  KDLEGENIEIVFA---KPPDQKRKERKAQRQAASGPS 101

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 77.2 bits (190), Expect = 6e-19
 Identities = 27/82 (32%), Positives = 41/82 (50%), Gaps = 5/82 (6%)

Query: 13  MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDAL 72
              + V NL       +L R F   G +  +++ R+       GFAFV F D RDA DA+
Sbjct: 73  DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAV 127

Query: 73  DAMDGRMLDGRELRVQMARYGR 94
             +DGR L G  +RV+++   +
Sbjct: 128 RELDGRTLCGCRVRVELSNGEK 149

>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 = 78.1 bits (193), Expect = 7e-19
 Identities = 17/73 (23%), Positives = 33/73 (45%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
           +  L      D ++ +    G +    + +D  T  S+G+AF  + D    + A+  ++G
Sbjct: 119 IGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNG 178

Query: 78  RMLDGRELRVQMA 90
             L  ++L VQ A
Sbjct: 179 MQLGDKKLLVQRA 191

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 69.7 bits (171), Expect = 1e-15
 Identities = 18/109 (16%), Positives = 36/109 (33%), Gaps = 7/109 (6%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPR-----DRFTRESRGFAFVRFFDKRDAEDAL 72
           V N+ +  T + +   F     +G +              + + FAF+ F    +   A+
Sbjct: 9   VGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM 68

Query: 73  DAMDGRMLDGRELRVQMAR-YGRPPSSSRSRGGRDRDRRRDRSRSRDRR 120
            A DG +  G+ L+++    Y   P  S +                  +
Sbjct: 69  -AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHK 116

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

 Score = 76.1 bits (187), Expect = 9e-19
 Identities = 20/112 (17%), Positives = 41/112 (36%), Gaps = 10/112 (8%)

Query: 4   GRPPPRIEGMVSLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAF 59
           G  PP  E    + + N+      + L+     +    G++ DI +     + ++ G A+
Sbjct: 20  GSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAY 76

Query: 60  VRFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRR 111
           + F  +  A+  ++A  G    G  L +    +   P S  +  G       
Sbjct: 77  IVFATQESAQAFVEAFQGYPFQGNPLVIT---FSETPQSQVAEDGSLEHHHH 125

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 79.0 bits (195), Expect = 9e-19
 Identities = 31/89 (34%), Positives = 44/89 (49%), Gaps = 6/89 (6%)

Query: 5  RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
                     L V NL    T +D +R+FER GE  +++I RDR      GF F+R   
Sbjct: 14 PGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRLES 67

Query: 65 KRDAEDALDAMDGRMLDGRELRVQMARYG 93
          +  AE A   +DG +L  R LR++ A +G
Sbjct: 68 RTLAEIAKAELDGTILKSRPLRIRFATHG 96

>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 = 58.2 bits (141), Expect = 4e-11
 Identities = 21/104 (20%), Positives = 35/104 (33%), Gaps = 2/104 (1%)

Query: 16  LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
           L V NL+   + + L + F + G V    +  D   R + G  FV F  K  A  AL+  
Sbjct: 99  LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGR-ATGKGFVEFAAKPPARKALERC 157

Query: 76  DGRM-LDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRD 118
                L     R  +               +   + +   + R+
Sbjct: 158 GDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQKTQQYHKERE 201

>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 = 75.9 bits (187), Expect = 9e-19
 Identities = 25/97 (25%), Positives = 38/97 (39%), Gaps = 1/97 (1%)

Query: 5   RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
                +E    L V NL +  +  D++ +F   G +    +  DR  R S G A V F  
Sbjct: 27  GGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGR-SLGTADVHFER 85

Query: 65  KRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRS 101
           + DA  A+    G  LDGR + +Q+            
Sbjct: 86  RADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHH 122

>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 = 74.9 bits (185), Expect = 1e-18
 Identities = 22/84 (26%), Positives = 43/84 (51%), Gaps = 8/84 (9%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
           V N++   T  +LR +FER G V +  + +         +AFV    + DA+ A+  ++G
Sbjct: 14  VGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEADAKAAIAQLNG 65

Query: 78  RMLDGRELRVQMARYGRPPSSSRS 101
           + + G+ + V+++  G+  S   S
Sbjct: 66  KEVKGKRINVELSTKGQKKSGPSS 89

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 75.0 bits (185), Expect = 1e-18
 Identities = 27/90 (30%), Positives = 49/90 (54%), Gaps = 3/90 (3%)

Query: 2   SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
           S+     + +    L V N+ +R    DLR++F + G++ D+ I  +   R S+GF FV 
Sbjct: 19  SHMNTENKSQPK-RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVT 75

Query: 62  FFDKRDAEDALDAMDGRMLDGRELRVQMAR 91
           F +  DA+ A + + G +++GR++ V  A 
Sbjct: 76  FENSADADRAREKLHGTVVEGRKIEVNNAT 105

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 74.7 bits (184), Expect = 2e-18
 Identities = 27/88 (30%), Positives = 40/88 (45%), Gaps = 5/88 (5%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGE-VGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
          SL + +L      + + R F   GE V  + I R+R T    G+ FV F D   AE  L 
Sbjct: 11 SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70

Query: 74 AMDGRMLDG----RELRVQMARYGRPPS 97
           ++G+ L G    +  ++  A Y  P S
Sbjct: 71 KINGKPLPGATPAKRFKLNYATYSGPSS 98

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 73.8 bits (182), Expect = 3e-18
 Identities = 19/90 (21%), Positives = 37/90 (41%), Gaps = 9/90 (10%)

Query: 18  VDNL-TYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD 76
           + NL     + +DL R+F   G +  I I           F F++F + +   DA++   
Sbjct: 15  IGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAIECES 66

Query: 77  GRMLDGRELRVQMARYGRPPSSSRSRGGRD 106
             M  G++L ++++     P       G +
Sbjct: 67  QEMNFGKKLILEVSSSNARPQFDHGDHGTN 96

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 73.8 bits (182), Expect = 3e-18
 Identities = 29/91 (31%), Positives = 40/91 (43%), Gaps = 2/91 (2%)

Query: 8  PRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRD 67
              G   + V NL +  T   L+  F  CG V    I  +    +S+G   V+F     
Sbjct: 3  SGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEV 60

Query: 68 AEDALDAMDGRMLDGRELRVQMARYGRPPSS 98
          AE A   M+G  L GRE+ V++ R    PSS
Sbjct: 61 AERACRMMNGMKLSGREIDVRIDRNASGPSS 91

>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 = 75.7 bits (187), Expect = 3e-18
 Identities = 20/88 (22%), Positives = 37/88 (42%), Gaps = 2/88 (2%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRE--SRGFAFVRFFDKRDAEDALDAM 75
           V  +    +  DLR +FE+ G V +I + RDR      S+G  FV F+ ++ A +A +A+
Sbjct: 8   VGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNAL 67

Query: 76  DGRMLDGRELRVQMARYGRPPSSSRSRG 103
               +          +      ++    
Sbjct: 68  HNMKVLPGMHHPIQMKPADSEKNNAVED 95

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

 Score = 66.9 bits (164), Expect = 7e-15
 Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 4/76 (5%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
           +  ++ + T +D+R +F   G++ +  I R      SRG AFV F  +  A+ A+ AM  
Sbjct: 100 IGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQ 158

Query: 78  RML---DGRELRVQMA 90
                     + V+ A
Sbjct: 159 AQTMEGCSSPMVVKFA 174

>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 = 75.3 bits (186), Expect = 4e-18
 Identities = 19/86 (22%), Positives = 36/86 (41%)

Query: 5   RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
                + G   L +  L      D ++ +    G +    + +D  T  S+G+AF  + D
Sbjct: 86  HDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVD 145

Query: 65  KRDAEDALDAMDGRMLDGRELRVQMA 90
               + A+  ++G  L  ++L VQ A
Sbjct: 146 INVTDQAIAGLNGMQLGDKKLLVQRA 171

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 69.2 bits (170), Expect = 1e-15
 Identities = 16/87 (18%), Positives = 34/87 (39%), Gaps = 6/87 (6%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPR-----DRFTRESRGFAFVRFFDKRDAEDAL 72
          V N+ +  T + +   F     +G +              + + FAF+ F    +   A+
Sbjct: 9  VGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM 68

Query: 73 DAMDGRMLDGRELRVQMARYGRPPSSS 99
           A DG +  G+ L+++     +P   +
Sbjct: 69 -AFDGIIFQGQSLKIRRPHDYQPLPGA 94

>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 = 73.0 bits (180), Expect = 5e-18
 Identities = 23/86 (26%), Positives = 37/86 (43%), Gaps = 8/86 (9%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
           V N++   T  +LR  FE  G V +  I +         +AFV      DA +A+  +D 
Sbjct: 15  VGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRGLDN 66

Query: 78  RMLDGRELRVQMARYGRPPSSSRSRG 103
               G+ + VQ++      +S  S G
Sbjct: 67  TEFQGKRMHVQLSTSRLRTASGPSSG 92

>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 = 73.4 bits (181), Expect = 5e-18
 Identities = 23/87 (26%), Positives = 38/87 (43%), Gaps = 3/87 (3%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
           V NL      + LR+ F   G +    +  +     S+GF FV F    +A  A+  M+G
Sbjct: 20  VKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNG 77

Query: 78  RMLDGRELRVQMARYGRPPSSSRSRGG 104
           R++  + L V +A+  +    S    G
Sbjct: 78  RIVATKPLYVALAQ-RKEERQSGPSSG 103

>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 = 73.3 bits (180), Expect = 6e-18
 Identities = 17/100 (17%), Positives = 34/100 (34%), Gaps = 6/100 (6%)

Query: 15  SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
            +   NL   T   +++  F R G +G + +P      E    A V F +  +A  A   
Sbjct: 12  VILAKNLPAGTLAAEIQETFSRFGSLGRVLLP------EGGITAIVEFLEPLEARKAFRH 65

Query: 75  MDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRS 114
           +         L ++ A  G   ++ + +  +         
Sbjct: 66  LAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEKAE 105

>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 = 72.3 bits (178), Expect = 1e-17
 Identities = 21/79 (26%), Positives = 34/79 (43%), Gaps = 6/79 (7%)

Query: 25  TTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRE 84
            TP  LR  F   G + D+ +   R        AFV +     A+ A+  ++G  ++  +
Sbjct: 25  MTPTLLRGAFSPFGNIIDLSMDPPR------NCAFVTYEKMESADQAVAELNGTQVESVQ 78

Query: 85  LRVQMARYGRPPSSSRSRG 103
           L+V +AR      S  S G
Sbjct: 79  LKVNIARKQPMLDSGPSSG 97

>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 = 72.3 bits (178), Expect = 1e-17
 Identities = 24/99 (24%), Positives = 41/99 (41%), Gaps = 11/99 (11%)

Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          + YG+  P       L V  L   T+   L R F+R G +  I   +         FA++
Sbjct: 9  IGYGKANPTT----RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD------SFAYI 58

Query: 61 RFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSS 99
          ++     A+ A   M G  L G + R+++  + +   SS
Sbjct: 59 QYESLDAAQAACAKMRGFPLGGPDRRLRV-DFAKSGPSS 96

>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 = 76.2 bits (188), Expect = 2e-17
 Identities = 18/75 (24%), Positives = 35/75 (46%), Gaps = 2/75 (2%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEV-GDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD 76
           + N     T  ++R + +    V   I +P  RF   SR FA++    K DA   ++ ++
Sbjct: 122 MTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNT-SRRFAYIDVTSKEDARYCVEKLN 180

Query: 77  GRMLDGRELRVQMAR 91
           G  ++G  L  +++ 
Sbjct: 181 GLKIEGYTLVTKVSN 195

>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 = 70.4 bits (173), Expect = 2e-15
 Identities = 24/79 (30%), Positives = 38/79 (48%), Gaps = 3/79 (3%)

Query: 14  VSLKVDNLTYRTTPDD-LRRVFERCGEVGDIYIPRDRF-TRESRGFAFVRFFDKRDAEDA 71
             + + NL+     ++ LR  FE  G +  I IP  +     +   AF+ F +K  AE A
Sbjct: 211 REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA 270

Query: 72  LDAMDGRMLDGRELRVQMA 90
           L  M+  +L  RE+ V +A
Sbjct: 271 L-QMNRSLLGNREISVSLA 288

>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 = 69.6 bits (171), Expect = 4e-15
 Identities = 14/84 (16%), Positives = 32/84 (38%), Gaps = 3/84 (3%)

Query: 4   GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFF 63
                R   + ++ V NL      + + + F+ CG +  + +      +++  FA + F 
Sbjct: 32  NEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIEFA 89

Query: 64  DKRDAEDALDAMDGRMLDGRELRV 87
               A  A+      ++   E+ V
Sbjct: 90  RYDGALAAITKTHK-VVGQNEIIV 112

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 71.8 bits (177), Expect = 2e-17
 Identities = 24/88 (27%), Positives = 38/88 (43%), Gaps = 2/88 (2%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGD-IYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD 76
           + NL        L   F   G +     I RD  T  S+G+AF+ F     ++ A++AM+
Sbjct: 10  IGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMN 69

Query: 77  GRMLDGRELRVQMARYGRPPSSSRSRGG 104
           G+ L  R + V  A + +    S    G
Sbjct: 70  GQYLCNRPITVSYA-FKKDSKGSGPSSG 96

>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 = 73.4 bits (181), Expect = 3e-17
 Identities = 25/89 (28%), Positives = 41/89 (46%), Gaps = 5/89 (5%)

Query: 2   SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
             GR   ++    +L   NL++  T D+L+ VFE   E     I       +S+G A++ 
Sbjct: 88  PKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALE-----IRLVSQDGKSKGIAYIE 142

Query: 62  FFDKRDAEDALDAMDGRMLDGRELRVQMA 90
           F  + DAE  L+   G  +DGR + +   
Sbjct: 143 FKSEADAEKNLEEKQGAEIDGRSVSLYYT 171

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 72.3 bits (178), Expect = 7e-17
 Identities = 19/90 (21%), Positives = 37/90 (41%), Gaps = 2/90 (2%)

Query: 2  SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          S+           +L + NL    +  +L+          D+ +   R T  +R F +V 
Sbjct: 2  SHMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVD 60

Query: 62 FFDKRDAEDALDAMDGRMLDGRELRVQMAR 91
          F    D E AL+ + G  + G E++++  +
Sbjct: 61 FESAEDLEKALE-LTGLKVFGNEIKLEKPK 89

>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 = 71.9 bits (177), Expect = 3e-17
 Identities = 23/105 (21%), Positives = 40/105 (38%), Gaps = 16/105 (15%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
           + NL        L   F   G +    +  D     S+G+ FV F  +  AE A++ M+G
Sbjct: 10  IKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNG 67

Query: 78  RMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRDRRYT 122
            +L+ R++ V   +               R  R     +R + +T
Sbjct: 68  MLLNDRKVFVGRFKS--------------RKEREAELGARAKEFT 98

>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 = 70.8 bits (174), Expect = 4e-17
 Identities = 22/78 (28%), Positives = 38/78 (48%), Gaps = 7/78 (8%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          +L V  L    T  DLR  F + GE+  I + +       +  AF++F  ++ AE A + 
Sbjct: 14 TLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEK 67

Query: 75 M-DGRMLDGRELRVQMAR 91
            +  +++GR L V+  R
Sbjct: 68 SFNKLIVNGRRLNVKWGR 85

>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 = 73.4 bits (180), Expect = 4e-17
 Identities = 26/110 (23%), Positives = 47/110 (42%), Gaps = 8/110 (7%)

Query: 18  VDNL-TYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD 76
           V NL   R TP  L  +F   G+V  + I  +      +  A V+  D   A+ A+  ++
Sbjct: 8   VSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADGNQAQLAMSHLN 62

Query: 77  GRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRDRRYTRSRS 126
           G  L G+ +R+ ++++          G  D+   +D   S   R+ +  S
Sbjct: 63  GHKLHGKPIRITLSKHQNVQ--LPREGQEDQGLTKDYGNSPLHRFKKPGS 110

>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 = 61.8 bits (150), Expect = 1e-12
 Identities = 16/77 (20%), Positives = 34/77 (44%), Gaps = 5/77 (6%)

Query: 16  LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
           L + N+    + +DL+ +F   G V    +   +F ++ R  A ++     +A  AL  +
Sbjct: 123 LHLSNIPPSVSEEDLKVLFSSNGGV----VKGFKFFQKDRKMALIQMGSVEEAVQALIDL 178

Query: 76  DG-RMLDGRELRVQMAR 91
               + +   LRV  ++
Sbjct: 179 HNHDLGENHHLRVSFSK 195

>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 = 70.8 bits (174), Expect = 5e-17
 Identities = 27/107 (25%), Positives = 43/107 (40%), Gaps = 8/107 (7%)

Query: 2   SYGRPPPRIEGMVSLK--VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAF 59
           S G       G    K  V  L  + + +D+ R+F+  G + +  + R      S+G AF
Sbjct: 2   SSGSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAF 60

Query: 60  VRFFDKRDAEDALDAMDGRML---DGRELRVQMARYGRPPSSSRSRG 103
           V+F    +A+ A+ A+ G          L V+ A       S  S G
Sbjct: 61  VKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFAD--TDKESGPSSG 105

>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 = 70.5 bits (173), Expect = 9e-17
 Identities = 25/87 (28%), Positives = 42/87 (48%), Gaps = 9/87 (10%)

Query: 18  VDNL-TYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD 76
           + NL T      D+  +F + G V    + +        G+AFV++ ++R A  A+   +
Sbjct: 32  IGNLNTALVKKSDVETIFSKYGRVAGCSVHK--------GYAFVQYSNERHARAAVLGEN 83

Query: 77  GRMLDGRELRVQMARYGRPPSSSRSRG 103
           GR+L G+ L + MA   +P  S  S G
Sbjct: 84  GRVLAGQTLDINMAGEPKPDRSGPSSG 110

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 70.4 bits (173), Expect = 1e-16
 Identities = 30/87 (34%), Positives = 45/87 (51%), Gaps = 1/87 (1%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
           V  L Y TT   LR+ FE  G++ +  +  DR T +SRG+ FV   D+  AE A    + 
Sbjct: 22  VGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP 81

Query: 78  RMLDGRELRVQMARYGRPPSSSRSRGG 104
            ++DGR+  V +A  G  P S ++   
Sbjct: 82  -IIDGRKANVNLAYLGAKPRSLQTGFA 107

>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 = 72.7 bits (178), Expect = 2e-16
 Identities = 28/128 (21%), Positives = 50/128 (39%), Gaps = 8/128 (6%)

Query: 4   GRPPPRIEGMVSLKVDNL-TYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRF 62
             P     G   L V NL   R TP  L  +F   G+V  +     +     +  A V+ 
Sbjct: 25  AIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRV-----KILFNKKENALVQM 79

Query: 63  FDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRDRRYT 122
            D   A+ A+  ++G  L G+ +R+ +++           G  D+   +D   S   R+ 
Sbjct: 80  ADGNQAQLAMSHLNGHKLHGKPIRITLSK--HQNVQLPREGQEDQGLTKDYGNSPLHRFK 137

Query: 123 RSRSFSSR 130
           +  S + +
Sbjct: 138 KPGSKNFQ 145

>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 = 60.0 bits (145), Expect = 9e-12
 Identities = 17/77 (22%), Positives = 34/77 (44%), Gaps = 5/77 (6%)

Query: 16  LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
           L + N+    + +DL+ +F   G V    +   +F ++ R  A ++     +A  AL  +
Sbjct: 154 LHLSNIPPSVSEEDLKVLFSSNGGV----VKGFKFFQKDRKMALIQMGSVEEAVQALIDL 209

Query: 76  DGRML-DGRELRVQMAR 91
               L +   LRV  ++
Sbjct: 210 HNHDLGENHHLRVSFSK 226

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 71.4 bits (176), Expect = 2e-16
 Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 2/73 (2%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          +  L + TT D+LR  F + G V D+ I +D  T  SRGF F+ F      ++ +     
Sbjct: 8  IGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ-- 65

Query: 78 RMLDGRELRVQMA 90
           +LDG+ +  + A
Sbjct: 66 HILDGKVIDPKRA 78

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 69.1 bits (170), Expect = 1e-15
 Identities = 20/88 (22%), Positives = 34/88 (38%), Gaps = 3/88 (3%)

Query: 5   RPPPRIEGMVSLK--VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRF 62
           R  PR E   + K  V  +     P +    F + G + D  +  D+ T +SRGF FV +
Sbjct: 77  RAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTY 136

Query: 63  FDKRDAEDALDAMDGRMLDGRELRVQMA 90
                 +             R++ ++ A
Sbjct: 137 DSADAVDRVC-QNKFIDFKDRKIEIKRA 163

>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 = 69.6 bits (171), Expect = 2e-16
 Identities = 28/117 (23%), Positives = 43/117 (36%), Gaps = 7/117 (5%)

Query: 2   SYGRPPPRIEGMVSLK--VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAF 59
           S G       G +     V NL Y+     L+ VF   G V    I  D+  + SRG   
Sbjct: 2   SSGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGK-SRGIGT 60

Query: 60  VRFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRS 116
           V F    +A  A+   +G++L  R + V+M     P    +         ++    S
Sbjct: 61  VTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALP----KGDFFPPERPQQSGPSS 113

>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 = 72.0 bits (176), Expect = 2e-16
 Identities = 19/110 (17%), Positives = 39/110 (35%), Gaps = 6/110 (5%)

Query: 18  VDNL-TYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD 76
           V  L   +   D +  VF   G V  +   + +      G A V   D    + A+  ++
Sbjct: 9   VYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRAITHLN 63

Query: 77  GRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRDRRYTRSRS 126
              + G+++ V +++                   +D S SR+ R++    
Sbjct: 64  NNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQ 113

>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 = 66.7 bits (162), Expect = 2e-14
 Identities = 8/70 (11%), Positives = 19/70 (27%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
             N     T ++   + +  G      +       E      + +  K DA + L  ++ 
Sbjct: 128 FFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNH 187

Query: 78  RMLDGRELRV 87
             +       
Sbjct: 188 YQMKNPNGPY 197

>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 = 69.6 bits (171), Expect = 2e-16
 Identities = 15/74 (20%), Positives = 25/74 (33%), Gaps = 1/74 (1%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
           + NL       +L  + +  G+V    I RD  +  SRG  F R       E  +   +G
Sbjct: 30  ISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNG 88

Query: 78  RMLDGRELRVQMAR 91
           + +           
Sbjct: 89  KFIKTPPGVSAPTE 102

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 68.8 bits (169), Expect = 3e-16
 Identities = 22/87 (25%), Positives = 41/87 (47%), Gaps = 2/87 (2%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
           V  + +     +LR  F++ G V ++ +  D   +  RGF F+ F D++  + A+  M  
Sbjct: 15  VGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV-NMHF 73

Query: 78  RMLDGRELRVQMARYGRPPSSSRSRGG 104
             + G+++ V+ A   R   SS    G
Sbjct: 74  HDIMGKKVEVKRAE-PRDSKSSGPSSG 99

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

 Score = 68.9 bits (169), Expect = 3e-16
 Identities = 16/74 (21%), Positives = 29/74 (39%), Gaps = 8/74 (10%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
           V          +L  +F   G + ++ I          GFAFV F +   A  A++ + G
Sbjct: 36  VRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAAKAIEEVHG 87

Query: 78  RMLDGRELRVQMAR 91
           +    + L V  ++
Sbjct: 88  KSFANQPLEVVYSK 101

>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 = 69.5 bits (170), Expect = 4e-16
 Identities = 24/93 (25%), Positives = 38/93 (40%), Gaps = 6/93 (6%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEV-----GDIYIPRDRFTRESRGFAFVRFFDKRDAEDAL 72
           V NL       DL+ +F R  +        ++  R       +G AF+   +++ A  AL
Sbjct: 50  VKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKAL 109

Query: 73  DAMDGRMLDGRELRVQMARYGRPPSSSRSRGGR 105
              +G +L G+ + VQ AR    P      G R
Sbjct: 110 KEANGYVLFGKPMVVQFAR-SARPKQDPKEGKR 141

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 67.5 bits (166), Expect = 4e-16
 Identities = 18/73 (24%), Positives = 33/73 (45%), Gaps = 1/73 (1%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V  L+  T  + +R  F   GEV  I +P D  T + RGF F+ F ++   +  +     
Sbjct: 4  VGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM-EKKY 62

Query: 78 RMLDGRELRVQMA 90
            +   +  +++A
Sbjct: 63 HNVGLSKCEIKVA 75

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 68.4 bits (168), Expect = 4e-16
 Identities = 27/99 (27%), Positives = 45/99 (45%), Gaps = 2/99 (2%)

Query: 5   RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
                 E   +  V NL + T   D+  +F+    +  + + RD+ T + +GF +V F +
Sbjct: 7   GKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDE 65

Query: 65  KRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRG 103
               ++AL   DG +L  R LRV +A   +   S  S G
Sbjct: 66  VDSLKEAL-TYDGALLGDRSLRVDIAEGRKQDKSGPSSG 103

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 68.4 bits (168), Expect = 5e-16
 Identities = 26/86 (30%), Positives = 39/86 (45%), Gaps = 2/86 (2%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
           V  L ++TT  DL+  F   GEV  + + +D  T  S+GF FVRF +       +     
Sbjct: 20  VLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRH- 78

Query: 78  RMLDGRELRVQMARYGRPPSSSRSRG 103
            M+DGR    ++    +   S  S G
Sbjct: 79  -MIDGRWCDCKLPNSKQSQDSGPSSG 103

>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 = 68.1 bits (167), Expect = 5e-16
 Identities = 17/93 (18%), Positives = 36/93 (38%), Gaps = 3/93 (3%)

Query: 6  PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
                G   +KV N+ +  + D++   F     +      +        G A V F  +
Sbjct: 8  ASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESR 67

Query: 66 RDAEDALDAMDGRMLDGRELRVQMARYGRPPSS 98
           +A  A+  ++ R +  R++++ +      PSS
Sbjct: 68 DEATAAVIDLNDRPIGSRKVKLVLG---SGPSS 97

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 67.5 bits (166), Expect = 5e-16
 Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 1/73 (1%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V  L+  TT +D++  FE+ G+V D  +  D+ T   RGF FV F  +   E     +  
Sbjct: 4  VGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EIHF 62

Query: 78 RMLDGRELRVQMA 90
            ++ + +  + A
Sbjct: 63 HEINNKMVECKKA 75

>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 = 67.7 bits (166), Expect = 6e-16
 Identities = 18/92 (19%), Positives = 38/92 (41%), Gaps = 5/92 (5%)

Query: 2  SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          S G+P P +     +KV N+ +  + D++   F     +      +        G A V 
Sbjct: 9  SSGKPGPTV-----IKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVA 63

Query: 62 FFDKRDAEDALDAMDGRMLDGRELRVQMARYG 93
          F  + +A  A+  ++ R +  R++++     G
Sbjct: 64 FESRDEATAAVIDLNDRPIGSRKVKLSGPSSG 95

>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 = 71.8 bits (175), Expect = 6e-16
 Identities = 29/141 (20%), Positives = 59/141 (41%), Gaps = 10/141 (7%)

Query: 6   PPPRIEGMVSLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVR 61
             P      ++ ++NL  +   D+L++    +F + G++ DI + R   + + RG AFV 
Sbjct: 2   AVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVI 58

Query: 62  FFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRDRRY 121
           F +   A +AL +M G     + +R+Q A   +  S   ++       R  +   R  + 
Sbjct: 59  FKEVSSATNALRSMQGFPFYDKPMRIQYA---KTDSDIIAKMKGTFVERDRKREKRKPKS 115

Query: 122 TRSRSFSSRSRSGSKSPRKAR 142
             + +     + G  +P    
Sbjct: 116 QETPATKKAVQGGGATPVVGA 136

>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 = 53.3 bits (127), Expect = 3e-09
 Identities = 16/73 (21%), Positives = 30/73 (41%), Gaps = 6/73 (8%)

Query: 20  NLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG-R 78
           NL   T    L  +F +     ++ +   R        AFV F ++  A  A DA+ G +
Sbjct: 214 NLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFK 268

Query: 79  MLDGRELRVQMAR 91
           +     +++  A+
Sbjct: 269 ITQNNAMKISFAK 281

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 68.0 bits (166), Expect = 1e-15
 Identities = 20/91 (21%), Positives = 39/91 (42%), Gaps = 10/91 (10%)

Query: 18  VDNLTYRTTPDDLRR---VFERCGEVGDIYIPRDRFTRESR---GFAFVRFFDKRDAEDA 71
           V  L+ R    ++ +    F + G++  + I        S+     A+V +    DA  A
Sbjct: 20  VVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRA 79

Query: 72  LDAMDGRMLDGRELRVQMA--RY--GRPPSS 98
           +  ++  ++DGR L+  +   +Y     PSS
Sbjct: 80  IQCVNNVVVDGRTLKASLGTTKYCSYSGPSS 110

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 66.4 bits (163), Expect = 2e-15
 Identities = 25/70 (35%), Positives = 39/70 (55%), Gaps = 1/70 (1%)

Query: 21 LTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRML 80
          L+++TT + LR  F + GEV +  + RD  T+ SRGF FV F D+   +  L A     L
Sbjct: 8  LSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQSRHEL 66

Query: 81 DGRELRVQMA 90
          D + +  ++A
Sbjct: 67 DSKTIDPKVA 76

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 69.2 bits (170), Expect = 2e-15
 Identities = 28/90 (31%), Positives = 44/90 (48%), Gaps = 1/90 (1%)

Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          MS    P   E +  L +  L++ TT + LR  FE+ G + D  + RD  T+ SRGF FV
Sbjct: 1  MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFV 60

Query: 61 RFFDKRDAEDALDAMDGRMLDGRELRVQMA 90
           +    + + A+       +DGR +  + A
Sbjct: 61 TYATVEEVDAAM-NARPHKVDGRVVEPKRA 89

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 66.5 bits (163), Expect = 2e-14
 Identities = 26/88 (29%), Positives = 39/88 (44%), Gaps = 3/88 (3%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
           V  +   T    LR  FE+ G++  I I  DR + + RGFAFV F D    +  +     
Sbjct: 109 VGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKY 167

Query: 78  RMLDGRELRVQMA--RYGRPPSSSRSRG 103
             ++G    V+ A  +     +SS  RG
Sbjct: 168 HTVNGHNCEVRKALSKQEMASASSSQRG 195

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 66.1 bits (162), Expect = 3e-15
 Identities = 27/70 (38%), Positives = 36/70 (51%), Gaps = 1/70 (1%)

Query: 21 LTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRML 80
          L++ T+  DL+  F + GEV D  I  D  T  SRGF F+ F D    E  LD  +   L
Sbjct: 19 LSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKE-HRL 77

Query: 81 DGRELRVQMA 90
          DGR +  + A
Sbjct: 78 DGRVIDPKKA 87

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 65.9 bits (161), Expect = 3e-15
 Identities = 15/72 (20%), Positives = 34/72 (47%), Gaps = 3/72 (4%)

Query: 17 KVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD 76
          +V         + + ++F + G++ + + P +    +++G+ F+ +     A DA+   D
Sbjct: 11 QVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAVDAVKNAD 68

Query: 77 GRMLDGRE-LRV 87
          G  LD +   RV
Sbjct: 69 GYKLDKQHTFRV 80

>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 = 65.4 bits (160), Expect = 5e-15
 Identities = 17/78 (21%), Positives = 35/78 (44%), Gaps = 9/78 (11%)

Query: 18 VDNLTYRT-TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD 76
          + NL  +  + +DL R+F   G +  I I           F F++F + +   DA++   
Sbjct: 27 IGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAIEXES 78

Query: 77 GRMLDGRELRVQMARYGR 94
            M  G++L ++++    
Sbjct: 79 QEMNFGKKLILEVSSSNA 96

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 65.4 bits (160), Expect = 7e-15
 Identities = 24/103 (23%), Positives = 43/103 (41%), Gaps = 4/103 (3%)

Query: 2   SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRE-SRGFAFV 60
           S G   P+     +  + NL Y  T + ++  F     +  + +PR+    E  +GF + 
Sbjct: 5   SSGSRLPK-SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYA 62

Query: 61  RFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRG 103
            F D      AL +++   L  + +RV +A   +   S  S G
Sbjct: 63  EFEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQDKDSGPSSG 104

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 64.9 bits (159), Expect = 8e-15
 Identities = 22/88 (25%), Positives = 40/88 (45%), Gaps = 4/88 (4%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
           V  +  R    ++R  F R G V ++ I  DR T  S+G+ FV F++  D +  ++    
Sbjct: 14  VGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQ 70

Query: 78  RMLDGRELRVQMARYGRPPSSSRSRGGR 105
               G++L++  A   +   S+     R
Sbjct: 71  INFHGKKLKLGPAI-RKQNLSTYHVQPR 97

>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 = 64.7 bits (158), Expect = 1e-14
 Identities = 15/86 (17%), Positives = 31/86 (36%), Gaps = 7/86 (8%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
           V NL   +   ++  + +           +  +   ++  AFV   +   A++A+     
Sbjct: 10  VKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQ 62

Query: 78  RMLDGRELRVQMARYGRPPSSSRSRG 103
               G++L VQ+        S  S G
Sbjct: 63  YSFRGKDLIVQLQPTDALLCSGPSSG 88

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

 Score = 64.4 bits (157), Expect = 1e-14
 Identities = 16/84 (19%), Positives = 30/84 (35%), Gaps = 3/84 (3%)

Query: 8  PRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRD 67
          P+ + +  L++ N+      + L  +  + G V                   V +  K  
Sbjct: 10 PKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTD---SETAVVNVTYSSKDQ 66

Query: 68 AEDALDAMDGRMLDGRELRVQMAR 91
          A  ALD ++G  L+   L+V    
Sbjct: 67 ARQALDKLNGFQLENFTLKVAYIP 90

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

 Score = 64.5 bits (157), Expect = 2e-14
 Identities = 23/81 (28%), Positives = 32/81 (39%), Gaps = 5/81 (6%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
           + V NL       DL+R     G V     P     +  R  AF+ + D   A+ A+  
Sbjct: 21 DVYVGNLPRDARVSDLKRALRELGSV-----PLRLTWQGPRRRAFLHYPDSAAAQQAVSC 75

Query: 75 MDGRMLDGRELRVQMARYGRP 95
          + G  L    LRV +AR  R 
Sbjct: 76 LQGLRLGTDTLRVALARQQRD 96

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 63.6 bits (155), Expect = 3e-14
 Identities = 15/75 (20%), Positives = 35/75 (46%), Gaps = 3/75 (4%)

Query: 17 KVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD 76
          +V         + + ++F + G++ + + P +    +++G+ F+ +     A DA+   D
Sbjct: 25 QVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAVDAVKNAD 82

Query: 77 GRMLDGRE-LRVQMA 90
          G  LD +   RV + 
Sbjct: 83 GYKLDKQHTFRVNLF 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 = 63.7 bits (155), Expect = 4e-14
 Identities = 16/83 (19%), Positives = 30/83 (36%), Gaps = 4/83 (4%)

Query: 18 VDNLTYRTTPDDLRRVFERCGE-VGDIYIPRD-RFTRESRGFAFVRFFDKRDAEDALDAM 75
          +  +      +++     +  E V D+ +        ++RGFAFV +   R A  A   +
Sbjct: 13 IGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKL 72

Query: 76 --DGRMLDGRELRVQMARYGRPP 96
                L G ++ V  A      
Sbjct: 73 MPGRIQLWGHQIAVDWAEPEIDV 95

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 63.0 bits (154), Expect = 6e-14
 Identities = 25/70 (35%), Positives = 39/70 (55%), Gaps = 1/70 (1%)

Query: 21  LTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRML 80
           L+++TT + LR  F + GEV +  + RD  T+ SRGF FV F D+   +  L A     L
Sbjct: 33  LSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQSRHEL 91

Query: 81  DGRELRVQMA 90
           D + +  ++A
Sbjct: 92  DSKTIDPKVA 101

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 62.6 bits (153), Expect = 8e-14
 Identities = 30/83 (36%), Positives = 39/83 (46%), Gaps = 1/83 (1%)

Query: 21  LTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRML 80
           L + TT + LR  F + GEV D  I +D+ T +SRGF FV+F D       L A     L
Sbjct: 24  LDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVL-ASRPHTL 82

Query: 81  DGRELRVQMARYGRPPSSSRSRG 103
           DGR +  +         S  S G
Sbjct: 83  DGRNIDPKPCTPRGMQPSGPSSG 105

>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 = 62.1 bits (151), Expect = 2e-13
 Identities = 24/108 (22%), Positives = 44/108 (40%), Gaps = 9/108 (8%)

Query: 2   SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
           S G+P P     + + V  + +    +D+R  F     V  +++ +D   R + G   V+
Sbjct: 5   SSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGR-NNGNGLVK 62

Query: 62  FFDKRDAEDALDAMDGRMLDGRELRV------QMARYGRPPSSSRSRG 103
           F   +D  +AL   +  ++  R + V      Q    G   +S  S G
Sbjct: 63  FLSPQDTFEALK-RNRMLMIQRYVEVSPATERQWVAAGGHITSGPSSG 109

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 62.1 bits (151), Expect = 2e-13
 Identities = 20/108 (18%), Positives = 38/108 (35%), Gaps = 9/108 (8%)

Query: 6   PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEV-GDIYIPRDRFTRESRGFAFVRFFD 64
                   V   + N+ +  T  D+ +  E        +++  D   +   G A V+F +
Sbjct: 8   EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQ-GLGQALVQFKN 66

Query: 65  KRDAEDALDAMDGRMLDGRELRV------QMARYGRPPSSSRSRGGRD 106
           + DA  +   +  + L+GRE  V       M    + P +    G   
Sbjct: 67  EDDARKSE-RLHRKKLNGREAFVHVVTLEDMREIEKNPPAQGKSGPSS 113

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 61.9 bits (151), Expect = 2e-13
 Identities = 27/84 (32%), Positives = 43/84 (51%), Gaps = 2/84 (2%)

Query: 21  LTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRML 80
           L++ TT + LR  +E+ G++ D  + RD  ++ SRGF FV F    + + A+ A     +
Sbjct: 35  LSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM-AARPHSI 93

Query: 81  DGRELRVQMARYGRPPSSSRSRGG 104
           DGR +  + A   R  S S    G
Sbjct: 94  DGRVVEPKRAV-AREESGSGPSSG 116

>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 = 61.5 bits (150), Expect = 2e-13
 Identities = 19/78 (24%), Positives = 35/78 (44%), Gaps = 3/78 (3%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRE-SRGFAFVRFFDKRDAEDALD 73
          +  + NL Y  T + ++  F     +  + +PR+    E  +GF +  F D      AL 
Sbjct: 21 TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL- 78

Query: 74 AMDGRMLDGRELRVQMAR 91
          +++   L  R +RV +A 
Sbjct: 79 SLNEESLGNRRIRVDVAD 96

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 59.9 bits (146), Expect = 6e-13
 Identities = 25/86 (29%), Positives = 39/86 (45%), Gaps = 7/86 (8%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
           V   T   T D+LR  F + G+V D++IP+       R FAFV F D + A+      + 
Sbjct: 10  VGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLC--GED 62

Query: 78  RMLDGRELRVQMARYGRPPSSSRSRG 103
            ++ G  + +  A      +S  S G
Sbjct: 63  LIIKGISVHISNAEPKHNSNSGPSSG 88

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 61.8 bits (150), Expect = 7e-13
 Identities = 24/97 (24%), Positives = 38/97 (39%), Gaps = 1/97 (1%)

Query: 5   RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
                +E    L V NL +  +  D++ +F   G +    +  DR +  S G A V F  
Sbjct: 80  GGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFER 138

Query: 65  KRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRS 101
           + DA  A+    G  LDGR + +Q+            
Sbjct: 139 RADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHH 175

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 59.6 bits (145), Expect = 1e-12
 Identities = 22/95 (23%), Positives = 36/95 (37%), Gaps = 8/95 (8%)

Query: 11  EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
            G+ S+ V           L   F   G V  + + +D+       FA V   D   A +
Sbjct: 6   SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDK-----GVFAIVEMGDV-GARE 59

Query: 71  ALDAMDGRMLDGRELRVQMA--RYGRPPSSSRSRG 103
           A+ +     L G  LRV+    +  + P+S   +G
Sbjct: 60  AVLSQSQHSLGGHRLRVRPREQKEFQSPASKSPKG 94

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 58.6 bits (142), Expect = 2e-12
 Identities = 15/74 (20%), Positives = 28/74 (37%), Gaps = 2/74 (2%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          +       T DD++   E  G+V +I + R    +  +G  FV F     A+  +    G
Sbjct: 16 IKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFV-ETPG 73

Query: 78 RMLDGRELRVQMAR 91
          +     +L +    
Sbjct: 74 QKYKETDLLILFKD 87

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 57.2 bits (139), Expect = 6e-12
 Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 7/73 (9%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V   T   T ++L++ F + GEV D++IP+       R FAFV F D + A+      + 
Sbjct: 16 VGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQSLC--GED 68

Query: 78 RMLDGRELRVQMA 90
           ++ G  + +  A
Sbjct: 69 LIIKGISVHISNA 81

>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 = 59.8 bits (144), Expect = 6e-12
 Identities = 16/90 (17%), Positives = 31/90 (34%), Gaps = 2/90 (2%)

Query: 1   MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
                         S+ +       T DD++   E  G+V +I + R    +  +G  FV
Sbjct: 97  PEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFV 155

Query: 61  RFFDKRDAEDALDAMDGRMLDGRELRVQMA 90
            F     A+  ++   G+     +L +   
Sbjct: 156 VFDSIESAKKFVETP-GQKYKETDLLILFK 184

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 58.5 bits (141), Expect = 6e-12
 Identities = 23/91 (25%), Positives = 42/91 (46%), Gaps = 6/91 (6%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
           V+NL Y  T D L ++F + G V  I      FT+ ++  A +++ D   A+ A  ++DG
Sbjct: 33  VENLFYPVTLDVLHQIFSKFGTVLKIIT----FTKNNQFQALLQYADPVSAQHAKLSLDG 88

Query: 78  RML--DGRELRVQMARYGRPPSSSRSRGGRD 106
           + +      LR+  ++         +   RD
Sbjct: 89  QNIYNACCTLRIDFSKLTSLNVKYNNDKSRD 119

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 56.9 bits (137), Expect = 2e-11
 Identities = 12/61 (19%), Positives = 29/61 (47%), Gaps = 6/61 (9%)

Query: 20 NLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRM 79
           L    + + L  V E+CG V  + +P ++       ++F R+    +++ A   ++G+ 
Sbjct: 34 GLGNGVSRNQLLPVLEKCGLVDALLMPPNK------PYSFARYRTTEESKRAYVTLNGKE 87

Query: 80 L 80
          +
Sbjct: 88 V 88

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 56.2 bits (136), Expect = 2e-11
 Identities = 18/84 (21%), Positives = 34/84 (40%), Gaps = 5/84 (5%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          ++K+    +  T  ++         V  I I R+       G+ FV F ++ + + AL  
Sbjct: 12 TVKLRGAPFNVTEKNVMEFLAPLKPV-AIRIVRNAHGN-KTGYIFVDFSNEEEVKQALK- 68

Query: 75 MDGRMLDGRELRVQMARYGRPPSS 98
           +   + GR + V   +    PSS
Sbjct: 69 CNREYMGGRYIEVFREK--SGPSS 90

>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 = 56.0 bits (135), Expect = 3e-11
 Identities = 16/91 (17%), Positives = 30/91 (32%), Gaps = 11/91 (12%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM-- 75
           V  L       DL    E+ G +  + +         +  A V F +   A++ +     
Sbjct: 20  VRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAAD 73

Query: 76  DGRMLDGRELRVQMARY---GRPPSSSRSRG 103
               + G++     +      RP +S  S G
Sbjct: 74  VPVYIAGQQAFFNYSTSKRITRPGNSGPSSG 104

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 55.4 bits (134), Expect = 4e-11
 Identities = 21/78 (26%), Positives = 36/78 (46%), Gaps = 3/78 (3%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERC-GEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
          SL V +LT       L   F +         +  D+ T  S+G+ FV+F D+ + + AL 
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALT 69

Query: 74 AMDGRM-LDGRELRVQMA 90
             G + L  + +R+ +A
Sbjct: 70 ECQGAVGLGSKPVRLSVA 87

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 54.4 bits (131), Expect = 8e-11
 Identities = 17/83 (20%), Positives = 32/83 (38%), Gaps = 11/83 (13%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPR-----DRFTRESRGFAFVRFFDKRDAEDAL 72
          V N+ +  T + +   F     +G +              + + FAF+ F    +   A+
Sbjct: 11 VGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM 70

Query: 73 DAMDGRMLDGRELRVQMARYGRP 95
           A DG +  G+ L++      RP
Sbjct: 71 -AFDGIIFQGQSLKI-----RRP 87

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 54.8 bits (132), Expect = 1e-10
 Identities = 21/97 (21%), Positives = 39/97 (40%), Gaps = 3/97 (3%)

Query: 8   PRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEV-GDIYIPRDRFTRESRGFAFVRFFDKR 66
           P       +++  L +  + +++ + F     V   + +P D   R S G AFV+F  + 
Sbjct: 10  PDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGR-STGEAFVQFASQE 68

Query: 67  DAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRG 103
            AE AL       +  R + +  +      +S  S G
Sbjct: 69  IAEKALK-KHKERIGHRYIEIFKSSRAEVRTSGPSSG 104

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 55.9 bits (134), Expect = 1e-10
 Identities = 23/93 (24%), Positives = 43/93 (46%), Gaps = 6/93 (6%)

Query: 16  LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
           + V+NL Y  T D L ++F + G V  I      FT+ ++  A +++ D   A+ A  ++
Sbjct: 49  IIVENLFYPVTLDVLHQIFSKFGTVLKII----TFTKNNQFQALLQYADPVSAQHAKLSL 104

Query: 76  DGRML--DGRELRVQMARYGRPPSSSRSRGGRD 106
           DG+ +      LR+  ++         +   RD
Sbjct: 105 DGQNIYNACCTLRIDFSKLTSLNVKYNNDKSRD 137

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 53.2 bits (128), Expect = 4e-10
 Identities = 18/72 (25%), Positives = 29/72 (40%), Gaps = 3/72 (4%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          + +  L YR T +D+   F     +  ++I      R   G A V F    DA  A+ A 
Sbjct: 18 VHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGR-VTGEADVEFATHEDAVAAM-AK 74

Query: 76 DGRMLDGRELRV 87
          D   +  R + +
Sbjct: 75 DKANMQHRYVEL 86

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3 Length = 104

 Score = 52.9 bits (127), Expect = 4e-10
 Identities = 13/61 (21%), Positives = 30/61 (49%), Gaps = 1/61 (1%)

Query: 28  DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV 87
           +    + E+ GEV ++ +  +       G  +V+F  + DAE A+  ++ R  +G+ +  
Sbjct: 42  EVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHA 100

Query: 88  Q 88
           +
Sbjct: 101 E 101

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 52.5 bits (126), Expect = 8e-10
 Identities = 21/118 (17%), Positives = 39/118 (33%), Gaps = 11/118 (9%)

Query: 1   MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEV-GDIYIPRDRFTRESRGFAF 59
               R     E    + +  L +      +   F++   V   IYI      + + G  F
Sbjct: 13  QKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGK-ATGEGF 71

Query: 60  VRFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSR 117
           V F ++ D + AL     + +  R ++V           ++       D  R R +S 
Sbjct: 72  VEFRNEADYKAAL-CRHKQYMGNRFIQVHP--------ITKKGMLEKIDMIRKRLQSG 120

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 52.2 bits (125), Expect = 9e-10
 Identities = 14/107 (13%), Positives = 37/107 (34%), Gaps = 13/107 (12%)

Query: 1   MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
                 P R+     + +  L    T  ++  +    G+V ++ + +       +  AF+
Sbjct: 9   HHGSGVPSRV-----IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFI 57

Query: 61  RFFDKRDAEDALDA--MDGRMLDGRELRVQMARYGRPPSSSRSRGGR 105
               +  A   ++       +L G+ + +Q + +    + S     R
Sbjct: 58  EMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTDSSPNQAR 104

>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 = 52.2 bits (125), Expect = 1e-09
 Identities = 22/112 (19%), Positives = 37/112 (33%), Gaps = 15/112 (13%)

Query: 5   RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERC---GEVGDIYIPRDRFTRESRGFAFVR 61
              P       +K+  L +  + +D++     C     V  ++    R  R   G AFV 
Sbjct: 9   MLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGR-QSGEAFVE 67

Query: 62  FFDKRDAEDALDAMDGRMLDGRELRV----------QMARYGRPPSSSRSRG 103
              + D + AL   D   +  R + V           +   G   +S  S G
Sbjct: 68  LESEDDVKLAL-KKDRESMGHRYIEVFKSHRTEMDWVLKHSGPNSASGPSSG 118

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 52.2 bits (125), Expect = 1e-09
 Identities = 20/91 (21%), Positives = 35/91 (38%), Gaps = 3/91 (3%)

Query: 1   MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEV-GDIYIPRDRFTRESRGFAF 59
           M  G           +++  L +  T +++ + F     V   I +P D   +   G AF
Sbjct: 30  MGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGK-ITGEAF 88

Query: 60  VRFFDKRDAEDALDAMDGRMLDGRELRVQMA 90
           V+F  +  AE AL       +  R + V  +
Sbjct: 89  VQFASQELAEKALG-KHKERIGHRYIEVFKS 118

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 51.7 bits (124), Expect = 1e-09
 Identities = 30/116 (25%), Positives = 38/116 (32%), Gaps = 8/116 (6%)

Query: 4   GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFF 63
              PP       + V  L    +  DL+      G+V    + RD       G   V F 
Sbjct: 7   RYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFV 59

Query: 64  DKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRDR 119
            K D   A+  +D       E      R  +         GR R R R RSRSR R
Sbjct: 60  RKEDMTYAVRKLDNTKFRSHEGETAYIRV-KVDGPRSPSYGRSRSRSRSRSRSRSR 114

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 51.7 bits (124), Expect = 1e-09
 Identities = 25/116 (21%), Positives = 32/116 (27%), Gaps = 12/116 (10%)

Query: 2   SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
                PP       + V  L    +  DL+      G+V    + RD       G   V 
Sbjct: 4   GSSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVE 56

Query: 62  FFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSR 117
           F  K D   A+  +D       E      R       S S G     R R    S 
Sbjct: 57  FVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSYG-----RSRSSGPSS 107

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 50.5 bits (121), Expect = 3e-09
 Identities = 12/77 (15%), Positives = 23/77 (29%), Gaps = 8/77 (10%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          +  L       DL    +  G +  + +         +  A V F D   A +A++    
Sbjct: 26 IRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEFEDVLGACNAVNYAAD 79

Query: 78 R--MLDGRELRVQMARY 92
              + G    V  +  
Sbjct: 80 NQIYIAGHPAFVNYSTS 96

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A Length = 105

 Score = 50.6 bits (121), Expect = 4e-09
 Identities = 22/82 (26%), Positives = 33/82 (40%), Gaps = 4/82 (4%)

Query: 10 IEGMVSLK--VDNLTYRTTPDDLRRVFERCGEVGDIYIPR--DRFTRESRGFAFVRFFDK 65
          +  MV  +  +D+  Y    +D+R    + G V  I IPR  D       G  FV F   
Sbjct: 10 LMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSV 69

Query: 66 RDAEDALDAMDGRMLDGRELRV 87
           D + A+  + GR    R +  
Sbjct: 70 FDCQKAMQGLTGRKFANRVVVT 91

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 50.3 bits (120), Expect = 6e-09
 Identities = 12/90 (13%), Positives = 33/90 (36%), Gaps = 8/90 (8%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD--AM 75
           +  L    T  ++  +    G+V ++ + +       +  AF+    +  A   ++    
Sbjct: 36  IRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTS 89

Query: 76  DGRMLDGRELRVQMARYGRPPSSSRSRGGR 105
              +L G+ + +Q + +    + S     R
Sbjct: 90  VTPVLRGQPIYIQFSNHKELKTDSSPNQAR 119

>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 = 49.8 bits (119), Expect = 7e-09
 Identities = 13/88 (14%), Positives = 33/88 (37%), Gaps = 8/88 (9%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD--AM 75
           +  L    T  ++  +    G+V +I + +       +  AF+    +  A   ++  + 
Sbjct: 20  IRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSA 73

Query: 76  DGRMLDGRELRVQMARYGRPPSSSRSRG 103
               L  + + +Q + +    +S  S G
Sbjct: 74  VTPHLRNQPIYIQYSNHKELKTSGPSSG 101

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 50.6 bits (121), Expect = 7e-09
 Identities = 19/104 (18%), Positives = 35/104 (33%), Gaps = 6/104 (5%)

Query: 4   GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFF 63
                +      + +  L Y+ T +D+   F     V  ++I      R   G A V F 
Sbjct: 37  SEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPV-RVHIEIGPDGR-VTGEADVEFA 94

Query: 64  DKRDAEDALDAMDGRMLDGRELRVQMARYG---RPPSSSRSRGG 104
              +A  A+ + D   +  R + + +           SS+   G
Sbjct: 95  THEEAVAAM-SKDRANMQHRYIELFLNSTTGASNGAYSSQVMQG 137

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 50.3 bits (120), Expect = 7e-09
 Identities = 17/91 (18%), Positives = 33/91 (36%), Gaps = 6/91 (6%)

Query: 4   GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGD----IYIPRDRFTRESRGFAF 59
                  E  V +++  L +  T +++   F +   +      I        R   G AF
Sbjct: 14  VAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGR-PTGDAF 72

Query: 60  VRFFDKRDAEDALDAMDGRMLDGRELRVQMA 90
           V F  +  A++AL      +L  R + +  +
Sbjct: 73  VLFACEEYAQNAL-RKHKDLLGKRYIELFRS 102

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 49.5 bits (118), Expect = 9e-09
 Identities = 15/75 (20%), Positives = 29/75 (38%), Gaps = 5/75 (6%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVG---DIYIPRDRFTRESRGFAFVRFFDKRDAEDAL 72
          ++   L +  T +D+   F  C        I+   +R  +  RG A +    ++D + AL
Sbjct: 14 IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGK-RRGDALIEMESEQDVQKAL 72

Query: 73 DAMDGRMLDGRELRV 87
                 +  R + V
Sbjct: 73 -EKHRMYMGQRYVEV 86

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 112

 Score = 48.9 bits (117), Expect = 2e-08
 Identities = 17/62 (27%), Positives = 29/62 (46%), Gaps = 4/62 (6%)

Query: 28 DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV 87
          +DLR    + G++  + +      R   G A V F D  +A+  +  +DGR   GR++  
Sbjct: 41 EDLRVECSKFGQIRKLLLFD----RHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITA 96

Query: 88 QM 89
          Q 
Sbjct: 97 QA 98

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 48.5 bits (115), Expect = 2e-08
 Identities = 19/89 (21%), Positives = 43/89 (48%), Gaps = 7/89 (7%)

Query: 14 VSLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAE 69
            ++V N+ YR +  +L++     F R G+V  + +       + +  A V+  + +DA 
Sbjct: 10 ADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHT---DYQLKAVVQMENLQDAI 66

Query: 70 DALDAMDGRMLDGRELRVQMARYGRPPSS 98
           A++++    +  +++ V +A     PSS
Sbjct: 67 GAVNSLHRYKIGSKKILVSLATGASGPSS 95

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A Length = 114

 Score = 47.0 bits (112), Expect = 1e-07
 Identities = 15/80 (18%), Positives = 32/80 (40%), Gaps = 6/80 (7%)

Query: 10 IEGMVSLK--VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRD 67
          +  M + +   +        DD+     + G V  IY+ +      ++G  +V+      
Sbjct: 12 LSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDK----NSAQGNVYVKCPSIAA 67

Query: 68 AEDALDAMDGRMLDGRELRV 87
          A  A++A+ GR   G+ +  
Sbjct: 68 AIAAVNALHGRWFAGKMITA 87

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 46.7 bits (111), Expect = 1e-07
 Identities = 14/96 (14%), Positives = 28/96 (29%), Gaps = 3/96 (3%)

Query: 4   GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFF 63
                       + + NL    +  DL+ +                 TR+  G   + F 
Sbjct: 19  SHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTF---SSVNTRDFDGTGALEFP 75

Query: 64  DKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSS 99
            +    +AL+ ++     G  + V+      P   S
Sbjct: 76  SEEILVEALERLNNIEFRGSVITVERDDNPPPIRRS 111

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 46.5 bits (110), Expect = 2e-07
 Identities = 17/90 (18%), Positives = 31/90 (34%), Gaps = 5/90 (5%)

Query: 4   GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGD---IYIPRDRFTRESRGFAFV 60
               P       +K+  L +  + +D++     C        ++    R  R   G AFV
Sbjct: 35  MMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGR-QSGEAFV 93

Query: 61  RFFDKRDAEDALDAMDGRMLDGRELRVQMA 90
               + D + AL   D   +  R + V  +
Sbjct: 94  ELGSEDDVKMALK-KDRESMGHRYIEVFKS 122

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 46.2 bits (109), Expect = 3e-07
 Identities = 21/91 (23%), Positives = 32/91 (35%), Gaps = 7/91 (7%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
           + N  Y  T D L  V    G+V      R    + +   A V F     A+ A  A++G
Sbjct: 30  IQNPLYPITVDVLYTVCNPVGKV-----QRIVIFKRNGIQAMVEFESVLCAQKAKAALNG 84

Query: 78  RMLDGRE--LRVQMARYGRPPSSSRSRGGRD 106
             +      L+++ AR  R           D
Sbjct: 85  ADIYAGCCTLKIEYARPTRLNVIRNDNDSWD 115

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 46.3 bits (109), Expect = 6e-07
 Identities = 18/77 (23%), Positives = 30/77 (38%), Gaps = 6/77 (7%)

Query: 15  SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
           +L   +L        +R VF R G++  I     +         FV+F  + +AE A +A
Sbjct: 145 ALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESK------NCGFVKFKYQANAEFAKEA 198

Query: 75  MDGRMLDGRELRVQMAR 91
           M  + L     +    R
Sbjct: 199 MSNQTLLLPSDKEWDDR 215

>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} PDB: 3us5_A 2dny_A Length = 118

 Score = 44.0 bits (104), Expect = 1e-06
 Identities = 13/64 (20%), Positives = 25/64 (39%), Gaps = 4/64 (6%)

Query: 28  DDLRRVFERCGEVGDIYIPR----DRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGR 83
            ++     + G V  + I +    +    E     FV F    +   A+ A++GR   GR
Sbjct: 40  GEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGR 99

Query: 84  ELRV 87
           ++  
Sbjct: 100 KVVA 103

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 41.9 bits (98), Expect = 8e-06
 Identities = 12/59 (20%), Positives = 25/59 (42%), Gaps = 2/59 (3%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRD--RFTRESRGFAFVRFFDKRDAEDALDA 74
          V  L      D++   F R G +   +  +   +     +G+AF+ F ++   +  +DA
Sbjct: 13 VGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDA 71

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A Length = 105

 Score = 39.4 bits (92), Expect = 5e-05
 Identities = 13/61 (21%), Positives = 24/61 (39%), Gaps = 1/61 (1%)

Query: 28 DDLRRVFERCGEVGDIYIPR-DRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR 86
           + +   E+ G+VG   I        +     F+ F     A  A+  ++GR   GR ++
Sbjct: 28 VETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVVK 87

Query: 87 V 87
           
Sbjct: 88 A 88

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 41.0 bits (95), Expect = 6e-05
 Identities = 20/116 (17%), Positives = 41/116 (35%), Gaps = 10/116 (8%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
           VDN   +   D  + +  +  E+  I + +D  +   R F  +    +   +  ++  + 
Sbjct: 30  VDNFDCKDVQDMPKSILSK-EEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVE--EV 86

Query: 78  RMLDGRELRVQMARYGRPPS-------SSRSRGGRDRDRRRDRSRSRDRRYTRSRS 126
             ++ + L   +    R PS         R R   D       + SR + Y + R 
Sbjct: 87  LRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQ 142

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster} Length = 89

 Score = 37.7 bits (87), Expect = 2e-04
 Identities = 14/79 (17%), Positives = 31/79 (39%), Gaps = 6/79 (7%)

Query: 12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDA 71
          G   L + NLT +     LR +  + G +   +         ++G A  ++  + +A  A
Sbjct: 6  GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKA 59

Query: 72 LDAMDGRMLDGRELRVQMA 90
            A++  +L    +  +  
Sbjct: 60 QMALNNCVLANTTIFAESP 78

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 35.9 bits (82), Expect = 8e-04
 Identities = 15/79 (18%), Positives = 32/79 (40%), Gaps = 9/79 (11%)

Query: 26  TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGREL 85
           + D L R+ ++ GEV ++ +   +      G A V F   + AE A+    G +    + 
Sbjct: 30  SKDVLLRLLQKYGEVLNLVLSSKK-----PGTAVVEFATVKAAELAVQNEVGLV----DN 80

Query: 86  RVQMARYGRPPSSSRSRGG 104
            ++++     P  +     
Sbjct: 81  PLKISWLEGQPQDASGPSS 99

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	158
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.93
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.93
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.92
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.92
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.91
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.91
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.91
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.91
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.91
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.91
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.91
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.91
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.9
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.9
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.9
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.9
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.9
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.9
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.9
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.9
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.9
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.9
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.9
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.9
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.9
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.9
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.9
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.9
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.9
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.89
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.89
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.89
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.89
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.89
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.89
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.89
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.89
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.89
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.89
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.89
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.89
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.89
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.89
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.89
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.89
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.89
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.89
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.89
2div_A	99	TRNA selenocysteine associated protein; structural	99.89
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.89
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.89
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.89
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.89
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.88
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.88
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.88
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.88
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.88
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.88
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.88
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.88
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.88
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.88
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.88
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.88
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.87
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.87
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.87
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.87
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.87
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.87
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.87
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.87
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.87
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.87
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.87
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.87
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.87
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.87
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.87
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.87
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.87
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.87
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.87
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.87
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.87
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.86
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.86
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.86
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.86
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.86
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.86
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.86
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.86
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.86
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.86
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.86
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.86
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.86
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.86
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.86
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.86
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.86
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.86
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.85
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.85
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.85
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.85
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.85
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.85
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.85
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.85
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.85
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.85
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.85
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.85
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.85
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.85
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.85
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.85
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.85
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.85
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.84
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.84
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.74
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.84
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.84
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.84
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.84
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.84
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.84
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.83
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.83
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.83
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.83
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.83
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.83
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.83
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.82
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.82
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.82
1x5p_A	97	Negative elongation factor E; structure genomics,	99.82
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.82
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.82
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.82
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.82
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.82
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.82
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.81
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.81
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.81
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.81
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.81
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.81
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.8
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.8
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.8
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.8
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.8
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.8
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.8
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.79
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.79
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.79
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.78
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.78
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.78
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.78
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.77
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.77
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.77
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.77
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.77
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.77
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.76
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.76
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.76
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.75
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.75
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.74
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.74
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.73
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.73
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.73
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.71
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.71
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.71
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.7
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.69
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.69
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.69
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.69
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.69
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.68
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.68
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.66
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	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
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.65
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.64
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.63
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.61
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.55
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.49
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.42
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.27
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	99.24
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.95
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	98.49
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	98.47
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	98.33
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.25
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	98.23
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	98.17
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	98.05
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	97.55
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	97.18
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	96.85
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	96.72
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	96.36
2g0c_A	76	ATP-dependent RNA helicase DBPA; RNA recognition m	93.5
3lpe_A	92	Putative transcription antitermination protein NU;	84.97
4eyt_A	129	Telomerase associated protein P65; RNA, LA protein	84.16

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

Probab=99.93  E-value=1.9e-25  Score=143.44  Aligned_cols=96  Identities=67%  Similarity=1.111  Sum_probs=89.3

Q ss_pred             CCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccC
Q psy7051           2 SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLD   81 (158)
Q Consensus         2 ~~~~p~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~   81 (158)
                      +++.|++..++..+|||+|||..+++++|+++|++||.|..|.|+.++.++..+|||||+|.+.++|+.|++.||+..|.
T Consensus         2 ~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~   81 (103)
T 2dnm_A            2 SSGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELD   81 (103)
T ss_dssp             CCCCCSSCCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBT
T ss_pred             CCCCCCCCCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEEC
Confidence            46788888899999999999999999999999999999999999999888999999999999999999999999999999


Q ss_pred             CceEEEEeeecCCCCC
Q psy7051          82 GRELRVQMARYGRPPS   97 (158)
Q Consensus        82 g~~i~v~~a~~~~~~~   97 (158)
                      |+.|.|.+++...+..
T Consensus        82 g~~l~V~~a~~~~~~~   97 (103)
T 2dnm_A           82 GRELRVQVARYGRRDL   97 (103)
T ss_dssp             TBCCEEEECSSCCSCC
T ss_pred             CcEEEEEECCcCCCCC
Confidence            9999999998655443

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

Probab=99.93  E-value=1.6e-24  Score=170.80  Aligned_cols=83  Identities=31%  Similarity=0.526  Sum_probs=78.9

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      ..+.++|||+|||+.|++++|+++|++||.|+.|.|+.++.++.++|||||+|.+.++|++||+.|||..|+|+.|.|.+
T Consensus        99 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~  178 (437)
T 3pgw_S           99 GDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  178 (437)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34568999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             eec
Q psy7051          90 ARY   92 (158)
Q Consensus        90 a~~   92 (158)
                      +..
T Consensus       179 a~~  181 (437)
T 3pgw_S          179 ERG  181 (437)
T ss_pred             eCC
Confidence            974

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

Probab=99.92  E-value=6.9e-25  Score=140.12  Aligned_cols=80  Identities=33%  Similarity=0.549  Sum_probs=77.0

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeec
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARY   92 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~   92 (158)
                      .++|||+|||..+++++|+++|++||+|..|.++.++.++.++|||||+|.+.++|+.|++.|||..|.|+.|.|++|++
T Consensus        19 gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~AkP   98 (99)
T 4fxv_A           19 GTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARP   98 (99)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCB
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            47899999999999999999999999999999999998999999999999999999999999999999999999999973

>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=99.92  E-value=1.6e-24  Score=143.88  Aligned_cols=90  Identities=26%  Similarity=0.416  Sum_probs=82.5

Q ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEE
Q psy7051           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR   86 (158)
Q Consensus         7 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~   86 (158)
                      |....+..+|||+|||..+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|+.||+.||+..|.|+.|.
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            33455668999999999999999999999999999999999988999999999999999999999999999999999999


Q ss_pred             EEeeecCCCC
Q psy7051          87 VQMARYGRPP   96 (158)
Q Consensus        87 v~~a~~~~~~   96 (158)
                      |+++....+.
T Consensus        96 v~~a~~~~~~  105 (126)
T 3ex7_B           96 VDWCFVRGPP  105 (126)
T ss_dssp             EEESEESSSC
T ss_pred             EEEecCCCCC
Confidence            9999865444

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

Probab=99.91  E-value=1.5e-23  Score=133.66  Aligned_cols=90  Identities=20%  Similarity=0.323  Sum_probs=81.9

Q ss_pred             CCCCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCce
Q psy7051           5 RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRE   84 (158)
Q Consensus         5 ~p~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~   84 (158)
                      .+.....+..+|||+|||..+++++|+++|++||.|..|.|+.++.++..+|||||+|.+.++|+.|++ ||+..|.|+.
T Consensus         2 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~   80 (99)
T 2dgs_A            2 SSGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKK   80 (99)
T ss_dssp             CCCCCCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCB
T ss_pred             CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeE
Confidence            344455677899999999999999999999999999999999998889999999999999999999998 9999999999


Q ss_pred             EEEEeeecCCC
Q psy7051          85 LRVQMARYGRP   95 (158)
Q Consensus        85 i~v~~a~~~~~   95 (158)
                      |.|.+++....
T Consensus        81 l~V~~a~~~~~   91 (99)
T 2dgs_A           81 VEVKRAEPRDS   91 (99)
T ss_dssp             CEEEECCCCCC
T ss_pred             EEEEECCCCcc
Confidence            99999985443

>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=99.91  E-value=1.8e-23  Score=134.59  Aligned_cols=90  Identities=28%  Similarity=0.426  Sum_probs=82.9

Q ss_pred             CCCCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCce
Q psy7051           5 RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRE   84 (158)
Q Consensus         5 ~p~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~   84 (158)
                      .++....+..+|||+|||..+++++|+++|++||.|..|.|+.++.++..+|||||+|.+.++|+.|++.||+..|.|+.
T Consensus         7 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   86 (105)
T 1x5u_A            7 GPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKP   86 (105)
T ss_dssp             CCCCCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCB
T ss_pred             CCcccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeE
Confidence            34455667789999999999999999999999999999999999889999999999999999999999999999999999


Q ss_pred             EEEEeeecCC
Q psy7051          85 LRVQMARYGR   94 (158)
Q Consensus        85 i~v~~a~~~~   94 (158)
                      |.|.+++...
T Consensus        87 l~v~~a~~~~   96 (105)
T 1x5u_A           87 IRVNKASAHN   96 (105)
T ss_dssp             CEEEETTTTS
T ss_pred             EEEEECCCCC
Confidence            9999998543

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

Probab=99.91  E-value=1.2e-23  Score=134.99  Aligned_cols=91  Identities=31%  Similarity=0.531  Sum_probs=83.5

Q ss_pred             CCCCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCce
Q psy7051           5 RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRE   84 (158)
Q Consensus         5 ~p~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~   84 (158)
                      .|....++..+|||+|||..+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|+.|++.||+..|.|+.
T Consensus         7 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   86 (103)
T 2cq0_A            7 GPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLI   86 (103)
T ss_dssp             CSCCCCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEE
T ss_pred             CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcE
Confidence            34455667799999999999999999999999999999999999889999999999999999999999999999999999


Q ss_pred             EEEEeeecCCC
Q psy7051          85 LRVQMARYGRP   95 (158)
Q Consensus        85 i~v~~a~~~~~   95 (158)
                      |.|.+++....
T Consensus        87 l~v~~a~~~~~   97 (103)
T 2cq0_A           87 LNVEWAKPSTN   97 (103)
T ss_dssp             CEEEESSCCCC
T ss_pred             EEEEECCCCCC
Confidence            99999985443

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

Probab=99.91  E-value=9.8e-24  Score=137.21  Aligned_cols=80  Identities=20%  Similarity=0.252  Sum_probs=77.1

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeec
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARY   92 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~   92 (158)
                      ..+|||+||++.+++++|+++|++||.|..|.|+.++.+++++|||||+|.+.++|+.|++.|||..|.|+.|.|+++..
T Consensus         6 ~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a~~   85 (110)
T 3s8s_A            6 LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDIK   85 (110)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECST
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCC
Confidence            47899999999999999999999999999999999999999999999999999999999999999999999999999863

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

Probab=99.91  E-value=2.4e-24  Score=144.92  Aligned_cols=97  Identities=84%  Similarity=1.408  Sum_probs=89.9

Q ss_pred             CCCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCccc
Q psy7051           1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRML   80 (158)
Q Consensus         1 ~~~~~p~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i   80 (158)
                      |+++.|++..++..+|||+|||..+++++|+++|++||.|..|.|+.++.++..+|||||+|.+.++|+.||+.||+..|
T Consensus        35 ~~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i  114 (135)
T 2lea_A           35 MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVL  114 (135)
T ss_dssp             CCSCCSCSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCS
T ss_pred             CCcCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEE
Confidence            46788888888899999999999999999999999999999999999988899999999999999999999999999999


Q ss_pred             CCceEEEEeeecCCCCC
Q psy7051          81 DGRELRVQMARYGRPPS   97 (158)
Q Consensus        81 ~g~~i~v~~a~~~~~~~   97 (158)
                      .|+.|.|.+++...++.
T Consensus       115 ~g~~l~V~~a~~~~~~~  131 (135)
T 2lea_A          115 DGRELRVQMARYGRPPD  131 (135)
T ss_dssp             SSSCCEEEECCCCCCCT
T ss_pred             CCEEEEEEECCCCCCCc
Confidence            99999999998655443

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.91  E-value=3.6e-24  Score=135.73  Aligned_cols=85  Identities=25%  Similarity=0.418  Sum_probs=78.4

Q ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCc--eEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCc----ccC
Q psy7051           8 PRIEGMVSLKVDNLTYRTTPDDLRRVFERCGE--VGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGR----MLD   81 (158)
Q Consensus         8 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~--i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~----~i~   81 (158)
                      ...+...||||+|||+.+|+++|+++|++||.  |..|.++.++.++.++|||||+|.+.++|+.|++.|||.    .|+
T Consensus         4 ~~~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~   83 (95)
T 2lkz_A            4 HHHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKID   83 (95)
T ss_dssp             CSSCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEET
T ss_pred             ccCCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceEC
Confidence            44567899999999999999999999999995  678999999999999999999999999999999999997    489


Q ss_pred             CceEEEEeeec
Q psy7051          82 GRELRVQMARY   92 (158)
Q Consensus        82 g~~i~v~~a~~   92 (158)
                      |+.|.|+||+.
T Consensus        84 Gr~i~V~~Aks   94 (95)
T 2lkz_A           84 GKTIGVDFAKS   94 (95)
T ss_dssp             TEEEEEEECCC
T ss_pred             CEEEEEEEccC
Confidence            99999999974

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

Probab=99.91  E-value=3.5e-23  Score=130.87  Aligned_cols=83  Identities=34%  Similarity=0.531  Sum_probs=78.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      +..+|||+|||..+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|+.|++.||+..|.|+.|.|.+++
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   83 (95)
T 2dnz_A            4 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVT   83 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEESS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEcc
Confidence            45889999999999999999999999999999999998889999999999999999999999999999999999999998


Q ss_pred             cCC
Q psy7051          92 YGR   94 (158)
Q Consensus        92 ~~~   94 (158)
                      ...
T Consensus        84 ~~~   86 (95)
T 2dnz_A           84 ERL   86 (95)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            543

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

Probab=99.91  E-value=3.5e-23  Score=132.56  Aligned_cols=86  Identities=36%  Similarity=0.607  Sum_probs=80.3

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEE
Q psy7051           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ   88 (158)
Q Consensus         9 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~   88 (158)
                      ..++..+|||+|||..+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|+.|++.||+..|.|+.|.|.
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            34566899999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             eeecCC
Q psy7051          89 MARYGR   94 (158)
Q Consensus        89 ~a~~~~   94 (158)
                      +++...
T Consensus        88 ~a~~~~   93 (102)
T 1x5s_A           88 QAGKSS   93 (102)
T ss_dssp             EEECCC
T ss_pred             ECCCCC
Confidence            998544

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

Probab=99.90  E-value=2.3e-23  Score=132.79  Aligned_cols=90  Identities=24%  Similarity=0.296  Sum_probs=82.5

Q ss_pred             CCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEE--------EEEccCCCCCCcccEEEEEEcCHHHHHHHHH
Q psy7051           2 SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGD--------IYIPRDRFTRESRGFAFVRFFDKRDAEDALD   73 (158)
Q Consensus         2 ~~~~p~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~--------v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~   73 (158)
                      +...+++...+..+|||+|||..+++++|+++|++||.|..        |.++.++.++..+|||||+|.+.++|+.|++
T Consensus         2 ~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~   81 (99)
T 2la6_A            2 GHHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAID   81 (99)
T ss_dssp             CSSCSCCSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHH
Confidence            34455556667799999999999999999999999999999        9999998899999999999999999999999


Q ss_pred             HhCCcccCCceEEEEeee
Q psy7051          74 AMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        74 ~l~g~~i~g~~i~v~~a~   91 (158)
                      .|||..|.|+.|.|++|+
T Consensus        82 ~l~g~~~~g~~l~V~~A~   99 (99)
T 2la6_A           82 WFDGKEFSGNPIKVSFAT   99 (99)
T ss_dssp             HHTTCBSSSSBCEEEECC
T ss_pred             HhCCCEeCCcEEEEEecC
Confidence            999999999999999874

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

Probab=99.90  E-value=4.9e-23  Score=138.90  Aligned_cols=87  Identities=30%  Similarity=0.494  Sum_probs=80.8

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      .+...+|||+|||..+++++|+++|+.||.|..|.|+.++.++..+|||||+|.+.++|+.|++.||+..|.|+.|.|.+
T Consensus        39 ~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  118 (139)
T 1u6f_A           39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            34568999999999999999999999999999999999988899999999999999999999999999999999999999


Q ss_pred             eecCCCC
Q psy7051          90 ARYGRPP   96 (158)
Q Consensus        90 a~~~~~~   96 (158)
                      ++....+
T Consensus       119 a~~~~~~  125 (139)
T 1u6f_A          119 AASGHQR  125 (139)
T ss_dssp             SSCCCCC
T ss_pred             CCCCCCC
Confidence            9865444

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

Probab=99.90  E-value=6e-23  Score=130.78  Aligned_cols=86  Identities=31%  Similarity=0.562  Sum_probs=80.3

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      ..+..+|||+|||..+++++|+++|++||.|..|.|+.+..++..+|||||+|.+.++|+.|++.||+..|.|+.|.|.+
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            34568999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             eecCCC
Q psy7051          90 ARYGRP   95 (158)
Q Consensus        90 a~~~~~   95 (158)
                      ++....
T Consensus        85 a~~~~~   90 (99)
T 1whw_A           85 STIKKE   90 (99)
T ss_dssp             CCCCST
T ss_pred             cCCCcc
Confidence            986543

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

Probab=99.90  E-value=3e-23  Score=133.76  Aligned_cols=90  Identities=23%  Similarity=0.351  Sum_probs=82.4

Q ss_pred             CCCCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCce
Q psy7051           5 RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRE   84 (158)
Q Consensus         5 ~p~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~   84 (158)
                      .++....+..+|||+|||..+++++|+++|++||.|..|.|+.++.++..+|||||+|.+.++|+.|++.|||..|.|+.
T Consensus        15 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   94 (106)
T 1p27_B           15 PGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQP   94 (106)
T ss_dssp             CCBCCBTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSB
T ss_pred             CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcE
Confidence            34444556789999999999999999999999999999999999889999999999999999999999999999999999


Q ss_pred             EEEEeeecCC
Q psy7051          85 LRVQMARYGR   94 (158)
Q Consensus        85 i~v~~a~~~~   94 (158)
                      |.|.+++...
T Consensus        95 l~V~~a~~~~  104 (106)
T 1p27_B           95 ISVDWCFVRG  104 (106)
T ss_dssp             CEEEESEESS
T ss_pred             EEEEeecCCC
Confidence            9999998543

>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=99.90  E-value=3.1e-23  Score=142.52  Aligned_cols=85  Identities=27%  Similarity=0.550  Sum_probs=79.9

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      .++..+|||+|||..+++++|+++|++||.|..|.|+.++.++..+|||||+|.+.++|+.||+.||+..|.|+.|.|++
T Consensus        36 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  115 (156)
T 1h2v_Z           36 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDW  115 (156)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            34568999999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             eecCC
Q psy7051          90 ARYGR   94 (158)
Q Consensus        90 a~~~~   94 (158)
                      ++...
T Consensus       116 a~~~~  120 (156)
T 1h2v_Z          116 DAGFK  120 (156)
T ss_dssp             ESCCC
T ss_pred             CCCCC
Confidence            98543

>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=99.90  E-value=4e-23  Score=133.15  Aligned_cols=89  Identities=21%  Similarity=0.368  Sum_probs=81.5

Q ss_pred             CCCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCccc---CC
Q psy7051           6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRML---DG   82 (158)
Q Consensus         6 p~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i---~g   82 (158)
                      ++....+..+|||+|||..+++++|+++|++||.|..|.|+.++.++..+|||||+|.+.++|+.|++.||+..+   .|
T Consensus         6 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g   85 (106)
T 2dgp_A            6 SGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMN   85 (106)
T ss_dssp             CSCCCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCS
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCC
Confidence            444556678999999999999999999999999999999999988899999999999999999999999999987   88


Q ss_pred             ceEEEEeeecCC
Q psy7051          83 RELRVQMARYGR   94 (158)
Q Consensus        83 ~~i~v~~a~~~~   94 (158)
                      +.|.|.+++...
T Consensus        86 ~~l~v~~a~~~~   97 (106)
T 2dgp_A           86 RPIQVKPADSES   97 (106)
T ss_dssp             SCCEEEECCCCS
T ss_pred             ceEEEEECCccc
Confidence            999999998543

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

Probab=99.90  E-value=5.5e-23  Score=132.67  Aligned_cols=91  Identities=27%  Similarity=0.506  Sum_probs=82.4

Q ss_pred             CCCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccC-CCCCCcccEEEEEEcCHHHHHHHHHHh-CCcccCCc
Q psy7051           6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRD-RFTRESRGFAFVRFFDKRDAEDALDAM-DGRMLDGR   83 (158)
Q Consensus         6 p~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~-~~~~~~~g~afV~f~~~~~a~~a~~~l-~g~~i~g~   83 (158)
                      +++......+|||+|||..+++++|+++|++||.|..|.|+.+ ..++..+|||||+|.+.++|+.|++.| |+..|.|+
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~   87 (107)
T 2cph_A            8 QVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGR   87 (107)
T ss_dssp             SSCCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSC
T ss_pred             ccccCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCC
Confidence            3444566789999999999999999999999999999999988 778999999999999999999999999 99999999


Q ss_pred             eEEEEeeecCCCC
Q psy7051          84 ELRVQMARYGRPP   96 (158)
Q Consensus        84 ~i~v~~a~~~~~~   96 (158)
                      .|.|.+++.....
T Consensus        88 ~l~v~~a~~~~~~  100 (107)
T 2cph_A           88 RLVLEWADSEVTV  100 (107)
T ss_dssp             BCEEEECCCCCCC
T ss_pred             EEEEEeCCCCCCC
Confidence            9999999865443

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

Probab=99.90  E-value=1.4e-22  Score=132.44  Aligned_cols=89  Identities=31%  Similarity=0.561  Sum_probs=81.9

Q ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEE
Q psy7051           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR   86 (158)
Q Consensus         7 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~   86 (158)
                      .....+..+|||+|||..+++++|+++|++||.|..|.|+.++.++..+|||||+|.+.++|+.||+.||+..|.|+.|.
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            34455678999999999999999999999999999999999988999999999999999999999999999999999999


Q ss_pred             EEeeecCCC
Q psy7051          87 VQMARYGRP   95 (158)
Q Consensus        87 v~~a~~~~~   95 (158)
                      |.+++....
T Consensus        89 V~~a~~~~~   97 (115)
T 2dgo_A           89 TNWATRKPP   97 (115)
T ss_dssp             EEESSCCCC
T ss_pred             EEEccCCCC
Confidence            999985543

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

Probab=99.90  E-value=3.4e-23  Score=135.44  Aligned_cols=87  Identities=24%  Similarity=0.285  Sum_probs=80.5

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEE
Q psy7051           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ   88 (158)
Q Consensus         9 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~   88 (158)
                      ..++..+|||+|||..+++++|+++|++||.|..|.|+.++.++..+|||||+|.+.++|+.||+.||+..|.|+.|.|.
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            34456899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             eeecCCC
Q psy7051          89 MARYGRP   95 (158)
Q Consensus        89 ~a~~~~~   95 (158)
                      +++....
T Consensus       101 ~a~~~~~  107 (115)
T 2cpz_A          101 LKRSKND  107 (115)
T ss_dssp             CCCCSCC
T ss_pred             EcCCCCc
Confidence            9985443

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

Probab=99.90  E-value=2.3e-23  Score=133.42  Aligned_cols=88  Identities=35%  Similarity=0.417  Sum_probs=81.1

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEE
Q psy7051           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ   88 (158)
Q Consensus         9 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~   88 (158)
                      ...+..+|||+|||..+++++|+++|++||.|..|.|+.++.++..+|||||+|.+.++|+.|++.||+..|.|+.|.|.
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            34566899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             eeecCCCC
Q psy7051          89 MARYGRPP   96 (158)
Q Consensus        89 ~a~~~~~~   96 (158)
                      +++.....
T Consensus        88 ~a~~~~~~   95 (102)
T 2cqb_A           88 LAKPMRIK   95 (102)
T ss_dssp             ECCCCCCC
T ss_pred             eCCCCCCC
Confidence            99855433

>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=99.90  E-value=7.4e-23  Score=132.87  Aligned_cols=88  Identities=26%  Similarity=0.458  Sum_probs=81.5

Q ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhC------Cccc
Q psy7051           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD------GRML   80 (158)
Q Consensus         7 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~------g~~i   80 (158)
                      +....+..+|||+|||+.+++++|+++|.+||.|..|.|+.++.++..+|||||+|.+.++|+.|++.||      +..|
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~   88 (111)
T 1x4h_A            9 PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKL   88 (111)
T ss_dssp             CCCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEES
T ss_pred             CCcCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEE
Confidence            4455667899999999999999999999999999999999998899999999999999999999999999      9999


Q ss_pred             CCceEEEEeeecCC
Q psy7051          81 DGRELRVQMARYGR   94 (158)
Q Consensus        81 ~g~~i~v~~a~~~~   94 (158)
                      .|+.|.|.++....
T Consensus        89 ~g~~l~v~~a~~~~  102 (111)
T 1x4h_A           89 DGRQLKVDLAVTRD  102 (111)
T ss_dssp             SSCEEEEECCCCCC
T ss_pred             cCEEEEEEECCCCc
Confidence            99999999998543

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

Probab=99.90  E-value=2.8e-23  Score=131.56  Aligned_cols=85  Identities=27%  Similarity=0.361  Sum_probs=79.1

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEE-EEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDI-YIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v-~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      .+..+|||+|||..+++++|+++|++||.|..| .|+.++.++..+|||||+|.+.++|+.|++.||+..|.|+.|.|.+
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            345899999999999999999999999999999 9999988999999999999999999999999999999999999999


Q ss_pred             eecCCC
Q psy7051          90 ARYGRP   95 (158)
Q Consensus        90 a~~~~~   95 (158)
                      +.....
T Consensus        83 a~~~~~   88 (96)
T 1x5t_A           83 AFKKDS   88 (96)
T ss_dssp             SCCCCC
T ss_pred             ecccCC
Confidence            985443

>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=99.90  E-value=7e-23  Score=134.33  Aligned_cols=82  Identities=32%  Similarity=0.567  Sum_probs=77.4

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      +...+|||+|||..+++++|+++|++||.|..|.|+.+. ++..+|||||+|.+.++|+.|++.|||..|.|+.|.|+++
T Consensus         5 ~~~~~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            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQA   83 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            455899999999999999999999999999999999987 8899999999999999999999999999999999999999


Q ss_pred             ecC
Q psy7051          91 RYG   93 (158)
Q Consensus        91 ~~~   93 (158)
                      +..
T Consensus        84 ~~~   86 (116)
T 2fy1_A           84 KKP   86 (116)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            844

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

Probab=99.90  E-value=4.9e-23  Score=129.92  Aligned_cols=86  Identities=31%  Similarity=0.512  Sum_probs=79.5

Q ss_pred             CCCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceE
Q psy7051           6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGREL   85 (158)
Q Consensus         6 p~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i   85 (158)
                      +....++..+|||+|||..+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|+.|++.||+..|.|+.|
T Consensus         9 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   88 (94)
T 2e5h_A            9 SGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVI   88 (94)
T ss_dssp             CCSCCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEE
T ss_pred             CCCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEE
Confidence            33444556899999999999999999999999999999999998889999999999999999999999999999999999


Q ss_pred             EEEeee
Q psy7051          86 RVQMAR   91 (158)
Q Consensus        86 ~v~~a~   91 (158)
                      .|++|+
T Consensus        89 ~v~~ak   94 (94)
T 2e5h_A           89 KASIAI   94 (94)
T ss_dssp             EEEECC
T ss_pred             EEEecC
Confidence            999985

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

Probab=99.90  E-value=4.9e-23  Score=130.14  Aligned_cols=86  Identities=38%  Similarity=0.535  Sum_probs=79.9

Q ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEE
Q psy7051           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR   86 (158)
Q Consensus         7 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~   86 (158)
                      ....++..+|||+|||..+++++|+++|++||.|..|.++.++.++..+|||||+|.+.++|+.|++.||+..|.|+.|.
T Consensus         9 ~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   88 (95)
T 2cqc_A            9 RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR   88 (95)
T ss_dssp             CCSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            33445668999999999999999999999999999999999988899999999999999999999999999999999999


Q ss_pred             EEeeec
Q psy7051          87 VQMARY   92 (158)
Q Consensus        87 v~~a~~   92 (158)
                      |++++.
T Consensus        89 v~~a~~   94 (95)
T 2cqc_A           89 VSGPSS   94 (95)
T ss_dssp             EECCSC
T ss_pred             EEecCC
Confidence            999874

>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=99.90  E-value=6.8e-23  Score=132.95  Aligned_cols=89  Identities=25%  Similarity=0.339  Sum_probs=82.0

Q ss_pred             CCCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceE
Q psy7051           6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGREL   85 (158)
Q Consensus         6 p~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i   85 (158)
                      ++....+..+|||+|||..+++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|+.|++.|||..|.|+.|
T Consensus        19 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l   98 (110)
T 1oo0_B           19 GPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTI   98 (110)
T ss_dssp             CBCCBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEE
Confidence            34445667899999999999999999999999999999999998899999999999999999999999999999999999


Q ss_pred             EEEeeecCC
Q psy7051          86 RVQMARYGR   94 (158)
Q Consensus        86 ~v~~a~~~~   94 (158)
                      .|.++....
T Consensus        99 ~V~~a~~~~  107 (110)
T 1oo0_B           99 QVDWCFVKG  107 (110)
T ss_dssp             EEEESEESS
T ss_pred             EEEEcccCC
Confidence            999998544

>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=99.90  E-value=8.7e-23  Score=131.24  Aligned_cols=87  Identities=20%  Similarity=0.368  Sum_probs=79.1

Q ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCC-CCcccEEEEEEcCHHHHHHHHHHhCCcccCCceE
Q psy7051           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFT-RESRGFAFVRFFDKRDAEDALDAMDGRMLDGREL   85 (158)
Q Consensus         7 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~-~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i   85 (158)
                      +....+..+|||+|||..+++++|+++|++|| |..|.|+.++.+ +..+|||||+|.+.++|+.|| .||+..|.|+.|
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l   86 (104)
T 1wi8_A            9 RLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRI   86 (104)
T ss_dssp             CCCSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEEC
T ss_pred             CCCCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEE
Confidence            33445668999999999999999999999999 999999999877 889999999999999999999 999999999999


Q ss_pred             EEEeeecCCC
Q psy7051          86 RVQMARYGRP   95 (158)
Q Consensus        86 ~v~~a~~~~~   95 (158)
                      .|.+++....
T Consensus        87 ~V~~a~~~~~   96 (104)
T 1wi8_A           87 RVDVADQAQD   96 (104)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEEccCCCC
Confidence            9999985443

>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=99.89  E-value=6.1e-23  Score=127.13  Aligned_cols=81  Identities=37%  Similarity=0.484  Sum_probs=77.0

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      .+..+|||+|||..+++++|+++|++||.|..|.++.++.++..+|||||+|.+.++|+.|++.|||..|.|+.|.|+++
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            35589999999999999999999999999999999999889999999999999999999999999999999999999998


Q ss_pred             e
Q psy7051          91 R   91 (158)
Q Consensus        91 ~   91 (158)
                      +
T Consensus        85 k   85 (85)
T 3mdf_A           85 K   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            5

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

Probab=99.89  E-value=1.4e-22  Score=129.97  Aligned_cols=85  Identities=27%  Similarity=0.418  Sum_probs=78.2

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      ..+..+|||+|||+.+++++|+++|++||.|..|.|+.+  ++..++||||+|.+.++|+.|++.||+..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2d9p_A           12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVAL   89 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            345689999999999999999999999999999999887  788999999999999999999999999999999999999


Q ss_pred             eecCCCC
Q psy7051          90 ARYGRPP   96 (158)
Q Consensus        90 a~~~~~~   96 (158)
                      ++....+
T Consensus        90 a~~~~~~   96 (103)
T 2d9p_A           90 AQRKEER   96 (103)
T ss_dssp             CSSCCCC
T ss_pred             ecccccC
Confidence            9855433

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

Probab=99.89  E-value=2.7e-22  Score=131.31  Aligned_cols=86  Identities=33%  Similarity=0.532  Sum_probs=79.7

Q ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEE
Q psy7051           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR   86 (158)
Q Consensus         7 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~   86 (158)
                      +.......+|||+|||..+++++|+++|++||.|..|.|+.++.++..+|||||+|.+.++|+.||+.|++ .|.|+.|.
T Consensus        11 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~   89 (116)
T 2cqd_A           11 SQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKAN   89 (116)
T ss_dssp             CCCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECE
T ss_pred             CcCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEE
Confidence            34455678999999999999999999999999999999999988999999999999999999999999998 89999999


Q ss_pred             EEeeecC
Q psy7051          87 VQMARYG   93 (158)
Q Consensus        87 v~~a~~~   93 (158)
                      |+++...
T Consensus        90 V~~a~~~   96 (116)
T 2cqd_A           90 VNLAYLG   96 (116)
T ss_dssp             EEESTTT
T ss_pred             EEEcccC
Confidence            9999754

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

Probab=99.89  E-value=1.7e-22  Score=129.59  Aligned_cols=84  Identities=29%  Similarity=0.483  Sum_probs=77.9

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEE
Q psy7051           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ   88 (158)
Q Consensus         9 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~   88 (158)
                      ..++..+|||+|||..+++++|+++|++|| |..|.|+.++.++.++|||||+|.+.++|+.|+ .||+..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~   88 (103)
T 2dng_A           11 PTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVD   88 (103)
T ss_dssp             CSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEE
Confidence            345668999999999999999999999996 999999999889999999999999999999999 899999999999999


Q ss_pred             eeecCC
Q psy7051          89 MARYGR   94 (158)
Q Consensus        89 ~a~~~~   94 (158)
                      +++...
T Consensus        89 ~a~~~~   94 (103)
T 2dng_A           89 IAEGRK   94 (103)
T ss_dssp             ECCCCC
T ss_pred             EecCCC
Confidence            998543

>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=99.89  E-value=7.6e-23  Score=129.30  Aligned_cols=86  Identities=26%  Similarity=0.342  Sum_probs=77.9

Q ss_pred             CCCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceE
Q psy7051           6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGREL   85 (158)
Q Consensus         6 p~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i   85 (158)
                      .+...++..+|||+|||..+++++|+++|++||+|..|.|+.++. +.++|||||+|.+.++|+.|++.||+..|.|+.|
T Consensus         9 ~~~~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   87 (95)
T 2ywk_A            9 FPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPI   87 (95)
T ss_dssp             ---CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEE
Confidence            344556678999999999999999999999999999999999874 8899999999999999999999999999999999


Q ss_pred             EEEeeec
Q psy7051          86 RVQMARY   92 (158)
Q Consensus        86 ~v~~a~~   92 (158)
                      .|.+++.
T Consensus        88 ~V~~a~~   94 (95)
T 2ywk_A           88 NVSGPSS   94 (95)
T ss_dssp             EEECCCC
T ss_pred             EEEEcCC
Confidence            9999874

>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=99.89  E-value=2.3e-22  Score=129.33  Aligned_cols=86  Identities=24%  Similarity=0.341  Sum_probs=79.0

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCC---ceEE
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDG---RELR   86 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g---~~i~   86 (158)
                      .++..+|||+|||..+++++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|+.||+.||+..|.|   +.|.
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~   90 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLV   90 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEE
Confidence            3456899999999999999999999999999999999987 78899999999999999999999999999988   9999


Q ss_pred             EEeeecCCCC
Q psy7051          87 VQMARYGRPP   96 (158)
Q Consensus        87 v~~a~~~~~~   96 (158)
                      |.+++....+
T Consensus        91 V~~a~~~~~~  100 (105)
T 2dnh_A           91 VKFADTDKES  100 (105)
T ss_dssp             EEESCSSCCC
T ss_pred             EEECccCccc
Confidence            9999865443

>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=99.89  E-value=4.8e-23  Score=134.89  Aligned_cols=74  Identities=24%  Similarity=0.329  Sum_probs=65.6

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCce-----E
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRE-----L   85 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~-----i   85 (158)
                      ....+|||+|||+.+++++|+++|++||+|..|.|+.+       |||||+|.+.++|+.||+.||+..|+|+.     |
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i   86 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   86 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEE
Confidence            34578999999999999999999999999999999765       79999999999999999999999999998     6


Q ss_pred             EEEeee
Q psy7051          86 RVQMAR   91 (158)
Q Consensus        86 ~v~~a~   91 (158)
                      +|..+.
T Consensus        87 ~v~~~~   92 (115)
T 3beg_B           87 RVKVDG   92 (115)
T ss_dssp             EEEECC
T ss_pred             EeccCC
Confidence            666554

>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=99.89  E-value=2.9e-22  Score=129.69  Aligned_cols=75  Identities=23%  Similarity=0.278  Sum_probs=70.5

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCC-----ceE
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDG-----REL   85 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g-----~~i   85 (158)
                      ....+|||+|||+.+++++|+++|++||+|+.|.|+.+       |||||+|.+.++|+.||+.||+..|.|     +.|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i   85 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   85 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEE
Confidence            45689999999999999999999999999999999765       799999999999999999999999999     999


Q ss_pred             EEEeeec
Q psy7051          86 RVQMARY   92 (158)
Q Consensus        86 ~v~~a~~   92 (158)
                      .|++++.
T Consensus        86 ~V~~a~~   92 (108)
T 1x4c_A           86 RVKVDGP   92 (108)
T ss_dssp             EEEESSC
T ss_pred             EEEeCCC
Confidence            9999984

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.89  E-value=2.3e-23  Score=131.08  Aligned_cols=80  Identities=24%  Similarity=0.375  Sum_probs=74.5

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcC-ceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhC-CcccCCceEEEEeee
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCG-EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD-GRMLDGRELRVQMAR   91 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G-~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~-g~~i~g~~i~v~~a~   91 (158)
                      .+|||+|||..+++++|+++|++|| .|..|.|+.++.++.++|||||+|.+.++|+.|++.|+ +..|.|+.|.|++|+
T Consensus         2 ~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a~   81 (91)
T 2lxi_A            2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSD   81 (91)
T ss_dssp             CEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEcC
Confidence            6899999999999999999999999 89999999999999999999999999999999998774 567999999999997


Q ss_pred             cC
Q psy7051          92 YG   93 (158)
Q Consensus        92 ~~   93 (158)
                      ..
T Consensus        82 ~~   83 (91)
T 2lxi_A           82 PK   83 (91)
T ss_dssp             SC
T ss_pred             CC
Confidence            44

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

Probab=99.89  E-value=1.3e-22  Score=132.24  Aligned_cols=86  Identities=31%  Similarity=0.409  Sum_probs=80.0

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceE--------EEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCccc
Q psy7051           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVG--------DIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRML   80 (158)
Q Consensus         9 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~--------~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i   80 (158)
                      ...+..+|||+|||..+++++|+++|++||.|.        .|.|+.++.++..+|||||+|.+.++|+.||+.||+..|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   90 (113)
T 2cpe_A           11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   90 (113)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCcc
Confidence            455678999999999999999999999999998        699999988999999999999999999999999999999


Q ss_pred             CCceEEEEeeecCC
Q psy7051          81 DGRELRVQMARYGR   94 (158)
Q Consensus        81 ~g~~i~v~~a~~~~   94 (158)
                      .|+.|.|.+++...
T Consensus        91 ~g~~l~V~~a~~~~  104 (113)
T 2cpe_A           91 QGSKLKVSLARKKP  104 (113)
T ss_dssp             TTEECEEECSSCCC
T ss_pred             CCCEEEEEECCCCC
Confidence            99999999998544

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

Probab=99.89  E-value=1.3e-22  Score=126.16  Aligned_cols=81  Identities=32%  Similarity=0.554  Sum_probs=76.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      +..+|||+|||..+++++|+++|++||.|..|.++.++.++..+|||||+|.+.++|+.|++.|||..|.|+.|.|.+++
T Consensus         5 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   84 (87)
T 3bs9_A            5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWAT   84 (87)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEecC
Confidence            45789999999999999999999999999999999998899999999999999999999999999999999999999997


Q ss_pred             c
Q psy7051          92 Y   92 (158)
Q Consensus        92 ~   92 (158)
                      .
T Consensus        85 ~   85 (87)
T 3bs9_A           85 R   85 (87)
T ss_dssp             -
T ss_pred             C
Confidence            3

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

Probab=99.89  E-value=5.9e-23  Score=137.10  Aligned_cols=88  Identities=39%  Similarity=0.553  Sum_probs=81.4

Q ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEE
Q psy7051           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR   86 (158)
Q Consensus         7 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~   86 (158)
                      +...++..+|||+|||..+++++|+++|++||+|..|.|+.++.++..+|||||+|.+.++|+.||+.|||..|.|+.|.
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            33455678999999999999999999999999999999999988899999999999999999999999999999999999


Q ss_pred             EEeeecCC
Q psy7051          87 VQMARYGR   94 (158)
Q Consensus        87 v~~a~~~~   94 (158)
                      |++++..+
T Consensus       120 V~~a~~~~  127 (129)
T 2kxn_B          120 VDFSITKR  127 (129)
T ss_dssp             ESCCSSSS
T ss_pred             EEEecCCC
Confidence            99998544

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

Probab=99.89  E-value=2.5e-22  Score=128.16  Aligned_cols=83  Identities=22%  Similarity=0.421  Sum_probs=77.8

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      ..+..+|||+|||..+++++|+++|++||.|..|.|+.+. ++..+|||||+|.+.++|+.|++.||+..|.|+.|.|.+
T Consensus        14 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   92 (100)
T 2do4_A           14 SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAI   92 (100)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3456789999999999999999999999999999999987 889999999999999999999999999999999999999


Q ss_pred             eecC
Q psy7051          90 ARYG   93 (158)
Q Consensus        90 a~~~   93 (158)
                      ++..
T Consensus        93 a~~~   96 (100)
T 2do4_A           93 SNSG   96 (100)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            9844

>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=99.89  E-value=1.4e-22  Score=130.83  Aligned_cols=84  Identities=30%  Similarity=0.418  Sum_probs=78.6

Q ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEE
Q psy7051           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR   86 (158)
Q Consensus         7 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~   86 (158)
                      ++..++..+|||+|||..+++++|+++|++||.|..|.|+.+. ++..+|||||+|.+.++|+.|++.||+..|.|+.|.
T Consensus        23 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  101 (107)
T 3ulh_A           23 GAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMN  101 (107)
T ss_dssp             -CCCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEE
Confidence            4455677899999999999999999999999999999999998 899999999999999999999999999999999999


Q ss_pred             EEeee
Q psy7051          87 VQMAR   91 (158)
Q Consensus        87 v~~a~   91 (158)
                      |++++
T Consensus       102 V~~a~  106 (107)
T 3ulh_A          102 IQLVT  106 (107)
T ss_dssp             EEEEC
T ss_pred             EEEeC
Confidence            99986

>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=99.89  E-value=1.2e-22  Score=140.85  Aligned_cols=89  Identities=26%  Similarity=0.373  Sum_probs=80.9

Q ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEE
Q psy7051           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR   86 (158)
Q Consensus         7 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~   86 (158)
                      |....+..+|||+|||+.+++++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|+.||+.|||..|.|+.|.
T Consensus        66 ~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~  145 (165)
T 1rk8_A           66 PQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQ  145 (165)
T ss_dssp             CCCCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            33455668999999999999999999999999999999999988999999999999999999999999999999999999


Q ss_pred             EEeeecCCC
Q psy7051          87 VQMARYGRP   95 (158)
Q Consensus        87 v~~a~~~~~   95 (158)
                      |.++....+
T Consensus       146 V~~a~~~~~  154 (165)
T 1rk8_A          146 VDWCFVKGP  154 (165)
T ss_dssp             EEESEECC-
T ss_pred             EEEecCCCC
Confidence            999985543

>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=99.89  E-value=3.1e-22  Score=129.65  Aligned_cols=85  Identities=38%  Similarity=0.511  Sum_probs=75.8

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEE
Q psy7051           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ   88 (158)
Q Consensus         9 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~   88 (158)
                      ...+..+|||+|||..+++++|+++|++||.|..|.|..+   +.+++||||+|.+.++|+.||+.||+..|.|+.|.|+
T Consensus        18 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   94 (109)
T 1x4a_A           18 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVE   94 (109)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            3455689999999999999999999999999999998654   4468999999999999999999999999999999999


Q ss_pred             eeecCCCC
Q psy7051          89 MARYGRPP   96 (158)
Q Consensus        89 ~a~~~~~~   96 (158)
                      +++.....
T Consensus        95 ~a~~~~~~  102 (109)
T 1x4a_A           95 FPRSGRGT  102 (109)
T ss_dssp             CCCCCCCC
T ss_pred             EcccCCCC
Confidence            99865433

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

Probab=99.89  E-value=1.9e-22  Score=124.36  Aligned_cols=79  Identities=33%  Similarity=0.481  Sum_probs=76.2

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeec
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARY   92 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~   92 (158)
                      .+|||+|||..+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|+.|++.|||..|.|+.|.|.+++.
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 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK   80 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCc
Confidence            6899999999999999999999999999999999988999999999999999999999999999999999999999974

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

Probab=99.89  E-value=1e-22  Score=129.41  Aligned_cols=84  Identities=29%  Similarity=0.527  Sum_probs=76.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCC---CCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEE
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRF---TRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ   88 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~   88 (158)
                      +..+|||+|||..+++++|+++|++||.|..|.|+.+..   ++..+|||||+|.+.++|+.|++.||+..|.|+.|.|.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   83 (98)
T 2cpf_A            4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVR   83 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            457899999999999999999999999999999988765   55789999999999999999999999999999999999


Q ss_pred             eeecCCC
Q psy7051          89 MARYGRP   95 (158)
Q Consensus        89 ~a~~~~~   95 (158)
                      +++....
T Consensus        84 ~a~~~~~   90 (98)
T 2cpf_A           84 ISERATK   90 (98)
T ss_dssp             CSSCSSC
T ss_pred             EccCCCC
Confidence            9985443

>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=99.89  E-value=5.5e-22  Score=127.18  Aligned_cols=87  Identities=26%  Similarity=0.375  Sum_probs=77.9

Q ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEE
Q psy7051           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR   86 (158)
Q Consensus         7 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~   86 (158)
                      +....+..+|||+|||..+++++|+++|++||.|..|.|+.+..+  .+|||||+|.+.++|+.|++.||+..|.|+.|.
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   86 (103)
T 2cqi_A            9 MEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVK   86 (103)
T ss_dssp             CCCSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC--CCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEE
Confidence            334556789999999999999999999999999999999988543  589999999999999999999999999999999


Q ss_pred             EEeeecCCC
Q psy7051          87 VQMARYGRP   95 (158)
Q Consensus        87 v~~a~~~~~   95 (158)
                      |.+++....
T Consensus        87 V~~a~~~~~   95 (103)
T 2cqi_A           87 VNWATTPSS   95 (103)
T ss_dssp             EEECCCTTC
T ss_pred             EEECCCCcc
Confidence            999986443

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

Probab=99.89  E-value=1.2e-22  Score=129.35  Aligned_cols=84  Identities=29%  Similarity=0.439  Sum_probs=79.1

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceE-EEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCce----E
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVG-DIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRE----L   85 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~-~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~----i   85 (158)
                      .+..+|||+|||..+++++|+++|++||.|. .|.|+.++.++.++|||||+|.+.++|+.|++.|||..|.|+.    |
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l   86 (99)
T 2div_A            7 GMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRF   86 (99)
T ss_dssp             SSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEEC
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcceeE
Confidence            4568999999999999999999999999999 9999999889999999999999999999999999999999999    9


Q ss_pred             EEEeeecCC
Q psy7051          86 RVQMARYGR   94 (158)
Q Consensus        86 ~v~~a~~~~   94 (158)
                      +|.+++...
T Consensus        87 ~v~~a~~~~   95 (99)
T 2div_A           87 KLNYATYSG   95 (99)
T ss_dssp             CEEETTCCS
T ss_pred             EEeecCCCC
Confidence            999998554

>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=99.89  E-value=2.1e-22  Score=127.66  Aligned_cols=81  Identities=21%  Similarity=0.352  Sum_probs=77.4

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeec
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARY   92 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~   92 (158)
                      ..+|||+|||..+++++|+++|++||.|..|.++.++.++..+|||||+|.+.++|+.|++.|||..|.|+.|.|.+++.
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   81 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSN   81 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCC
Confidence            47899999999999999999999999999999999988899999999999999999999999999999999999999985


Q ss_pred             C
Q psy7051          93 G   93 (158)
Q Consensus        93 ~   93 (158)
                      .
T Consensus        82 ~   82 (96)
T 2x1f_A           82 S   82 (96)
T ss_dssp             S
T ss_pred             C
Confidence            4

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

Probab=99.89  E-value=7.3e-22  Score=126.62  Aligned_cols=87  Identities=29%  Similarity=0.458  Sum_probs=77.7

Q ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEE
Q psy7051           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR   86 (158)
Q Consensus         7 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~   86 (158)
                      +.......+|||+|||..+++++|+++|++||.|..|.|+.+..  ..+|||||+|.+.++|+.|++.||+..|.|+.|.
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   86 (103)
T 2cq3_A            9 SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIE   86 (103)
T ss_dssp             SCCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            33445668999999999999999999999999999999988753  3789999999999999999999999999999999


Q ss_pred             EEeeecCCC
Q psy7051          87 VQMARYGRP   95 (158)
Q Consensus        87 v~~a~~~~~   95 (158)
                      |.+++....
T Consensus        87 v~~a~~~~~   95 (103)
T 2cq3_A           87 VNNATARVM   95 (103)
T ss_dssp             EEECCSSCC
T ss_pred             EEEcccCCC
Confidence            999985443

>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=99.89  E-value=2.4e-23  Score=130.56  Aligned_cols=82  Identities=26%  Similarity=0.370  Sum_probs=72.7

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcC--ceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCG--EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G--~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      .+|||+|||..+++++|+++|++||  .|..|.++.++.++.++|||||+|.+.++|+.|++.|||..|.|+.|.|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            5799999999999999999999999  99999999999899999999999999999999999999999999999999998


Q ss_pred             cCCC
Q psy7051          92 YGRP   95 (158)
Q Consensus        92 ~~~~   95 (158)
                      ...+
T Consensus        82 ~~~~   85 (90)
T 3p5t_L           82 KLEH   85 (90)
T ss_dssp             ----
T ss_pred             CCcc
Confidence            5543

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

Probab=99.89  E-value=2.7e-22  Score=128.78  Aligned_cols=85  Identities=25%  Similarity=0.294  Sum_probs=78.7

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhh-cCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcc-cCCceEE
Q psy7051           9 RIEGMVSLKVDNLTYRTTPDDLRRVFER-CGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRM-LDGRELR   86 (158)
Q Consensus         9 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~-~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~-i~g~~i~   86 (158)
                      ...+..+|||+|||..+++++|+++|++ ||.|..|.|+.+. ++..+|||||+|.+.++|+.|++.||+.. |.|+.|.
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~   83 (104)
T 2dhg_A            5 SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVR   83 (104)
T ss_dssp             CSSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEE
Confidence            3455688999999999999999999999 9999999999998 89999999999999999999999999999 9999999


Q ss_pred             EEeeecCC
Q psy7051          87 VQMARYGR   94 (158)
Q Consensus        87 v~~a~~~~   94 (158)
                      |.++....
T Consensus        84 v~~a~~~~   91 (104)
T 2dhg_A           84 LSVAIPKA   91 (104)
T ss_dssp             CCBCCCCC
T ss_pred             EEEccCCC
Confidence            99997443

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

Probab=99.88  E-value=1.7e-22  Score=132.66  Aligned_cols=82  Identities=28%  Similarity=0.313  Sum_probs=77.1

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      .++..+|||+|||..+++++|+++|++||.|..|.|+.++.++..+|||||+|.+.++|+.|++.|||..|.|+.|+|++
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            34568999999999999999999999999999999999988899999999999999999999999999999999999998


Q ss_pred             ee
Q psy7051          90 AR   91 (158)
Q Consensus        90 a~   91 (158)
                      ++
T Consensus       117 ak  118 (118)
T 2khc_A          117 KK  118 (118)
T ss_dssp             C-
T ss_pred             cC
Confidence            74

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

Probab=99.88  E-value=2.2e-22  Score=130.36  Aligned_cols=86  Identities=31%  Similarity=0.483  Sum_probs=80.2

Q ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEE
Q psy7051           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR   86 (158)
Q Consensus         7 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~   86 (158)
                      +...++..+|||+|||..+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|+.|++.|||..|.|+.|.
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            44456678999999999999999999999999999999999988899999999999999999999999999999999999


Q ss_pred             EEeeec
Q psy7051          87 VQMARY   92 (158)
Q Consensus        87 v~~a~~   92 (158)
                      |.+++.
T Consensus       100 V~~a~~  105 (108)
T 2jrs_A          100 VGHVTE  105 (108)
T ss_dssp             EECSCS
T ss_pred             EEEccc
Confidence            999873

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

Probab=99.88  E-value=3.7e-22  Score=125.38  Aligned_cols=84  Identities=31%  Similarity=0.423  Sum_probs=77.2

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      ..+..+|||+|||..+++++|+++|++||.|..|.++.+  ++..+|||||+|.+.++|+.|++.||+..|.|+.|.|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~   82 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRI   82 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            356689999999999999999999999999999999874  788899999999999999999999999999999999999


Q ss_pred             eecCCC
Q psy7051          90 ARYGRP   95 (158)
Q Consensus        90 a~~~~~   95 (158)
                      ++....
T Consensus        83 a~~~~~   88 (92)
T 2dgv_A           83 DRNASG   88 (92)
T ss_dssp             CSCCSS
T ss_pred             cCCCCC
Confidence            985543

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

Probab=99.88  E-value=1.6e-21  Score=127.14  Aligned_cols=87  Identities=26%  Similarity=0.315  Sum_probs=79.4

Q ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEE
Q psy7051           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR   86 (158)
Q Consensus         7 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~   86 (158)
                      .....+..+|||+|||..+++++|+++|.+||.|..|.|+.++ ++..+|||||+|.+.++|+.|++.||+..|.|+.|.
T Consensus         9 ~~~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   87 (114)
T 2do0_A            9 LQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMH   87 (114)
T ss_dssp             CCCCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEE
Confidence            3344566899999999999999999999999999999999887 688999999999999999999999999999999999


Q ss_pred             EEeeecCC
Q psy7051          87 VQMARYGR   94 (158)
Q Consensus        87 v~~a~~~~   94 (158)
                      |.+++...
T Consensus        88 v~~a~~~~   95 (114)
T 2do0_A           88 VKMDERAL   95 (114)
T ss_dssp             EEECSCCC
T ss_pred             EEEcccCC
Confidence            99997543

>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=99.88  E-value=2.1e-22  Score=125.37  Aligned_cols=83  Identities=29%  Similarity=0.502  Sum_probs=76.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCC-cccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRE-SRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~-~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      ...+|||+|||..+++++|+++|++||.|..|.++.+..++. .+|||||+|.+.++|+.|++.|||..|.|+.|.|+++
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            347899999999999999999999999999999998876665 7899999999999999999999999999999999999


Q ss_pred             ecCC
Q psy7051          91 RYGR   94 (158)
Q Consensus        91 ~~~~   94 (158)
                      ....
T Consensus        83 ~~~~   86 (88)
T 4a8x_A           83 LAPW   86 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7544

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

Probab=99.88  E-value=1.9e-22  Score=129.79  Aligned_cols=88  Identities=32%  Similarity=0.446  Sum_probs=80.5

Q ss_pred             CCCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceE
Q psy7051           6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGREL   85 (158)
Q Consensus         6 p~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i   85 (158)
                      .+...++..+|||+|||+.+++++|+++|++||.|..|.|+.++.++..+|||||+|.+.++|+.||+. ++..|.|+.|
T Consensus         9 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l   87 (105)
T 2dh8_A            9 NNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNI   87 (105)
T ss_dssp             CCCCSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEE
T ss_pred             CcCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEE
Confidence            344456678999999999999999999999999999999999988999999999999999999999988 9999999999


Q ss_pred             EEEeeecCC
Q psy7051          86 RVQMARYGR   94 (158)
Q Consensus        86 ~v~~a~~~~   94 (158)
                      .|.+++...
T Consensus        88 ~V~~a~~~~   96 (105)
T 2dh8_A           88 DPKPCTPRG   96 (105)
T ss_dssp             BCCCSCCSS
T ss_pred             EEEEccCCC
Confidence            999997443

>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=99.88  E-value=4.3e-22  Score=123.89  Aligned_cols=84  Identities=35%  Similarity=0.469  Sum_probs=75.8

Q ss_pred             CCCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceE
Q psy7051           6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGREL   85 (158)
Q Consensus         6 p~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i   85 (158)
                      ++....+..+|||+|||+.+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|+.|++ +++..|+|+.|
T Consensus         4 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i   82 (87)
T 3s7r_A            4 ASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVI   82 (87)
T ss_dssp             ---CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEE
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEE
Confidence            34455677899999999999999999999999999999999998899999999999999999999995 58889999999


Q ss_pred             EEEee
Q psy7051          86 RVQMA   90 (158)
Q Consensus        86 ~v~~a   90 (158)
                      .|++|
T Consensus        83 ~v~~A   87 (87)
T 3s7r_A           83 DPKKA   87 (87)
T ss_dssp             EEEEC
T ss_pred             EEEeC
Confidence            99875

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

Probab=99.88  E-value=8e-22  Score=125.05  Aligned_cols=81  Identities=20%  Similarity=0.303  Sum_probs=74.7

Q ss_pred             CCCcEEEEeCCCCCCCHHHHH----HHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEE
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLR----RVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR   86 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~----~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~   86 (158)
                      ...++|||+|||..+++++|+    ++|++||.|..|.|+.+..+   ++||||+|.+.++|+.|++.|||..|.|+.|.
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~   83 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKIL   83 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            445899999999999999999    99999999999999988655   78999999999999999999999999999999


Q ss_pred             EEeeecCC
Q psy7051          87 VQMARYGR   94 (158)
Q Consensus        87 v~~a~~~~   94 (158)
                      |++++...
T Consensus        84 V~~a~~~~   91 (96)
T 2dgx_A           84 VSLATGAS   91 (96)
T ss_dssp             EEECCCSS
T ss_pred             EEEcCCCC
Confidence            99997543

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

Probab=99.88  E-value=3.2e-22  Score=130.96  Aligned_cols=79  Identities=24%  Similarity=0.371  Sum_probs=73.4

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeec
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARY   92 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~   92 (158)
                      .++|||+|||+.+++++|+++|++||.|..|.|+.+.  +..+|||||+|.+.++|+.||+.||+..|.|+.|.|.++..
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~   82 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   82 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSC
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            4789999999999999999999999999999999885  34789999999999999999999999999999999999874


Q ss_pred             C
Q psy7051          93 G   93 (158)
Q Consensus        93 ~   93 (158)
                      .
T Consensus        83 ~   83 (115)
T 4f25_A           83 R   83 (115)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=99.88  E-value=5e-22  Score=124.00  Aligned_cols=80  Identities=33%  Similarity=0.630  Sum_probs=76.2

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeec
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARY   92 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~   92 (158)
                      ..+|||+|||..+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|+.|+ .||+..|.|+.|.|.+++.
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~~   84 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRT   84 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEccC
Confidence            468999999999999999999999999999999999889999999999999999999999 9999999999999999975


Q ss_pred             C
Q psy7051          93 G   93 (158)
Q Consensus        93 ~   93 (158)
                      .
T Consensus        85 ~   85 (89)
T 3ucg_A           85 N   85 (89)
T ss_dssp             T
T ss_pred             C
Confidence            4

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

Probab=99.88  E-value=2.8e-22  Score=130.33  Aligned_cols=84  Identities=14%  Similarity=0.161  Sum_probs=71.6

Q ss_pred             CCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcC-ceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccC
Q psy7051           3 YGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCG-EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLD   81 (158)
Q Consensus         3 ~~~p~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G-~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~   81 (158)
                      |+.+|+   ...+|||+|||+.+++++|+++|++|| +|..+.+...    .++|||||+|.+.++|+.||+.|||..|.
T Consensus        21 ~~~~p~---~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~----~~rGfaFV~F~~~e~A~~Ai~~lng~~l~   93 (111)
T 2jvr_A           21 MSKLPA---KRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR----DFDGTGALEFPSEEILVEALERLNNIEFR   93 (111)
T ss_dssp             ----CC---CCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC----SSSCCEEEEESSHHHHHHHHHHTTTEEET
T ss_pred             cCCCCC---CCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC----CCCCEEEEEECCHHHHHHHHHHcCCCEEC
Confidence            555544   348999999999999999999999999 8999988543    36899999999999999999999999999


Q ss_pred             CceEEEEeeecC
Q psy7051          82 GRELRVQMARYG   93 (158)
Q Consensus        82 g~~i~v~~a~~~   93 (158)
                      |+.|.|++++..
T Consensus        94 Gr~i~V~~a~~~  105 (111)
T 2jvr_A           94 GSVITVERDDNP  105 (111)
T ss_dssp             TEEEEEEESCC-
T ss_pred             CeEEEEEECCCC
Confidence            999999998743

>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=99.88  E-value=1.1e-21  Score=134.77  Aligned_cols=86  Identities=85%  Similarity=1.388  Sum_probs=80.6

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      ....+|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|+.||+.|||..|.|+.|.|.++
T Consensus        68 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  147 (158)
T 2kn4_A           68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA  147 (158)
T ss_dssp             CBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            44689999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q psy7051          91 RYGRPP   96 (158)
Q Consensus        91 ~~~~~~   96 (158)
                      +..+++
T Consensus       148 ~~~~~~  153 (158)
T 2kn4_A          148 RYGRPP  153 (158)
T ss_dssp             CCSSCC
T ss_pred             CCCCCC
Confidence            865544

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

Probab=99.87  E-value=1.7e-21  Score=122.44  Aligned_cols=83  Identities=25%  Similarity=0.374  Sum_probs=74.5

Q ss_pred             CCCCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCce
Q psy7051           5 RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRE   84 (158)
Q Consensus         5 ~p~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~   84 (158)
                      .++....+..+|||+|||..+++++|+++|++||.|..|.++.        +||||+|.+.++|+.|++.||+..|.|+.
T Consensus         2 ~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~   73 (92)
T 2dgt_A            2 SSGSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRGLDNTEFQGKR   73 (92)
T ss_dssp             CCSCCCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS--------SEEEEEESCHHHHHHHHHHHTTEEETTEE
T ss_pred             CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCeeCCcE
Confidence            3455566779999999999999999999999999999999863        49999999999999999999999999999


Q ss_pred             EEEEeeecCCC
Q psy7051          85 LRVQMARYGRP   95 (158)
Q Consensus        85 i~v~~a~~~~~   95 (158)
                      |.|.+++....
T Consensus        74 l~V~~a~~~~~   84 (92)
T 2dgt_A           74 MHVQLSTSRLR   84 (92)
T ss_dssp             EEEEESSCCCS
T ss_pred             EEEEEccCCCC
Confidence            99999985443

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

Probab=99.87  E-value=3e-22  Score=127.30  Aligned_cols=83  Identities=17%  Similarity=0.235  Sum_probs=77.2

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      .+...+|||+|||..+++++|+++|.+||.|..+.++.+..++.++|||||+|.+.++|+.|++.||+..|.|+.|.|++
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            34568999999999999999999999999998888888888999999999999999999999999999999999999999


Q ss_pred             eec
Q psy7051          90 ARY   92 (158)
Q Consensus        90 a~~   92 (158)
                      +..
T Consensus        92 a~~   94 (98)
T 2cqp_A           92 GSG   94 (98)
T ss_dssp             SSC
T ss_pred             cCC
Confidence            873

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

Probab=99.87  E-value=2.1e-21  Score=124.50  Aligned_cols=86  Identities=28%  Similarity=0.435  Sum_probs=78.1

Q ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEE
Q psy7051           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR   86 (158)
Q Consensus         7 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~   86 (158)
                      +....+..+|||+|||..+++++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|+.||+  ++..|+|+.|.
T Consensus         9 ~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~   86 (103)
T 2cqg_A            9 KRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCD   86 (103)
T ss_dssp             SCCCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEE
T ss_pred             CCccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEE
Confidence            3345567899999999999999999999999999999999998889999999999999999999997  57899999999


Q ss_pred             EEeeecCC
Q psy7051          87 VQMARYGR   94 (158)
Q Consensus        87 v~~a~~~~   94 (158)
                      |.++....
T Consensus        87 v~~a~~~~   94 (103)
T 2cqg_A           87 CKLPNSKQ   94 (103)
T ss_dssp             EECCCTTC
T ss_pred             EEecCCCC
Confidence            99998543

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

Probab=99.87  E-value=1.8e-22  Score=129.07  Aligned_cols=80  Identities=23%  Similarity=0.338  Sum_probs=76.6

Q ss_pred             CcEEEEeCCCC------CCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCC-ceE
Q psy7051          13 MVSLKVDNLTY------RTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDG-REL   85 (158)
Q Consensus        13 ~~~l~V~nl~~------~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g-~~i   85 (158)
                      ..+|||+|||.      .+++++|.++|++||.|..|.|+.++.++.++|||||+|.+.++|+.|++.|||..|.| +.|
T Consensus         6 ~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~l   85 (100)
T 3ns6_A            6 DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRL   85 (100)
T ss_dssp             GGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCBC
T ss_pred             CcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeEE
Confidence            47899999999      99999999999999999999999999899999999999999999999999999999999 999


Q ss_pred             EEEeeec
Q psy7051          86 RVQMARY   92 (158)
Q Consensus        86 ~v~~a~~   92 (158)
                      .|.++..
T Consensus        86 ~V~~a~~   92 (100)
T 3ns6_A           86 FLYTMKD   92 (100)
T ss_dssp             EEEESHH
T ss_pred             EEEECch
Confidence            9999863

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

Probab=99.87  E-value=3.3e-22  Score=133.71  Aligned_cols=88  Identities=20%  Similarity=0.382  Sum_probs=80.2

Q ss_pred             CCCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEE--EEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCc----c
Q psy7051           6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGD--IYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGR----M   79 (158)
Q Consensus         6 p~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~--v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~----~   79 (158)
                      ++....+..+|||+|||+.+++++|+++|++||.|..  |.|+.++.++.++|||||+|.+. +|+.|++.|||.    .
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            3344566789999999999999999999999999976  99999999999999999999999 999999999999    9


Q ss_pred             cCCceEEEEeeecCC
Q psy7051          80 LDGRELRVQMARYGR   94 (158)
Q Consensus        80 i~g~~i~v~~a~~~~   94 (158)
                      |.|+.|.|.+++...
T Consensus        95 ~~gr~l~V~~a~~~~  109 (131)
T 2m2b_A           95 IDGKTINVEFAKGSK  109 (131)
T ss_dssp             GGGCCCCCEECCCSC
T ss_pred             CCCEEEEEEECCCCC
Confidence            999999999998543

>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=99.87  E-value=9.3e-22  Score=126.16  Aligned_cols=82  Identities=21%  Similarity=0.220  Sum_probs=74.2

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEE
Q psy7051           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ   88 (158)
Q Consensus         9 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~   88 (158)
                      ......+|||+|||+.+++++|+++|++||. +.|.|+.++ +++++|||||+|.+.++|+.|| .+|+..|.++.|.|.
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~   87 (102)
T 1wez_A           11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAM-AKDKANMQHRYVELF   87 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHH-TTSSCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEECC-CCCEeeEEEEEECCHHHHHHHH-HhCCCeECCcEEEEE
Confidence            3445689999999999999999999999994 599999997 8999999999999999999999 579999999999999


Q ss_pred             eeecC
Q psy7051          89 MARYG   93 (158)
Q Consensus        89 ~a~~~   93 (158)
                      ++...
T Consensus        88 ~~~~~   92 (102)
T 1wez_A           88 LNSTA   92 (102)
T ss_dssp             EECCC
T ss_pred             ECCCC
Confidence            88743

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

Probab=99.87  E-value=7.3e-22  Score=135.80  Aligned_cols=79  Identities=23%  Similarity=0.416  Sum_probs=76.0

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcC--ceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCG--EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G--~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      ..+|||+|||+.+++++|+++|++||  .|..|.|+.++.++.++|||||+|.+.++|+.||+.|||..|.|+.|.|.++
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            46999999999999999999999999  9999999999999999999999999999999999999999999999999998


Q ss_pred             e
Q psy7051          91 R   91 (158)
Q Consensus        91 ~   91 (158)
                      .
T Consensus       135 ~  135 (156)
T 3n9u_C          135 T  135 (156)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.87  E-value=1.9e-22  Score=127.43  Aligned_cols=81  Identities=17%  Similarity=0.243  Sum_probs=75.3

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      +..+|||+|||+.+++++|+++|++||.|..+.++.+..++.++|||||+|.+.++|+.|++.||+..|.|+.|.|+++.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a~   93 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPS   93 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEecc
Confidence            35899999999999999999999999999888888888889999999999999999999999999999999999999886


Q ss_pred             c
Q psy7051          92 Y   92 (158)
Q Consensus        92 ~   92 (158)
                      .
T Consensus        94 s   94 (95)
T 2ek1_A           94 S   94 (95)
T ss_dssp             -
T ss_pred             C
Confidence            3

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

Probab=99.87  E-value=1.9e-21  Score=122.00  Aligned_cols=85  Identities=18%  Similarity=0.295  Sum_probs=77.6

Q ss_pred             CCCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceE
Q psy7051           6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGREL   85 (158)
Q Consensus         6 p~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i   85 (158)
                      +........+|||+|||..+++++|+++|++| .|..|.|+.+ .++.++|||||+|.+.++|+.|++ ||+..|.|+.|
T Consensus         3 ~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i   79 (91)
T 2dgw_A            3 SGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYI   79 (91)
T ss_dssp             CCCCCCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEE
T ss_pred             CCCCCCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEE
Confidence            33444567899999999999999999999999 9999999998 689999999999999999999999 99999999999


Q ss_pred             EEEeeecC
Q psy7051          86 RVQMARYG   93 (158)
Q Consensus        86 ~v~~a~~~   93 (158)
                      .|.+++..
T Consensus        80 ~v~~a~~~   87 (91)
T 2dgw_A           80 EVFREKSG   87 (91)
T ss_dssp             EEEEESSC
T ss_pred             EEEECCcC
Confidence            99999743

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

Probab=99.87  E-value=2.8e-21  Score=121.03  Aligned_cols=77  Identities=31%  Similarity=0.498  Sum_probs=71.3

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      ++..+|||+|||..+++++|+++|++||.|..|.++        ++||||+|.+.++|+.|++.||+..|.|+.|.|+++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   77 (90)
T 2dnq_A            6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEAS   77 (90)
T ss_dssp             SCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECS
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEEC
Confidence            456899999999999999999999999999999986        579999999999999999999999999999999999


Q ss_pred             ecCCC
Q psy7051          91 RYGRP   95 (158)
Q Consensus        91 ~~~~~   95 (158)
                      +....
T Consensus        78 ~~~~~   82 (90)
T 2dnq_A           78 KNKSK   82 (90)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            85443

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

Probab=99.87  E-value=4e-22  Score=130.49  Aligned_cols=81  Identities=30%  Similarity=0.498  Sum_probs=76.3

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeec
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARY   92 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~   92 (158)
                      ..+|||+|||..+++++|+++|.+||.|..|.|+.++.++..+|||||+|.+.++|+.||+. ++..|.|+.|.|.++..
T Consensus        27 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~~  105 (116)
T 1x4b_A           27 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVA  105 (116)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECCC
Confidence            47999999999999999999999999999999999988899999999999999999999987 99999999999999985


Q ss_pred             CC
Q psy7051          93 GR   94 (158)
Q Consensus        93 ~~   94 (158)
                      ..
T Consensus       106 ~~  107 (116)
T 1x4b_A          106 RE  107 (116)
T ss_dssp             CC
T ss_pred             Cc
Confidence            43

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

Probab=99.87  E-value=1.1e-21  Score=124.81  Aligned_cols=80  Identities=16%  Similarity=0.217  Sum_probs=71.2

Q ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcc--cCCce
Q psy7051           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRM--LDGRE   84 (158)
Q Consensus         7 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~--i~g~~   84 (158)
                      ....++..+|||+|||..+++++|.++|++||.|+.|.++..      +|+|||+|++.++|++|++.|++..  |.|+.
T Consensus        15 ~~~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~------kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~   88 (100)
T 3r27_A           15 PHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYAADNQIYIAGHP   88 (100)
T ss_dssp             --CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCEEETTEE
T ss_pred             cccCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhcCCCceeCCcE
Confidence            334566789999999999999999999999999999998753      6899999999999999999999875  78999


Q ss_pred             EEEEeeec
Q psy7051          85 LRVQMARY   92 (158)
Q Consensus        85 i~v~~a~~   92 (158)
                      |.|+|++.
T Consensus        89 i~V~~S~~   96 (100)
T 3r27_A           89 AFVNYSTS   96 (100)
T ss_dssp             EEEEECSC
T ss_pred             EEEEeccc
Confidence            99999974

>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=99.87  E-value=1.7e-22  Score=129.68  Aligned_cols=84  Identities=30%  Similarity=0.509  Sum_probs=78.6

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      .....+|||+|||..+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|+.|++.|||..|.|+.|.|.+
T Consensus         5 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   84 (104)
T 1p1t_A            5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDN   84 (104)
T ss_dssp             HHHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEE
T ss_pred             CCCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Confidence            34557899999999999999999999999999999999988899999999999999999999999999999999999999


Q ss_pred             eecC
Q psy7051          90 ARYG   93 (158)
Q Consensus        90 a~~~   93 (158)
                      +...
T Consensus        85 a~~~   88 (104)
T 1p1t_A           85 AASE   88 (104)
T ss_dssp             TTCT
T ss_pred             CCCc
Confidence            8744

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

Probab=99.87  E-value=1.2e-21  Score=125.32  Aligned_cols=87  Identities=31%  Similarity=0.428  Sum_probs=76.6

Q ss_pred             CCCCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCce
Q psy7051           5 RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRE   84 (158)
Q Consensus         5 ~p~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~   84 (158)
                      .|....++..+|||+|||..+++++|+++|++|+   .|.++.+..++..+|||||+|.+.++|+.||+.||+..|.|+.
T Consensus         7 ~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   83 (102)
T 2fc8_A            7 GPNARSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNK   83 (102)
T ss_dssp             TTSSSSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeE
Confidence            3445566778999999999999999999999884   5667777778889999999999999999999999999999999


Q ss_pred             EEEEeeecCC
Q psy7051          85 LRVQMARYGR   94 (158)
Q Consensus        85 i~v~~a~~~~   94 (158)
                      |.|.+++...
T Consensus        84 l~V~~a~~~~   93 (102)
T 2fc8_A           84 VTLDWAKPKG   93 (102)
T ss_dssp             CEEEECCCCC
T ss_pred             EEEEEecCCC
Confidence            9999998543

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

Probab=99.87  E-value=2.5e-21  Score=128.18  Aligned_cols=85  Identities=28%  Similarity=0.400  Sum_probs=79.3

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEE
Q psy7051           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ   88 (158)
Q Consensus         9 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~   88 (158)
                      ...+..+|||+|||..+++++|+++|++||.|..|.|+.+. ++..+|||||+|.+.++|+.|++.|||..|.|+.|.|+
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  109 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ  109 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            44566899999999999999999999999999999999988 88899999999999999999999999999999999999


Q ss_pred             eeecCC
Q psy7051          89 MARYGR   94 (158)
Q Consensus        89 ~a~~~~   94 (158)
                      +|....
T Consensus       110 ~a~~~~  115 (124)
T 2kt5_A          110 LVASQI  115 (124)
T ss_dssp             EECCTT
T ss_pred             EeCCCC
Confidence            998544

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

Probab=99.87  E-value=1e-21  Score=129.98  Aligned_cols=82  Identities=32%  Similarity=0.624  Sum_probs=77.0

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeec
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARY   92 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~   92 (158)
                      ..+|||+|||..+++++|+++|++||.|..|.|+.++.++..+|||||+|.+.++|+.|+ .|||..|.|+.|.|.+++.
T Consensus        36 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~  114 (124)
T 2jwn_A           36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRT  114 (124)
T ss_dssp             HTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESSC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCC
Confidence            479999999999999999999999999999999999889999999999999999999999 7999999999999999985


Q ss_pred             CCC
Q psy7051          93 GRP   95 (158)
Q Consensus        93 ~~~   95 (158)
                      ..+
T Consensus       115 ~~~  117 (124)
T 2jwn_A          115 NMP  117 (124)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            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=99.87  E-value=6e-21  Score=122.40  Aligned_cols=79  Identities=23%  Similarity=0.433  Sum_probs=71.8

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEE
Q psy7051           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ   88 (158)
Q Consensus         9 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~   88 (158)
                      ...+..+|||+|||..+++++|+++|++||.|..|.++        ++||||+|.+.++|+.|++.||+..|.|+.|.|.
T Consensus         7 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   78 (103)
T 2dgu_A            7 GMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIV   78 (103)
T ss_dssp             CCCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEE
Confidence            34556899999999999999999999999999999985        3599999999999999999999999999999999


Q ss_pred             eeecCCC
Q psy7051          89 MARYGRP   95 (158)
Q Consensus        89 ~a~~~~~   95 (158)
                      +++....
T Consensus        79 ~a~~~~~   85 (103)
T 2dgu_A           79 FAKPPDQ   85 (103)
T ss_dssp             ECCCCCC
T ss_pred             EcCCCcc
Confidence            9985543

>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=99.87  E-value=9.6e-22  Score=127.87  Aligned_cols=87  Identities=18%  Similarity=0.297  Sum_probs=77.5

Q ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHH---HHhhhcCceEEEEEccCCCCC---CcccEEEEEEcCHHHHHHHHHHhCCccc
Q psy7051           7 PPRIEGMVSLKVDNLTYRTTPDDLR---RVFERCGEVGDIYIPRDRFTR---ESRGFAFVRFFDKRDAEDALDAMDGRML   80 (158)
Q Consensus         7 ~~~~~~~~~l~V~nl~~~~~~~~l~---~~f~~~G~i~~v~~~~~~~~~---~~~g~afV~f~~~~~a~~a~~~l~g~~i   80 (158)
                      ........+|||+|||+.+++++|.   ++|++||+|..|.|+.+..++   .++|||||+|.+.++|+.||+.||+..|
T Consensus         9 ~~r~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~   88 (111)
T 2cpi_A            9 SVRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVV   88 (111)
T ss_dssp             CCCCCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEE
T ss_pred             cccccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEE
Confidence            3345566899999999999999999   999999999999998887644   4569999999999999999999999999


Q ss_pred             CCceEEEEeeecC
Q psy7051          81 DGRELRVQMARYG   93 (158)
Q Consensus        81 ~g~~i~v~~a~~~   93 (158)
                      .|+.|.|.+++..
T Consensus        89 ~gr~l~V~~a~~k  101 (111)
T 2cpi_A           89 DGRTLKASLGTTK  101 (111)
T ss_dssp             TTEEEEEESCCCC
T ss_pred             CCEEEEEEecccc
Confidence            9999999999844

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

Probab=99.87  E-value=7.8e-22  Score=126.74  Aligned_cols=79  Identities=20%  Similarity=0.273  Sum_probs=74.2

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      ....+|||+|||+.+++++|+++|++||+|..|.|+.++. +.++|||||+|.+.++|+.||+ +++..|+|+.|.|.++
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 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFK   86 (103)
T ss_dssp             SGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEc
Confidence            3457899999999999999999999999999999999986 8899999999999999999997 8999999999999987


Q ss_pred             e
Q psy7051          91 R   91 (158)
Q Consensus        91 ~   91 (158)
                      .
T Consensus        87 ~   87 (103)
T 1s79_A           87 D   87 (103)
T ss_dssp             H
T ss_pred             h
Confidence            5

>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=99.87  E-value=4.8e-22  Score=129.76  Aligned_cols=78  Identities=31%  Similarity=0.465  Sum_probs=75.3

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeec
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARY   92 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~   92 (158)
                      .+|||+|||..+++++|+++|++||.|..|.|+.++.++..+|||||+|.+.++|+.|| .||+..|.|+.|.|.+++.
T Consensus        26 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~  103 (114)
T 2cq4_A           26 RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQA  103 (114)
T ss_dssp             TEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHHH
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecCC
Confidence            69999999999999999999999999999999999888999999999999999999999 9999999999999999874

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

Probab=99.87  E-value=1.5e-22  Score=125.41  Aligned_cols=81  Identities=21%  Similarity=0.300  Sum_probs=75.4

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      ++..+|||+|||+.+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|+.|++.|||..|.|+.|+|.++
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            34589999999999999999999999999999999999889999999999999999999999999999999999887655


Q ss_pred             e
Q psy7051          91 R   91 (158)
Q Consensus        91 ~   91 (158)
                      .
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

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

Probab=99.86  E-value=2.9e-21  Score=123.42  Aligned_cols=82  Identities=28%  Similarity=0.535  Sum_probs=73.4

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEE
Q psy7051           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ   88 (158)
Q Consensus         9 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~   88 (158)
                      ...+..+|||+|||..+++++|+++|++||.|   .++.+ .++..+|||||+|.+.++|+.|++.||+..|.|+.|.|+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   86 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLE   86 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEE
Confidence            44567899999999999999999999999987   45555 578899999999999999999999999999999999999


Q ss_pred             eeecCC
Q psy7051          89 MARYGR   94 (158)
Q Consensus        89 ~a~~~~   94 (158)
                      +++...
T Consensus        87 ~a~~~~   92 (101)
T 2fc9_A           87 LQGPRG   92 (101)
T ss_dssp             ECSSCC
T ss_pred             EcCCCC
Confidence            998543

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

Probab=99.86  E-value=1.5e-21  Score=125.80  Aligned_cols=85  Identities=22%  Similarity=0.407  Sum_probs=76.1

Q ss_pred             CCCCCCCCCcEEEEeCCCCCC------CHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCc
Q psy7051           5 RPPPRIEGMVSLKVDNLTYRT------TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGR   78 (158)
Q Consensus         5 ~p~~~~~~~~~l~V~nl~~~~------~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~   78 (158)
                      .|+.......+|||+|||..+      ++++|+++|++||.|..|.|+  ..++.++|||||+|.+.++|+.|++.|||.
T Consensus         7 ~~~~~~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~   84 (105)
T 2nlw_A            7 RPQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGY   84 (105)
T ss_dssp             CCCSCCSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSE
T ss_pred             CCCCCCCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCc
Confidence            344444556899999999999      789999999999999999888  357889999999999999999999999999


Q ss_pred             ccCCc-eEEEEeee
Q psy7051          79 MLDGR-ELRVQMAR   91 (158)
Q Consensus        79 ~i~g~-~i~v~~a~   91 (158)
                      .|.|+ .|.|.++.
T Consensus        85 ~~~g~~~l~V~~a~   98 (105)
T 2nlw_A           85 KLDKQHTFRVNLFT   98 (105)
T ss_dssp             ECSTTCEEEEECSC
T ss_pred             ccCCCceEEEEEcc
Confidence            99998 99999986

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

Probab=99.86  E-value=5.6e-22  Score=129.53  Aligned_cols=86  Identities=30%  Similarity=0.329  Sum_probs=72.5

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      ++..+|||+|||..+++++|+++|.+||.|..|.+..+..++..+|||||+|.+.++|+.|++.||+..|.|+.|.|.++
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a  102 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG  102 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEc
Confidence            45689999999999999999999999999843322222226778899999999999999999999999999999999999


Q ss_pred             ecCCCC
Q psy7051          91 RYGRPP   96 (158)
Q Consensus        91 ~~~~~~   96 (158)
                      +.....
T Consensus       103 ~~~~~~  108 (115)
T 2cpx_A          103 KNKKQR  108 (115)
T ss_dssp             CCCSCC
T ss_pred             cCCCCC
Confidence            865443

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

Probab=99.86  E-value=2.1e-21  Score=125.93  Aligned_cols=84  Identities=30%  Similarity=0.494  Sum_probs=75.1

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      .++..+|||+|||..+++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|+.|++.+ +..|+|+.|.|.+
T Consensus        22 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~~  100 (109)
T 2rs2_A           22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPKV  100 (109)
T ss_dssp             ----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEEE
Confidence            445689999999999999999999999999999999999888999999999999999999999875 5899999999999


Q ss_pred             eecCC
Q psy7051          90 ARYGR   94 (158)
Q Consensus        90 a~~~~   94 (158)
                      +....
T Consensus       101 a~~~~  105 (109)
T 2rs2_A          101 AFPRR  105 (109)
T ss_dssp             CCCCC
T ss_pred             ccCCC
Confidence            98543

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

Probab=99.86  E-value=5.6e-21  Score=122.83  Aligned_cols=82  Identities=21%  Similarity=0.313  Sum_probs=75.0

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEE-EEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEE
Q psy7051           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGD-IYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV   87 (158)
Q Consensus         9 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~-v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v   87 (158)
                      ......+|||+|||+.+++++|+++|++||.|.. |.|+.+ .+++++|||||+|.+.++|+.||+. |+..|.|+.|.|
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v   88 (104)
T 1wg5_A           11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEI   88 (104)
T ss_dssp             SCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEE
Confidence            3455689999999999999999999999999987 888888 6899999999999999999999986 999999999999


Q ss_pred             Eeeec
Q psy7051          88 QMARY   92 (158)
Q Consensus        88 ~~a~~   92 (158)
                      .++..
T Consensus        89 ~~~~~   93 (104)
T 1wg5_A           89 FKSSR   93 (104)
T ss_dssp             EEECT
T ss_pred             EECCH
Confidence            98863

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

Probab=99.86  E-value=1.2e-21  Score=125.41  Aligned_cols=78  Identities=18%  Similarity=0.269  Sum_probs=70.6

Q ss_pred             CCCCcEEEEeCCCC-CCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCc--ccCCceEE
Q psy7051          10 IEGMVSLKVDNLTY-RTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGR--MLDGRELR   86 (158)
Q Consensus        10 ~~~~~~l~V~nl~~-~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~--~i~g~~i~   86 (158)
                      .++..+|||+|||+ .+++++|+++|++||.|..|.|+.+      ++||||+|++.++|+.|++.||+.  .|.|+.|.
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~   85 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   85 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEE
Confidence            45678999999999 9999999999999999999999865      479999999999999999998864  59999999


Q ss_pred             EEeeecC
Q psy7051          87 VQMARYG   93 (158)
Q Consensus        87 v~~a~~~   93 (158)
                      |++|+..
T Consensus        86 V~~a~~~   92 (102)
T 1x4d_A           86 VHLSQKY   92 (102)
T ss_dssp             EEEECCC
T ss_pred             EEECCCC
Confidence            9999843

>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=99.86  E-value=4.8e-22  Score=126.98  Aligned_cols=82  Identities=22%  Similarity=0.403  Sum_probs=73.8

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCC-CCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEE
Q psy7051           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDR-FTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV   87 (158)
Q Consensus         9 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~-~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v   87 (158)
                      ......+|||+|||..+++++|+++|++|| |..|.|+.+. .++..+|||||+|.+.++|+.|+ .|||..|.|+.|.|
T Consensus        15 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V   92 (100)
T 2j76_E           15 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRV   92 (100)
T ss_dssp             -----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEE
Confidence            345568999999999999999999999999 9999999987 58999999999999999999999 89999999999999


Q ss_pred             Eeeec
Q psy7051          88 QMARY   92 (158)
Q Consensus        88 ~~a~~   92 (158)
                      ++++.
T Consensus        93 ~~a~~   97 (100)
T 2j76_E           93 DVADQ   97 (100)
T ss_dssp             EECCC
T ss_pred             EeccC
Confidence            99874

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

Probab=99.86  E-value=6e-22  Score=119.92  Aligned_cols=75  Identities=27%  Similarity=0.431  Sum_probs=71.6

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        15 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      +|||+|||+.+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|++|++ ||+..|+|+.|.|.+|
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            48999999999999999999999999999999998889999999999999999999997 9999999999999875

>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=99.86  E-value=7.2e-21  Score=123.08  Aligned_cols=84  Identities=21%  Similarity=0.244  Sum_probs=77.0

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCc-eEEEEEc-cCCCCCCcccEEEEEEcCHHHHHHHHHHhC--CcccCCceEE
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGE-VGDIYIP-RDRFTRESRGFAFVRFFDKRDAEDALDAMD--GRMLDGRELR   86 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~-i~~v~~~-~~~~~~~~~g~afV~f~~~~~a~~a~~~l~--g~~i~g~~i~   86 (158)
                      .+..+|||+|||..+++++|+++|.+||. |..|.++ .+..++..+|||||+|.+.++|+.|++.|+  +..|.|+.|.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~   85 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIA   85 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCE
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEE
Confidence            45689999999999999999999999998 9999998 788788899999999999999999999996  5899999999


Q ss_pred             EEeeecCC
Q psy7051          87 VQMARYGR   94 (158)
Q Consensus        87 v~~a~~~~   94 (158)
                      |.+++...
T Consensus        86 V~~a~~~~   93 (109)
T 2dis_A           86 VDWAEPEI   93 (109)
T ss_dssp             EEESCSSC
T ss_pred             EEEcCCCC
Confidence            99998544

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

Probab=99.86  E-value=1.5e-21  Score=126.63  Aligned_cols=86  Identities=21%  Similarity=0.372  Sum_probs=77.4

Q ss_pred             CCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCC
Q psy7051           3 YGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDG   82 (158)
Q Consensus         3 ~~~p~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g   82 (158)
                      .+.|++......+|||+|||+.+++++|+++|++| .|..|.|+.++. ++++|||||+|.+.++|++|| .||+..|+|
T Consensus         6 ~~~~~~~~~~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al-~~~~~~~~g   82 (109)
T 2dnn_A            6 SGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQ   82 (109)
T ss_dssp             CCCCCCCCHHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHH-HTTTEEETT
T ss_pred             CCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHH-hcCCCeECC
Confidence            34555555566899999999999999999999999 899999999874 889999999999999999999 699999999


Q ss_pred             ceEEEEeee
Q psy7051          83 RELRVQMAR   91 (158)
Q Consensus        83 ~~i~v~~a~   91 (158)
                      +.|.|..+.
T Consensus        83 r~i~V~~a~   91 (109)
T 2dnn_A           83 RYVEVSPAT   91 (109)
T ss_dssp             EEEEEEECC
T ss_pred             eEEEEEECC
Confidence            999998875

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

Probab=99.86  E-value=1.8e-21  Score=124.93  Aligned_cols=76  Identities=13%  Similarity=0.241  Sum_probs=69.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCC--cccCCceEEEEe
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG--RMLDGRELRVQM   89 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g--~~i~g~~i~v~~   89 (158)
                      +..+|||+|||+.+++++|+++|++||+|..|.|+.+      +|||||+|.+.++|+.|++.|++  ..|.|+.|.|.+
T Consensus        15 ~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~   88 (105)
T 1sjq_A           15 PSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQF   88 (105)
T ss_dssp             CCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEE
Confidence            3588999999999999999999999999999999875      68999999999999999998864  689999999999


Q ss_pred             eecC
Q psy7051          90 ARYG   93 (158)
Q Consensus        90 a~~~   93 (158)
                      ++..
T Consensus        89 A~~~   92 (105)
T 1sjq_A           89 SNHK   92 (105)
T ss_dssp             CSSS
T ss_pred             cCCC
Confidence            9743

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

Probab=99.86  E-value=5.7e-21  Score=121.19  Aligned_cols=77  Identities=30%  Similarity=0.407  Sum_probs=71.0

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccC--CceEEEE
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLD--GRELRVQ   88 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~--g~~i~v~   88 (158)
                      ++..+|||+|||..+++++|+++|++||.|..|.++.+      ++||||+|.+.++|+.|++.||+..|.  |+.|.|+
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~   88 (97)
T 1why_A           15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD   88 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEE
Confidence            34578999999999999999999999999999998754      679999999999999999999999999  9999999


Q ss_pred             eeecC
Q psy7051          89 MARYG   93 (158)
Q Consensus        89 ~a~~~   93 (158)
                      +++..
T Consensus        89 ~a~~~   93 (97)
T 1why_A           89 FAKSG   93 (97)
T ss_dssp             ECCCC
T ss_pred             ECCCC
Confidence            99854

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

Probab=99.86  E-value=3.8e-21  Score=129.50  Aligned_cols=81  Identities=37%  Similarity=0.470  Sum_probs=76.1

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      ..+..+|||+|||..+++++|+++|++||.|..|.++.++.++..+|||||+|.+.++|+.|++.||+..|.|+.|.|.+
T Consensus        60 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  139 (140)
T 2ku7_A           60 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL  139 (140)
T ss_dssp             CSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEEC
T ss_pred             CCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            34568999999999999999999999999999999999988999999999999999999999999999999999999987


Q ss_pred             e
Q psy7051          90 A   90 (158)
Q Consensus        90 a   90 (158)
                      |
T Consensus       140 A  140 (140)
T 2ku7_A          140 A  140 (140)
T ss_dssp             -
T ss_pred             C
Confidence            5

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

Probab=99.86  E-value=2.9e-21  Score=125.26  Aligned_cols=84  Identities=31%  Similarity=0.528  Sum_probs=76.0

Q ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEE
Q psy7051           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR   86 (158)
Q Consensus         7 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~   86 (158)
                      +.......+|||+|||..+++++|+++|++||.|..|.++.+.  +..+|||||+|.+.++|+.|++.|||..|+|+.|.
T Consensus        23 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~  100 (109)
T 2err_A           23 TENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIE  100 (109)
T ss_dssp             CSCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECE
T ss_pred             ccCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            3344566899999999999999999999999999999998875  34789999999999999999999999999999999


Q ss_pred             EEeeec
Q psy7051          87 VQMARY   92 (158)
Q Consensus        87 v~~a~~   92 (158)
                      |++++.
T Consensus       101 V~~a~~  106 (109)
T 2err_A          101 VNNATA  106 (109)
T ss_dssp             EEECCC
T ss_pred             EEECCC
Confidence            999873

>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=99.86  E-value=8.4e-21  Score=122.07  Aligned_cols=79  Identities=14%  Similarity=0.177  Sum_probs=71.0

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCc--ccCCceEE
Q psy7051           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGR--MLDGRELR   86 (158)
Q Consensus         9 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~--~i~g~~i~   86 (158)
                      ..++..+|||+|||+.+++++|+++|++||.|..|.|+.+      +|||||+|.+.++|+.|++.|++.  .|.|+.|.
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~   84 (104)
T 1wex_A           11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAF   84 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            4566789999999999999999999999999999988764      689999999999999999988754  59999999


Q ss_pred             EEeeecC
Q psy7051          87 VQMARYG   93 (158)
Q Consensus        87 v~~a~~~   93 (158)
                      |++++..
T Consensus        85 V~~a~~~   91 (104)
T 1wex_A           85 FNYSTSK   91 (104)
T ss_dssp             EEECSSS
T ss_pred             EEEccCc
Confidence            9999854

>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=99.86  E-value=8.1e-21  Score=120.91  Aligned_cols=80  Identities=33%  Similarity=0.551  Sum_probs=73.1

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEE
Q psy7051           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ   88 (158)
Q Consensus         9 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~   88 (158)
                      ...+..+|||+|||..+++++|+++|++||.|..|.++.+      +|||||+|.+.++|+.|++.||+..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~   84 (99)
T 2cpj_A           11 TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVR   84 (99)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEE
Confidence            3455689999999999999999999999999999998754      6899999999999999999999999999999999


Q ss_pred             eeecCC
Q psy7051          89 MARYGR   94 (158)
Q Consensus        89 ~a~~~~   94 (158)
                      +++...
T Consensus        85 ~a~~~~   90 (99)
T 2cpj_A           85 FACHSA   90 (99)
T ss_dssp             ESSCCS
T ss_pred             EcCCCC
Confidence            998543

>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=99.86  E-value=4.7e-21  Score=118.59  Aligned_cols=80  Identities=28%  Similarity=0.412  Sum_probs=72.5

Q ss_pred             CCCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHh-CCcccCCce
Q psy7051           6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM-DGRMLDGRE   84 (158)
Q Consensus         6 p~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l-~g~~i~g~~   84 (158)
                      .++......+|||+|||..+++++|+++|++||.|..|.++.+      +|||||+|.+.++|+.|++.| ++..|.|+.
T Consensus         5 ~~~~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~   78 (85)
T 2ytc_A            5 SSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRR   78 (85)
T ss_dssp             CCCSCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEE
T ss_pred             CCCCCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCE
Confidence            3444566789999999999999999999999999999999764      689999999999999999988 999999999


Q ss_pred             EEEEeee
Q psy7051          85 LRVQMAR   91 (158)
Q Consensus        85 i~v~~a~   91 (158)
                      |.|++++
T Consensus        79 l~v~~ak   85 (85)
T 2ytc_A           79 LNVKWGR   85 (85)
T ss_dssp             CCEEECC
T ss_pred             EEEEecC
Confidence            9999975

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

Probab=99.86  E-value=1.2e-20  Score=120.66  Aligned_cols=80  Identities=14%  Similarity=0.143  Sum_probs=71.2

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhC--CcccCCceEE
Q psy7051           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD--GRMLDGRELR   86 (158)
Q Consensus         9 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~--g~~i~g~~i~   86 (158)
                      ..++..+|||+|||+.+++++|+++|++||.|..|.++.+      +|||||+|.+.++|+.|++.|+  +..|.|+.|.
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~   84 (101)
T 2cq1_A           11 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIY   84 (101)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEEE
Confidence            3456689999999999999999999999999999988764      6899999999999999999774  6789999999


Q ss_pred             EEeeecCC
Q psy7051          87 VQMARYGR   94 (158)
Q Consensus        87 v~~a~~~~   94 (158)
                      |.+++...
T Consensus        85 V~~a~~~~   92 (101)
T 2cq1_A           85 IQYSNHKE   92 (101)
T ss_dssp             EEECSCSS
T ss_pred             EEEcCccc
Confidence            99998543

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

Probab=99.85  E-value=5.8e-21  Score=125.31  Aligned_cols=80  Identities=13%  Similarity=0.202  Sum_probs=72.0

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCC--cccCCceEE
Q psy7051           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG--RMLDGRELR   86 (158)
Q Consensus         9 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g--~~i~g~~i~   86 (158)
                      ..++..+|||+|||+.+++++|+++|++||.|+.|.|+.+      +|||||+|++.++|++|++.|++  ..|.|+.|.
T Consensus        27 ~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~  100 (119)
T 2ad9_A           27 AGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIY  100 (119)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEE
Confidence            4456689999999999999999999999999999999875      68999999999999999998874  689999999


Q ss_pred             EEeeecCC
Q psy7051          87 VQMARYGR   94 (158)
Q Consensus        87 v~~a~~~~   94 (158)
                      |.+++...
T Consensus       101 V~~a~~k~  108 (119)
T 2ad9_A          101 IQFSNHKE  108 (119)
T ss_dssp             EEECSSSS
T ss_pred             EEEccCCC
Confidence            99998543

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

Probab=99.85  E-value=8.5e-22  Score=130.49  Aligned_cols=80  Identities=18%  Similarity=0.210  Sum_probs=73.5

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      ....+|||+|||+.+++++|+++|++||.|..+.++.+..++.++|||||+|.+.++|+.||+ ||+..|+|+.|.|.++
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            455899999999999999999999999999886566666689999999999999999999998 9999999999999998


Q ss_pred             e
Q psy7051          91 R   91 (158)
Q Consensus        91 ~   91 (158)
                      .
T Consensus       102 ~  102 (124)
T 1wel_A          102 T  102 (124)
T ss_dssp             C
T ss_pred             C
Confidence            6

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

Probab=99.85  E-value=1.3e-20  Score=118.02  Aligned_cols=77  Identities=26%  Similarity=0.488  Sum_probs=70.7

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      ..+..+|||+|||..+++++|+++|++||.|..|.++.        +||||+|.+.++|+.|++.||+..|.|+.|.|.+
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   77 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVEL   77 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            34568899999999999999999999999999999963        4999999999999999999999999999999999


Q ss_pred             eecCC
Q psy7051          90 ARYGR   94 (158)
Q Consensus        90 a~~~~   94 (158)
                      ++...
T Consensus        78 a~~~~   82 (90)
T 2dnp_A           78 STKGQ   82 (90)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            98543

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

Probab=99.85  E-value=8.2e-21  Score=126.25  Aligned_cols=83  Identities=19%  Similarity=0.377  Sum_probs=73.9

Q ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHH----HHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCC
Q psy7051           7 PPRIEGMVSLKVDNLTYRTTPDDLR----RVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDG   82 (158)
Q Consensus         7 ~~~~~~~~~l~V~nl~~~~~~~~l~----~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g   82 (158)
                      ++..++..+|||+|||+.+++++|+    ++|++||.|..|.+..   ++..+|||||+|.+.++|+.|++.|||..|.|
T Consensus        23 ~~~~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~g   99 (127)
T 2a3j_A           23 PPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQG   99 (127)
T ss_dssp             CCCCSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTT
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCC
Confidence            3445667899999999999999876    6999999999987753   56789999999999999999999999999999


Q ss_pred             ceEEEEeeec
Q psy7051          83 RELRVQMARY   92 (158)
Q Consensus        83 ~~i~v~~a~~   92 (158)
                      +.|.|.+++.
T Consensus       100 r~l~V~~a~~  109 (127)
T 2a3j_A          100 NPLVITFSET  109 (127)
T ss_dssp             SCCEEEECCC
T ss_pred             CEEEEEEccC
Confidence            9999999974

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

Probab=99.85  E-value=2.4e-21  Score=140.90  Aligned_cols=80  Identities=26%  Similarity=0.393  Sum_probs=75.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcC--ceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCG--EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G--~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      ..++|||+||++.+++++|+++|++||  .|+.|.|+.++.+++++|||||+|.+.++|++||+.||+..|.|+.|+|.+
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~  146 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP  146 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEE
Confidence            456899999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             ee
Q psy7051          90 AR   91 (158)
Q Consensus        90 a~   91 (158)
                      ++
T Consensus       147 a~  148 (229)
T 3q2s_C          147 VN  148 (229)
T ss_dssp             CC
T ss_pred             CC
Confidence            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

Probab=99.85  E-value=8.2e-21  Score=123.16  Aligned_cols=76  Identities=28%  Similarity=0.511  Sum_probs=70.0

Q ss_pred             CCcEEEEeCCCCC-CCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          12 GMVSLKVDNLTYR-TTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        12 ~~~~l~V~nl~~~-~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      ...+|||+|||+. +++++|+++|++||.|..|.+        .++||||+|.+.++|+.|++.||+..|+|+.|.|+++
T Consensus        26 ~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   97 (110)
T 1wf1_A           26 INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMA   97 (110)
T ss_dssp             CSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEES
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            3479999999999 999999999999999999988        3689999999999999999999999999999999999


Q ss_pred             ecCCC
Q psy7051          91 RYGRP   95 (158)
Q Consensus        91 ~~~~~   95 (158)
                      +..+.
T Consensus        98 ~~~~~  102 (110)
T 1wf1_A           98 GEPKP  102 (110)
T ss_dssp             CCCCS
T ss_pred             CCCCC
Confidence            85443

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

Probab=99.85  E-value=1.3e-21  Score=118.86  Aligned_cols=76  Identities=32%  Similarity=0.592  Sum_probs=72.6

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      .+|||+|||..+++++|+++|++||+|..|.++.++.++.++|||||+|.+.++|+.|++.++ ..|+|+.|.|++|
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            369999999999999999999999999999999998889999999999999999999999998 9999999999886

>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=99.85  E-value=1.4e-20  Score=121.87  Aligned_cols=78  Identities=18%  Similarity=0.381  Sum_probs=72.3

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      ....+|||+|||..+++++|+++|++||.|..|.|+.+      +|||||+|.+.++|+.|++.|||..|.|+.|.|.++
T Consensus        23 ~~~~~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           23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG   96 (109)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEec
Confidence            34579999999999999999999999999999999876      689999999999999999999999999999999999


Q ss_pred             ecCC
Q psy7051          91 RYGR   94 (158)
Q Consensus        91 ~~~~   94 (158)
                      +...
T Consensus        97 ~~~~  100 (109)
T 1x4g_A           97 KESP  100 (109)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8544

>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=99.85  E-value=8.8e-22  Score=123.23  Aligned_cols=80  Identities=28%  Similarity=0.513  Sum_probs=73.9

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeecC
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARYG   93 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~~   93 (158)
                      .+|||+|||..+++++|+++|++||.|..|.++.++.++.++|||||+|.+.+ |+.|++.|||..|.|+.|.|++|...
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~   80 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPK   80 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC---
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            58999999999999999999999999999999999888999999999999999 99999999999999999999999754


Q ss_pred             C
Q psy7051          94 R   94 (158)
Q Consensus        94 ~   94 (158)
                      .
T Consensus        81 ~   81 (90)
T 2ki2_A           81 K   81 (90)
T ss_dssp             -
T ss_pred             C
Confidence            3

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

Probab=99.85  E-value=5.6e-21  Score=121.09  Aligned_cols=79  Identities=24%  Similarity=0.412  Sum_probs=70.6

Q ss_pred             CCCCCcEEEEeCCCC-CCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEE
Q psy7051           9 RIEGMVSLKVDNLTY-RTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV   87 (158)
Q Consensus         9 ~~~~~~~l~V~nl~~-~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v   87 (158)
                      ..++..+|||+|||+ .+++++|+++|++||.|..|.+.        +|||||+|.+.++|+.|++.||+..|.|+.|.|
T Consensus         6 ~~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   77 (96)
T 2kvi_A            6 NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLIL   77 (96)
T ss_dssp             ---CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCE
T ss_pred             cCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEE
Confidence            345678999999998 99999999999999999999883        679999999999999999999999999999999


Q ss_pred             EeeecCCC
Q psy7051          88 QMARYGRP   95 (158)
Q Consensus        88 ~~a~~~~~   95 (158)
                      ++++....
T Consensus        78 ~~a~~~~~   85 (96)
T 2kvi_A           78 EVSSSNAR   85 (96)
T ss_dssp             EEEECCCC
T ss_pred             EEcCcCCC
Confidence            99985543

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

Probab=99.85  E-value=1.1e-20  Score=123.17  Aligned_cols=81  Identities=21%  Similarity=0.369  Sum_probs=75.9

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCccc--------C
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRML--------D   81 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i--------~   81 (158)
                      ..+..+|||+|||..+++++|+++|++||.|..|.|+.+. ++..+|||||+|.+.++|+.|++.|||..|        .
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~  100 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP  100 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCC
Confidence            3456899999999999999999999999999999999998 889999999999999999999999999999        5


Q ss_pred             CceEEEEeee
Q psy7051          82 GRELRVQMAR   91 (158)
Q Consensus        82 g~~i~v~~a~   91 (158)
                      ++.|.|.|++
T Consensus       101 ~~~l~v~~a~  110 (114)
T 1x5o_A          101 TEPLLCKFSG  110 (114)
T ss_dssp             SSCBEEEECC
T ss_pred             CCceeEEccC
Confidence            7889999997

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

Probab=99.85  E-value=2.8e-20  Score=118.39  Aligned_cols=77  Identities=30%  Similarity=0.519  Sum_probs=70.0

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhhc--CceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEE
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDLRRVFERC--GEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV   87 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~--G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v   87 (158)
                      ..+..+|||+|||+.+++++|+++|++|  |.|..|.++        ++||||+|.+.++|+.|++.||+..|.|+.|.|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   83 (99)
T 2cpd_A           12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEV   83 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEE
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            3456899999999999999999999999  899998874        569999999999999999999999999999999


Q ss_pred             EeeecCC
Q psy7051          88 QMARYGR   94 (158)
Q Consensus        88 ~~a~~~~   94 (158)
                      .+++...
T Consensus        84 ~~a~~~~   90 (99)
T 2cpd_A           84 TLAKPVD   90 (99)
T ss_dssp             ECCCCCC
T ss_pred             EECCCCC
Confidence            9998543

>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=99.85  E-value=3.1e-21  Score=126.01  Aligned_cols=81  Identities=21%  Similarity=0.281  Sum_probs=75.3

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhhcCce-EEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEE
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEV-GDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ   88 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i-~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~   88 (158)
                      ..+..+|||+|||+.+++++|+++|++||.| ..|.|+.+. ++..+|||||+|.+.++|+.||+. |+..|.|+.|.|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~   89 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVH   89 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEE
Confidence            3456899999999999999999999999999 889999998 899999999999999999999976 9999999999999


Q ss_pred             eeec
Q psy7051          89 MARY   92 (158)
Q Consensus        89 ~a~~   92 (158)
                      ++..
T Consensus        90 ~a~~   93 (114)
T 2cpy_A           90 VVTL   93 (114)
T ss_dssp             EECH
T ss_pred             ECCH
Confidence            9874

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

Probab=99.85  E-value=3.7e-21  Score=126.46  Aligned_cols=79  Identities=20%  Similarity=0.263  Sum_probs=74.2

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCc---eEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEE
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGE---VGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV   87 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~---i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v   87 (158)
                      ....+|||+|||+.+++++|+++|++||.   |..|.|+.+.. ++++|||||+|.+.++|+.||+ ||+..|+|+.|.|
T Consensus        15 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V   92 (118)
T 2db1_A           15 GEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEV   92 (118)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEE
Confidence            45688999999999999999999999998   89999998875 8899999999999999999998 9999999999999


Q ss_pred             Eeee
Q psy7051          88 QMAR   91 (158)
Q Consensus        88 ~~a~   91 (158)
                      .++.
T Consensus        93 ~~a~   96 (118)
T 2db1_A           93 FKSH   96 (118)
T ss_dssp             EEEC
T ss_pred             EECC
Confidence            9986

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

Probab=99.85  E-value=8.3e-21  Score=120.47  Aligned_cols=79  Identities=27%  Similarity=0.368  Sum_probs=70.4

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      .+...+|||+|||..+++++|+++|++||.|. +.++.+    ..+|||||+|.+.++|+.|++.|||..|.|+.|.|.+
T Consensus        16 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   90 (97)
T 2e5j_A           16 APLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVAL   90 (97)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE----TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC----CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            34468999999999999999999999999996 556543    4679999999999999999999999999999999999


Q ss_pred             eecC
Q psy7051          90 ARYG   93 (158)
Q Consensus        90 a~~~   93 (158)
                      ++..
T Consensus        91 a~~~   94 (97)
T 2e5j_A           91 ARQQ   94 (97)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9854

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

Probab=99.85  E-value=7.2e-21  Score=117.50  Aligned_cols=73  Identities=18%  Similarity=0.218  Sum_probs=68.9

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ..-|||+||++.+++++|+++|.+||+|..+.+..      ++|||||+|.+.++|+.|++.||+..|.|+.|.|++|.
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            46799999999999999999999999999999865      47999999999999999999999999999999999984

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

Probab=99.85  E-value=8.9e-21  Score=132.91  Aligned_cols=82  Identities=29%  Similarity=0.432  Sum_probs=77.2

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      .++.++|||+|||..+++++|+++|++||.|..|.|+.+. ++..+|||||+|.+.++|+.|++.||+..|.|+.|+|++
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~~  163 (177)
T 2f3j_A           85 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  163 (177)
T ss_dssp             CTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3446899999999999999999999999999999999988 888999999999999999999999999999999999999


Q ss_pred             eec
Q psy7051          90 ARY   92 (158)
Q Consensus        90 a~~   92 (158)
                      +..
T Consensus       164 a~~  166 (177)
T 2f3j_A          164 VAS  166 (177)
T ss_dssp             ESS
T ss_pred             ecC
Confidence            874

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

Probab=99.85  E-value=7.7e-21  Score=121.39  Aligned_cols=76  Identities=36%  Similarity=0.612  Sum_probs=71.0

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeecC
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARYG   93 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~~   93 (158)
                      ++|||+|||..+++++|+++|++||+|..|.++.+     .+|||||+|.+.++|+.|++.||+..|.|+.|.|.+++..
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   75 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGM   75 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCC
Confidence            47999999999999999999999999999999876     5789999999999999999999999999999999999854


Q ss_pred             C
Q psy7051          94 R   94 (158)
Q Consensus        94 ~   94 (158)
                      .
T Consensus        76 ~   76 (101)
T 2hvz_A           76 P   76 (101)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=4.3e-21  Score=121.60  Aligned_cols=83  Identities=30%  Similarity=0.512  Sum_probs=73.5

Q ss_pred             CCCCCCcEEEEeCCCCCCCHHHHH----HHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCc
Q psy7051           8 PRIEGMVSLKVDNLTYRTTPDDLR----RVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGR   83 (158)
Q Consensus         8 ~~~~~~~~l~V~nl~~~~~~~~l~----~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~   83 (158)
                      +..++..+|||+|||..+++++|+    ++|++||.|..|.++.   ++..+|||||+|.+.++|+.|++.|||..|.|+
T Consensus         3 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   79 (97)
T 1nu4_A            3 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK   79 (97)
T ss_dssp             ---CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCc
Confidence            345667899999999999999999    9999999999998863   456789999999999999999999999999999


Q ss_pred             eEEEEeeecC
Q psy7051          84 ELRVQMARYG   93 (158)
Q Consensus        84 ~i~v~~a~~~   93 (158)
                      .|.|.+++..
T Consensus        80 ~l~v~~a~~~   89 (97)
T 1nu4_A           80 PMRIQYAKTD   89 (97)
T ss_dssp             ECEEEECSSC
T ss_pred             EEEEEEccCC
Confidence            9999999854

>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=99.84  E-value=5e-21  Score=128.69  Aligned_cols=79  Identities=19%  Similarity=0.256  Sum_probs=74.3

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCc---eEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEE
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGE---VGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV   87 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~---i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v   87 (158)
                      ....+|||+|||+.+|+++|+++|++||.   |..|.|+.++. ++++|||||+|.+.++|+.||+ ||+..|+|+.|.|
T Consensus        42 ~~~~~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           42 GEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEV  119 (136)
T ss_dssp             CTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEE
Confidence            45689999999999999999999999999   88999999876 9999999999999999999998 9999999999999


Q ss_pred             Eeee
Q psy7051          88 QMAR   91 (158)
Q Consensus        88 ~~a~   91 (158)
                      .++.
T Consensus       120 ~~a~  123 (136)
T 2hgl_A          120 FKSH  123 (136)
T ss_dssp             EECC
T ss_pred             EECC
Confidence            9875

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

Probab=99.74  E-value=1.1e-22  Score=133.30  Aligned_cols=85  Identities=26%  Similarity=0.321  Sum_probs=78.6

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEE--------EEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccC
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGD--------IYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLD   81 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~--------v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~   81 (158)
                      ..+..+|||+|||..+++++|+++|++||.|..        |.|+.++.++..+|||||+|.+.++|+.|++.||+..|.
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            345688999999999999999999999999998        889988888999999999999999999999999999999


Q ss_pred             CceEEEEeeecCC
Q psy7051          82 GRELRVQMARYGR   94 (158)
Q Consensus        82 g~~i~v~~a~~~~   94 (158)
                      |+.|.|.+++...
T Consensus        84 g~~l~V~~a~~~~   96 (116)
T 2lcw_A           84 GNPIKVSFATRRA   96 (116)
Confidence            9999999998543

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

Probab=99.84  E-value=1.1e-20  Score=122.29  Aligned_cols=77  Identities=22%  Similarity=0.387  Sum_probs=71.2

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      ..+..+|||+|||..+++++|+++|++||.|..|.++        +|||||+|.+.++|+.|++.|||..|.|+.|.|.+
T Consensus        28 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   99 (108)
T 2jvo_A           28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVY   99 (108)
T ss_dssp             CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEES
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            3456899999999999999999999999999999886        58999999999999999999999999999999999


Q ss_pred             eecCC
Q psy7051          90 ARYGR   94 (158)
Q Consensus        90 a~~~~   94 (158)
                      ++...
T Consensus       100 a~~~~  104 (108)
T 2jvo_A          100 SKLPA  104 (108)
T ss_dssp             CSCCC
T ss_pred             ecCCC
Confidence            98543

>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=99.84  E-value=1.2e-20  Score=118.81  Aligned_cols=76  Identities=29%  Similarity=0.433  Sum_probs=67.9

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCc-eEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCC-cccCCceEEEE
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGE-VGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG-RMLDGRELRVQ   88 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~-i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g-~~i~g~~i~v~   88 (158)
                      ++..+|||+|||..+++++|+++|++||. |..+.+.       .+|||||+|.+.++|+.|++.||+ ..|.|+.|.|.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~   78 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVD   78 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEE
Confidence            45688999999999999999999999999 6555552       368999999999999999999999 99999999999


Q ss_pred             eeecC
Q psy7051          89 MARYG   93 (158)
Q Consensus        89 ~a~~~   93 (158)
                      +++..
T Consensus        79 ~a~~~   83 (93)
T 2cqh_A           79 YSVSK   83 (93)
T ss_dssp             ECCCC
T ss_pred             EccCc
Confidence            99854

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

Probab=99.84  E-value=1.9e-20  Score=134.63  Aligned_cols=86  Identities=33%  Similarity=0.430  Sum_probs=77.0

Q ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEE
Q psy7051           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR   86 (158)
Q Consensus         7 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~   86 (158)
                      .....+..+|||+|||+.+++++|+++|++||+|..|.|+.++.++.++|||||+|.+.++|+.||+.||+..+.|+.|.
T Consensus         9 ~~p~~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~   88 (213)
T 4f02_A            9 SAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVR   88 (213)
T ss_dssp             ------CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccc
Confidence            33345678999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeeec
Q psy7051          87 VQMARY   92 (158)
Q Consensus        87 v~~a~~   92 (158)
                      |.++..
T Consensus        89 ~~~~~~   94 (213)
T 4f02_A           89 IMWSQR   94 (213)
T ss_dssp             EEECCC
T ss_pred             cccccc
Confidence            998763

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

Probab=99.84  E-value=1.9e-21  Score=124.21  Aligned_cols=81  Identities=22%  Similarity=0.282  Sum_probs=73.3

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      ....+|||+|||..+++++|+++|++||.|.. .++.+..++.++|||||+|.+.++|+.||+ ||+..|.|+.|.|.++
T Consensus        15 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~a   92 (101)
T 1fj7_A           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   92 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEc
Confidence            35689999999999999999999999999877 566666678889999999999999999998 9999999999999999


Q ss_pred             ecC
Q psy7051          91 RYG   93 (158)
Q Consensus        91 ~~~   93 (158)
                      +..
T Consensus        93 ~~~   95 (101)
T 1fj7_A           93 KGR   95 (101)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            743

>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=99.84  E-value=4.4e-20  Score=117.23  Aligned_cols=75  Identities=24%  Similarity=0.402  Sum_probs=69.8

Q ss_pred             CCCCcEEEEeCCCC-CCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEE
Q psy7051          10 IEGMVSLKVDNLTY-RTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ   88 (158)
Q Consensus        10 ~~~~~~l~V~nl~~-~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~   88 (158)
                      ..+..+|||+|||. .+++++|+++|++||.|..|.+.        +|||||+|.+.++|+.|++.|||..|.|+.|.|+
T Consensus        19 ~~~~~~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           19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILE   90 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            45568999999998 99999999999999999999883        6899999999999999999999999999999999


Q ss_pred             eeec
Q psy7051          89 MARY   92 (158)
Q Consensus        89 ~a~~   92 (158)
                      +++.
T Consensus        91 ~a~~   94 (97)
T 2xnq_A           91 VSSS   94 (97)
T ss_dssp             ECCC
T ss_pred             ecCC
Confidence            9874

>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=99.84  E-value=3.7e-21  Score=116.35  Aligned_cols=75  Identities=24%  Similarity=0.414  Sum_probs=71.1

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        15 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      +|||+|||..+++++|+++|++||+|..|.++.++.++.++|||||+|.+.++|+.|++ +++..|.|+.|.|.+|
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            59999999999999999999999999999999998889999999999999999999997 5899999999999875

>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=99.83  E-value=6.7e-21  Score=123.08  Aligned_cols=80  Identities=19%  Similarity=0.312  Sum_probs=74.6

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhhcCc---eEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEE
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGE---VGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR   86 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~---i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~   86 (158)
                      .....+|||+|||+.+++++|+++|+.||.   |..|.|+.+.. +.++|||||+|.+.++|+.||+ ||+..|+|+.|.
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~   85 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVE   85 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCC
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEE
Confidence            455689999999999999999999999988   89999999876 8999999999999999999998 999999999999


Q ss_pred             EEeee
Q psy7051          87 VQMAR   91 (158)
Q Consensus        87 v~~a~   91 (158)
                      |.++.
T Consensus        86 V~~a~   90 (107)
T 2lmi_A           86 VYEIN   90 (107)
T ss_dssp             CEECC
T ss_pred             EEECC
Confidence            99886

>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=99.83  E-value=5.5e-20  Score=120.05  Aligned_cols=78  Identities=28%  Similarity=0.415  Sum_probs=72.2

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      +..+|||+|||..+++++|.++|++||.|..|.++.+   +..+|||||+|.+.++|+.|++.|||..|.|+.|.|.++.
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   83 (115)
T 3lqv_A            7 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYN   83 (115)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEec
Confidence            4579999999999999999999999999999999865   3458999999999999999999999999999999999987


Q ss_pred             c
Q psy7051          92 Y   92 (158)
Q Consensus        92 ~   92 (158)
                      .
T Consensus        84 ~   84 (115)
T 3lqv_A           84 A   84 (115)
T ss_dssp             H
T ss_pred             C
Confidence            4

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

Probab=99.83  E-value=9.2e-21  Score=116.42  Aligned_cols=72  Identities=24%  Similarity=0.480  Sum_probs=66.8

Q ss_pred             cEEEEeCCCCCC------CHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCc-eEE
Q psy7051          14 VSLKVDNLTYRT------TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGR-ELR   86 (158)
Q Consensus        14 ~~l~V~nl~~~~------~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~-~i~   86 (158)
                      .+|||+|||..+      ++++|+++|++||.|..|.++  ..++.++|||||+|.+.++|+.|++.|||..|.|+ .|+
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~   79 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFR   79 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEE
Confidence            589999999999      779999999999999999987  35788999999999999999999999999999999 887


Q ss_pred             E
Q psy7051          87 V   87 (158)
Q Consensus        87 v   87 (158)
                      |
T Consensus        80 V   80 (81)
T 2krb_A           80 V   80 (81)
T ss_dssp             C
T ss_pred             e
Confidence            6

>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=99.83  E-value=2.1e-20  Score=121.56  Aligned_cols=75  Identities=20%  Similarity=0.319  Sum_probs=69.8

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ..++|||+|||..+++++|+++|++||.|..|.|+.      .++||||+|.+.++|+.|++.|||..|.|+.|.|+|++
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   82 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            357999999999999999999999999999998864      36899999999999999999999999999999999997


Q ss_pred             c
Q psy7051          92 Y   92 (158)
Q Consensus        92 ~   92 (158)
                      .
T Consensus        83 ~   83 (111)
T 1whx_A           83 I   83 (111)
T ss_dssp             T
T ss_pred             C
Confidence            4

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

Probab=99.83  E-value=1.9e-20  Score=121.56  Aligned_cols=79  Identities=18%  Similarity=0.227  Sum_probs=70.0

Q ss_pred             CCCCcEEEEeCCCCC-CCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCC--cccCCceEE
Q psy7051          10 IEGMVSLKVDNLTYR-TTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG--RMLDGRELR   86 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~-~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g--~~i~g~~i~   86 (158)
                      .++..+|||+|||+. +++++|+++|++||+|..|.|+..      +|||||+|.+.++|+.|++.|++  ..|.|+.|.
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~   95 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   95 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            445689999999998 999999999999999999998643      68999999999999999998864  569999999


Q ss_pred             EEeeecCC
Q psy7051          87 VQMARYGR   94 (158)
Q Consensus        87 v~~a~~~~   94 (158)
                      |.+++...
T Consensus        96 V~~a~~~~  103 (112)
T 1x4f_A           96 VDLSEKYK  103 (112)
T ss_dssp             EEEECSCS
T ss_pred             EEECcccc
Confidence            99997443

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

Probab=99.83  E-value=1.5e-20  Score=120.19  Aligned_cols=84  Identities=25%  Similarity=0.428  Sum_probs=76.4

Q ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEE
Q psy7051           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR   86 (158)
Q Consensus         7 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~   86 (158)
                      |.......+|||+|||..+++++|+++|++||.|..|.++.+. ++..+|||||+|.+.++|+.|++  ++..|+|+.|.
T Consensus         3 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~   79 (102)
T 2xs2_A            3 PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLK   79 (102)
T ss_dssp             CCCEEEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCeECCEEEE
Confidence            3344456899999999999999999999999999999999998 89999999999999999999997  99999999999


Q ss_pred             EEeeecC
Q psy7051          87 VQMARYG   93 (158)
Q Consensus        87 v~~a~~~   93 (158)
                      |.++...
T Consensus        80 v~~a~~~   86 (102)
T 2xs2_A           80 LGPAIRK   86 (102)
T ss_dssp             EEEEEEC
T ss_pred             EEECCcC
Confidence            9998743

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

Probab=99.83  E-value=7.8e-20  Score=115.30  Aligned_cols=78  Identities=24%  Similarity=0.277  Sum_probs=68.7

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      .....+|||+|||..+++++|+++|++||.|..|  +.+..++.   ||||+|.+.++|+.|++ ||+..|.|+.|.|.+
T Consensus         5 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~   78 (94)
T 2e5g_A            5 SSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRP   78 (94)
T ss_dssp             CTTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBC
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEE
Confidence            3456799999999999999999999999999987  44544554   99999999999999998 999999999999998


Q ss_pred             eecC
Q psy7051          90 ARYG   93 (158)
Q Consensus        90 a~~~   93 (158)
                      +...
T Consensus        79 a~~~   82 (94)
T 2e5g_A           79 REQK   82 (94)
T ss_dssp             SCCS
T ss_pred             CCcC
Confidence            7643

>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=99.82  E-value=2.8e-20  Score=123.37  Aligned_cols=80  Identities=23%  Similarity=0.279  Sum_probs=72.1

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceE--EEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEE
Q psy7051           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVG--DIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR   86 (158)
Q Consensus         9 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~--~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~   86 (158)
                      ......+|||+|||+.+++++|+++|++| .|.  .|.|+.++. ++++|||||+|.+.++|++||+ +++..|+|+.|.
T Consensus        38 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~gR~I~  114 (126)
T 2hgm_A           38 DSANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALG-KHKERIGHRYIE  114 (126)
T ss_dssp             CSSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHT-TTTCCBTTBCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHH-HCCCEECCEEEE
Confidence            33456889999999999999999999999 677  899999876 9999999999999999999997 578999999999


Q ss_pred             EEeee
Q psy7051          87 VQMAR   91 (158)
Q Consensus        87 v~~a~   91 (158)
                      |..+.
T Consensus       115 V~~a~  119 (126)
T 2hgm_A          115 VFKSS  119 (126)
T ss_dssp             CEEEC
T ss_pred             EEECC
Confidence            98875

>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=99.82  E-value=4.2e-21  Score=129.45  Aligned_cols=80  Identities=18%  Similarity=0.179  Sum_probs=73.2

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      ....+|||+|||+.+++++|+++|++|| |+.|.|+.++. ++++|||||+|.+.++|+.|| .+|+..|.|+.|.|.++
T Consensus        44 ~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a  120 (139)
T 2hgn_A           44 TTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLN  120 (139)
T ss_dssp             -CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEEC
Confidence            4457899999999999999999999999 77999999975 899999999999999999999 78999999999999998


Q ss_pred             ecC
Q psy7051          91 RYG   93 (158)
Q Consensus        91 ~~~   93 (158)
                      ...
T Consensus       121 ~~~  123 (139)
T 2hgn_A          121 STT  123 (139)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            744

>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=99.82  E-value=7.4e-20  Score=125.87  Aligned_cols=81  Identities=23%  Similarity=0.339  Sum_probs=71.4

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCC--ceEE
Q psy7051           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDG--RELR   86 (158)
Q Consensus         9 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g--~~i~   86 (158)
                      ......+|||+||++.+++++|+++|++||+|..|.|....    ..|||||+|.+.++|+.|++.|||..|.|  +.|+
T Consensus        42 ~ps~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~----~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~  117 (164)
T 1sjr_A           42 GQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLR  117 (164)
T ss_dssp             CCCCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS----SCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEE
T ss_pred             CCCceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEE
Confidence            33445789999999999999999999999999999986442    46899999999999999999999999965  9999


Q ss_pred             EEeeecC
Q psy7051          87 VQMARYG   93 (158)
Q Consensus        87 v~~a~~~   93 (158)
                      |+|++..
T Consensus       118 V~~Ak~~  124 (164)
T 1sjr_A          118 IDFSKLT  124 (164)
T ss_dssp             EEECSSS
T ss_pred             EEEecCC
Confidence            9999854

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

Probab=99.82  E-value=2.4e-19  Score=113.69  Aligned_cols=78  Identities=26%  Similarity=0.350  Sum_probs=69.7

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      ..+..+|||+||  .+++++|+++|++||.|..|.|.      ..+|||||+|.+.++|+.||+.||+..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~   83 (97)
T 1x5p_A           12 PRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNI   83 (97)
T ss_dssp             CCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEEC
T ss_pred             CCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            345689999996  89999999999999999999884      2478999999999999999999999999999999999


Q ss_pred             eecCCC
Q psy7051          90 ARYGRP   95 (158)
Q Consensus        90 a~~~~~   95 (158)
                      ++....
T Consensus        84 a~~~~~   89 (97)
T 1x5p_A           84 ARKQPM   89 (97)
T ss_dssp             CSSCCC
T ss_pred             CCCCCC
Confidence            985443

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

Probab=99.82  E-value=2.5e-20  Score=117.87  Aligned_cols=78  Identities=28%  Similarity=0.491  Sum_probs=70.7

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      ..+..+|||+|||..+++++|+++|++||.|..+     ..++..+|||||+|.+.++|+.|++.|||..|.|+.|.|.+
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   87 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY   87 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            3456899999999999999999999999988766     23677899999999999999999999999999999999999


Q ss_pred             eec
Q psy7051          90 ARY   92 (158)
Q Consensus        90 a~~   92 (158)
                      +..
T Consensus        88 a~~   90 (96)
T 1fjc_A           88 TGE   90 (96)
T ss_dssp             CSS
T ss_pred             cCC
Confidence            974

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

Probab=99.82  E-value=1.7e-19  Score=123.87  Aligned_cols=83  Identities=31%  Similarity=0.467  Sum_probs=78.6

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEE
Q psy7051           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ   88 (158)
Q Consensus         9 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~   88 (158)
                      ...+..+|||+|||..+++++|+++|++||.|..+.++.+..++.++|||||+|.+.++|+.|++.|||..|+|+.|.|.
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            44556899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             eee
Q psy7051          89 MAR   91 (158)
Q Consensus        89 ~a~   91 (158)
                      ||+
T Consensus       163 ~a~  165 (166)
T 3md3_A          163 WAA  165 (166)
T ss_dssp             ESC
T ss_pred             ecC
Confidence            986

>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=99.82  E-value=9.4e-20  Score=124.28  Aligned_cols=80  Identities=34%  Similarity=0.534  Sum_probs=73.5

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEE
Q psy7051           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ   88 (158)
Q Consensus         9 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~   88 (158)
                      ...+..+|||+|||+.+++++|+++|++||.|..|.++.+     ++|||||+|.+.++|+.|++.|||..|.|+.|.|.
T Consensus        69 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  143 (150)
T 2i2y_A           69 SCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVE  143 (150)
T ss_dssp             SSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            3455689999999999999999999999999999999876     47899999999999999999999999999999999


Q ss_pred             eeecC
Q psy7051          89 MARYG   93 (158)
Q Consensus        89 ~a~~~   93 (158)
                      +++..
T Consensus       144 ~a~~~  148 (150)
T 2i2y_A          144 LSNGE  148 (150)
T ss_dssp             ECCCC
T ss_pred             EcCCC
Confidence            99743

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

Probab=99.82  E-value=3.9e-20  Score=118.11  Aligned_cols=74  Identities=20%  Similarity=0.304  Sum_probs=69.2

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeec
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARY   92 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~   92 (158)
                      ..+|||+|||..+++++|+++|++||.|..|.++.      .+|||||+|.+.++|+.|++.|||..|+|+.|.|.+++.
T Consensus        27 ~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  100 (101)
T 2la4_A           27 VTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP------EKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKE  100 (101)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCC
T ss_pred             CCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccC
Confidence            57999999999999999999999999999999873      468999999999999999999999999999999999863

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

Probab=99.82  E-value=9.5e-20  Score=115.20  Aligned_cols=79  Identities=22%  Similarity=0.255  Sum_probs=71.2

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEE-EEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDI-YIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v-~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      ....+|||+|||+.+++++|+++|++||.|..| .++.++.++    .|||+|.+.++|+.|++.|||..|.|+.|.|.+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~----~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   88 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETA----VVNVTYSSKDQARQALDKLNGFQLENFTLKVAY   88 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSE----EEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEE
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCC----EEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            445889999999999999999999999999999 587776443    499999999999999999999999999999999


Q ss_pred             eecC
Q psy7051          90 ARYG   93 (158)
Q Consensus        90 a~~~   93 (158)
                      +...
T Consensus        89 a~~~   92 (96)
T 2e44_A           89 IPDE   92 (96)
T ss_dssp             CCCC
T ss_pred             cCcc
Confidence            9743

>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=99.82  E-value=9.5e-21  Score=128.27  Aligned_cols=87  Identities=29%  Similarity=0.368  Sum_probs=73.1

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEE--EccC---CCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCce
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIY--IPRD---RFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRE   84 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~--~~~~---~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~   84 (158)
                      ..+..+|||+|||+.+++++|+++|++||.|..|.  ++.+   ..++..+|||||+|.+.++|+.|++.|||..|.|+.
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            45568999999999999999999999999887641  1111   236778999999999999999999999999999999


Q ss_pred             EEEEeeecCCCC
Q psy7051          85 LRVQMARYGRPP   96 (158)
Q Consensus        85 i~v~~a~~~~~~   96 (158)
                      |.|.+++...++
T Consensus       122 l~V~~a~~~~~~  133 (143)
T 3egn_A          122 MVVQFARSARPK  133 (143)
T ss_dssp             CEEEECCCSCC-
T ss_pred             EEEEECCCCCCc
Confidence            999999865443

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

Probab=99.81  E-value=6.2e-20  Score=120.63  Aligned_cols=80  Identities=15%  Similarity=0.196  Sum_probs=72.3

Q ss_pred             cEEEEeCC----CCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcC----HHH----HHHHHH--HhCCcc
Q psy7051          14 VSLKVDNL----TYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD----KRD----AEDALD--AMDGRM   79 (158)
Q Consensus        14 ~~l~V~nl----~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~----~~~----a~~a~~--~l~g~~   79 (158)
                      +.|||+||    |+.+++++|+++|+.||+|..|.++.|+.||.++|||||+|.+    +++    |..|+.  .|||..
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            67999999    9999999999999999999999999999999999999999996    433    788888  789999


Q ss_pred             cCCceEEEEeeecC
Q psy7051          80 LDGRELRVQMARYG   93 (158)
Q Consensus        80 i~g~~i~v~~a~~~   93 (158)
                      |+|+.|+|.+.+.+
T Consensus        83 I~Gr~irV~ln~~g   96 (136)
T 2j8a_A           83 IMGFKFEVILNKHS   96 (136)
T ss_dssp             ETTEEEEEEECCTT
T ss_pred             ecCcEEEEEECccc
Confidence            99999999987643

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=1.2e-19  Score=118.08  Aligned_cols=77  Identities=21%  Similarity=0.409  Sum_probs=69.2

Q ss_pred             CCCCcEEEE--eCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCccc-----CC
Q psy7051          10 IEGMVSLKV--DNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRML-----DG   82 (158)
Q Consensus        10 ~~~~~~l~V--~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i-----~g   82 (158)
                      .++..+|||  +||++.+++++|+++|++||+|..|.|+.+      +|||||+|.+.++|++|++.|||.+|     .|
T Consensus        22 ~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~------rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g   95 (114)
T 2cq2_A           22 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   95 (114)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             CCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHhCCCEEccccCCC
Confidence            345688999  779999999999999999999999988643      68999999999999999999999988     68


Q ss_pred             ceEEEEeeec
Q psy7051          83 RELRVQMARY   92 (158)
Q Consensus        83 ~~i~v~~a~~   92 (158)
                      ..|.|.+++.
T Consensus        96 ~~l~v~~a~~  105 (114)
T 2cq2_A           96 ITLYLNFVEK  105 (114)
T ss_dssp             EECEEEEESC
T ss_pred             cEEEEEeccc
Confidence            8999999873

>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=99.81  E-value=1.3e-19  Score=127.88  Aligned_cols=92  Identities=32%  Similarity=0.487  Sum_probs=78.7

Q ss_pred             CCCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCccc
Q psy7051           1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRML   80 (158)
Q Consensus         1 ~~~~~p~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i   80 (158)
                      |+-...+...+...+|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|+.|++. ++..|
T Consensus         1 ms~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~   79 (196)
T 1l3k_A            1 MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKV   79 (196)
T ss_dssp             -------CCCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEE
T ss_pred             CCcccCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEE
Confidence            44445555667789999999999999999999999999999999999988999999999999999999999975 99999


Q ss_pred             CCceEEEEeeecC
Q psy7051          81 DGRELRVQMARYG   93 (158)
Q Consensus        81 ~g~~i~v~~a~~~   93 (158)
                      .|+.|.|.++...
T Consensus        80 ~g~~l~v~~~~~~   92 (196)
T 1l3k_A           80 DGRVVEPKRAVSR   92 (196)
T ss_dssp             TTEECEEEECCC-
T ss_pred             CCEEeeeecccCc
Confidence            9999999998643

>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=99.81  E-value=1.6e-19  Score=124.92  Aligned_cols=80  Identities=24%  Similarity=0.409  Sum_probs=76.5

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      ....+|||+|||..+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|+.|++.|||..|+|+.|.|.+|
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            44688999999999999999999999999999999999889999999999999999999999999999999999999987

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

Probab=99.81  E-value=3.3e-19  Score=127.57  Aligned_cols=84  Identities=25%  Similarity=0.402  Sum_probs=79.0

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ...+|||+|||..+++++|+++|++||.|..|.++.+..++.++|||||+|.+.++|..|++.|||..|.|+.|.|.++.
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            45799999999999999999999999999999999998899999999999999999999999999999999999999998


Q ss_pred             cCCC
Q psy7051          92 YGRP   95 (158)
Q Consensus        92 ~~~~   95 (158)
                      ....
T Consensus       204 ~~~~  207 (216)
T 2qfj_A          204 TPPM  207 (216)
T ss_dssp             SCSS
T ss_pred             CCCC
Confidence            6543

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

Probab=99.81  E-value=4.4e-20  Score=122.06  Aligned_cols=79  Identities=20%  Similarity=0.282  Sum_probs=71.9

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCce----EEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEE
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEV----GDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR   86 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i----~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~   86 (158)
                      +...+|||+|||+.+++++|+++|++||.|    ..|.|+.+. +++++|||||+|.+.++|+.||+. |+..|.++.|.
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~   98 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP-DGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIE   98 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECT-TSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECC-CCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEE
Confidence            445899999999999999999999999875    688888884 899999999999999999999975 99999999999


Q ss_pred             EEeee
Q psy7051          87 VQMAR   91 (158)
Q Consensus        87 v~~a~   91 (158)
                      |..+.
T Consensus        99 V~~a~  103 (123)
T 2dha_A           99 LFRST  103 (123)
T ss_dssp             CEEEC
T ss_pred             EEECC
Confidence            98875

>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=99.80  E-value=4.3e-19  Score=121.92  Aligned_cols=80  Identities=31%  Similarity=0.574  Sum_probs=76.5

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeec
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARY   92 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~   92 (158)
                      .++|||+|||+.+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|+.|++.||+..|.|+.|.|.++..
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   81 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCC
Confidence            47899999999999999999999999999999999988999999999999999999999999999999999999999874

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

Probab=99.80  E-value=3.8e-19  Score=122.52  Aligned_cols=87  Identities=32%  Similarity=0.527  Sum_probs=79.5

Q ss_pred             CCCCCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCC-
Q psy7051           4 GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDG-   82 (158)
Q Consensus         4 ~~p~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g-   82 (158)
                      ..|........+|||+|||..+++++|+++|++||.|..+.++.+..++.++|||||+|.+.++|..|++.|||..|.| 
T Consensus        80 ~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~  159 (168)
T 1b7f_A           80 ARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGG  159 (168)
T ss_dssp             CCCCSSTTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTC
T ss_pred             cCCCcccCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCC
Confidence            3455555667899999999999999999999999999999999998889999999999999999999999999999988 


Q ss_pred             -ceEEEEee
Q psy7051          83 -RELRVQMA   90 (158)
Q Consensus        83 -~~i~v~~a   90 (158)
                       +.|.|.+|
T Consensus       160 ~~~l~V~~A  168 (168)
T 1b7f_A          160 SQPLSVRLA  168 (168)
T ss_dssp             SSCCEEEEC
T ss_pred             CeEEEEEeC
Confidence             99999886

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=3.5e-19  Score=111.03  Aligned_cols=74  Identities=31%  Similarity=0.425  Sum_probs=65.3

Q ss_pred             CCCcE-EEEeCCCCCCCHHH----HHHHhhhcC-ceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCce
Q psy7051          11 EGMVS-LKVDNLTYRTTPDD----LRRVFERCG-EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRE   84 (158)
Q Consensus        11 ~~~~~-l~V~nl~~~~~~~~----l~~~f~~~G-~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~   84 (158)
                      ++..| |||+|||..+++++    |.++|++|| +|..|       ++   |+|||+|.+.++|+.|++.|||..|.|+.
T Consensus         6 ~p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~   75 (96)
T 2diu_A            6 SGCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGNR   75 (96)
T ss_dssp             CCSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSC
T ss_pred             CCcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCce
Confidence            44555 99999999999988    558999995 99887       23   89999999999999999999999999999


Q ss_pred             EEEEeeecCC
Q psy7051          85 LRVQMARYGR   94 (158)
Q Consensus        85 i~v~~a~~~~   94 (158)
                      |+|.+|+...
T Consensus        76 i~v~~A~~~s   85 (96)
T 2diu_A           76 IIVSFTPKNR   85 (96)
T ss_dssp             CEEESSCCSC
T ss_pred             EEEEecCCCc
Confidence            9999998543

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

Probab=99.80  E-value=4.3e-19  Score=122.25  Aligned_cols=82  Identities=30%  Similarity=0.440  Sum_probs=77.3

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      +..+|||+|||..+++++|+++|++||+|..|.++.++.++.++|||||+|.+.++|+.|++.|++..|.|+.|.|.++.
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            35789999999999999999999999999999999998889999999999999999999999999999999999999987


Q ss_pred             cC
Q psy7051          92 YG   93 (158)
Q Consensus        92 ~~   93 (158)
                      ..
T Consensus        82 ~~   83 (168)
T 1b7f_A           82 PG   83 (168)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

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

Probab=99.80  E-value=6e-19  Score=124.64  Aligned_cols=83  Identities=23%  Similarity=0.404  Sum_probs=78.7

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      .+..+|||+|||..+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|+.|++.|||..|+|+.|.|.++
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            45689999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             ecC
Q psy7051          91 RYG   93 (158)
Q Consensus        91 ~~~   93 (158)
                      +..
T Consensus       192 ~~~  194 (198)
T 2yh0_A          192 SVG  194 (198)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            854

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

Probab=99.80  E-value=5.1e-19  Score=117.53  Aligned_cols=77  Identities=26%  Similarity=0.421  Sum_probs=69.4

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccE-EEEEEcCHHHHHHHHHHhCCcccCC--ceEEEE
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGF-AFVRFFDKRDAEDALDAMDGRMLDG--RELRVQ   88 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~-afV~f~~~~~a~~a~~~l~g~~i~g--~~i~v~   88 (158)
                      ....|||+||++.+++++|+++|++||+|..|.++..     .+|+ |||+|.+.++|+.|++.|||..|.|  +.|+|+
T Consensus        27 ~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~-----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~  101 (130)
T 3zzy_A           27 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID  101 (130)
T ss_dssp             SEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE-----TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEE
T ss_pred             ceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC-----CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEE
Confidence            3467889999999999999999999999999988754     2577 9999999999999999999999988  899999


Q ss_pred             eeecC
Q psy7051          89 MARYG   93 (158)
Q Consensus        89 ~a~~~   93 (158)
                      |++..
T Consensus       102 ~ak~~  106 (130)
T 3zzy_A          102 FSKLT  106 (130)
T ss_dssp             ECSCS
T ss_pred             ecCCC
Confidence            99843

>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=99.80  E-value=5e-19  Score=121.59  Aligned_cols=87  Identities=29%  Similarity=0.457  Sum_probs=78.0

Q ss_pred             CCCCCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCc
Q psy7051           4 GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGR   83 (158)
Q Consensus         4 ~~p~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~   83 (158)
                      ..|........+|||+|||..+++++|+++|++||.|..+.++.+..++.++|||||+|.+.++|+.|++.|||..|.|+
T Consensus        79 ~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~  158 (167)
T 1fxl_A           79 ARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGA  158 (167)
T ss_dssp             CCCCCGGGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTC
T ss_pred             cCCCcccCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCC
Confidence            34444455668999999999999999999999999999999999888899999999999999999999999999999996


Q ss_pred             e--EEEEee
Q psy7051          84 E--LRVQMA   90 (158)
Q Consensus        84 ~--i~v~~a   90 (158)
                      .  |.|.||
T Consensus       159 ~~~i~v~~A  167 (167)
T 1fxl_A          159 TEPITVKFA  167 (167)
T ss_dssp             SSCCEEEEC
T ss_pred             ccceEEEeC
Confidence            5  888875

>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=99.79  E-value=4.6e-19  Score=125.03  Aligned_cols=82  Identities=27%  Similarity=0.361  Sum_probs=75.1

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ...+|||+|||..+++++|+++|++||.|..|.++.+..++.++|||||+|.+.++|+.|++. ++..|+|+.|.|.++.
T Consensus       103 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a~  181 (196)
T 1l3k_A          103 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKAL  181 (196)
T ss_dssp             CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEECC
T ss_pred             CcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEecC
Confidence            457999999999999999999999999999999999988999999999999999999999975 8999999999999997


Q ss_pred             cCC
Q psy7051          92 YGR   94 (158)
Q Consensus        92 ~~~   94 (158)
                      ...
T Consensus       182 ~k~  184 (196)
T 1l3k_A          182 SKQ  184 (196)
T ss_dssp             ---
T ss_pred             Chh
Confidence            543

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

Probab=99.79  E-value=2.7e-19  Score=111.49  Aligned_cols=75  Identities=19%  Similarity=0.375  Sum_probs=68.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ...+|||+|||+.+++++|+++|++| .|..|.+.      ..+|||||+|.+.++|+.|++.|||..|.|+.|.|+++.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   76 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcC
Confidence            34789999999999999999999999 99999884      368999999999999999999999999999999999987


Q ss_pred             cC
Q psy7051          92 YG   93 (158)
Q Consensus        92 ~~   93 (158)
                      ..
T Consensus        77 ~~   78 (88)
T 1wg1_A           77 TD   78 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

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

Probab=99.79  E-value=1.3e-18  Score=115.00  Aligned_cols=74  Identities=30%  Similarity=0.345  Sum_probs=66.4

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccE-EEEEEcCHHHHHHHHHHhCCcccCC--ceEEEEee
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGF-AFVRFFDKRDAEDALDAMDGRMLDG--RELRVQMA   90 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~-afV~f~~~~~a~~a~~~l~g~~i~g--~~i~v~~a   90 (158)
                      ..|||+||++.+++++|+++|++||.|..|.|+..      .|| |||+|.+.++|+.|++.|||..|.|  +.|.|++|
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~------~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~A   99 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR------NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYA   99 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES------SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECC
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEe
Confidence            45789999999999999999999999999988642      276 9999999999999999999999987  68999999


Q ss_pred             ecC
Q psy7051          91 RYG   93 (158)
Q Consensus        91 ~~~   93 (158)
                      +..
T Consensus       100 k~~  102 (124)
T 2e5i_A          100 RPT  102 (124)
T ss_dssp             SCS
T ss_pred             cCC
Confidence            844

>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=99.78  E-value=1e-18  Score=125.05  Aligned_cols=77  Identities=19%  Similarity=0.284  Sum_probs=71.3

Q ss_pred             CCcEEEEeCCC-CCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          12 GMVSLKVDNLT-YRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        12 ~~~~l~V~nl~-~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      +..+|||+||+ ..+++++|.++|++||.|..|.++.+.     +|||||+|.+.++|+.||+.|||..|.|+.|.|.++
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s   77 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVS   77 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTS-----TTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEc
Confidence            45789999999 899999999999999999999998753     689999999999999999999999999999999999


Q ss_pred             ecC
Q psy7051          91 RYG   93 (158)
Q Consensus        91 ~~~   93 (158)
                      +..
T Consensus        78 ~~~   80 (205)
T 3tyt_A           78 KQP   80 (205)
T ss_dssp             SCS
T ss_pred             cCC
Confidence            743

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

Probab=99.78  E-value=1.1e-18  Score=125.40  Aligned_cols=78  Identities=24%  Similarity=0.393  Sum_probs=72.7

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeec
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARY   92 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~   92 (158)
                      ..+|||+|||..+++++|+++|++||.|..|.|+.+.  +..+|||||+|.+.++|+.||+.|||..|+|+.|.|.+++.
T Consensus       103 ~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~  180 (213)
T 4f02_A          103 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS  180 (213)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC--CCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            4689999999999999999999999999999998874  34689999999999999999999999999999999999863

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

Probab=99.78  E-value=1.1e-18  Score=113.80  Aligned_cols=76  Identities=21%  Similarity=0.305  Sum_probs=64.8

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCC---CCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEE
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFT---RESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV   87 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~---~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v   87 (158)
                      ....+|||+|||+.+++++|+++|++||.|. +.++.+..+   +.++|||||+|.+.++|+.||+.|+  .++|..|.+
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~   82 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLC   82 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEe
Confidence            4458899999999999999999999999999 888887766   6899999999999999999999883  255555555


Q ss_pred             Ee
Q psy7051          88 QM   89 (158)
Q Consensus        88 ~~   89 (158)
                      ..
T Consensus        83 ~~   84 (114)
T 2dnl_A           83 VS   84 (114)
T ss_dssp             EC
T ss_pred             cc
Confidence            43

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

Probab=99.77  E-value=1.6e-18  Score=123.97  Aligned_cols=79  Identities=30%  Similarity=0.499  Sum_probs=72.6

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ..+|||+|||..+++++|+++|++||.|..|.|+.+..++..+|||||+|.+.++|+.|++.||+..|.|+.|.|.++.
T Consensus        28 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~  106 (216)
T 2qfj_A           28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPS  106 (216)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCS
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCC
Confidence            4789999999999999999999999999999999998889999999999999999999999999999999999998765

>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=99.77  E-value=8e-19  Score=120.85  Aligned_cols=80  Identities=19%  Similarity=0.272  Sum_probs=75.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ...+|||+|||..+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|+.|++ +++..|.|+.|.|.++.
T Consensus        86 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~  164 (167)
T 2cjk_A           86 KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAE  164 (167)
T ss_dssp             HCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECC
T ss_pred             CCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecC
Confidence            34689999999999999999999999999999999998889999999999999999999997 89999999999999987


Q ss_pred             c
Q psy7051          92 Y   92 (158)
Q Consensus        92 ~   92 (158)
                      .
T Consensus       165 p  165 (167)
T 2cjk_A          165 P  165 (167)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.77  E-value=1.9e-18  Score=107.13  Aligned_cols=70  Identities=27%  Similarity=0.525  Sum_probs=65.4

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhc----C-------ceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCccc
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERC----G-------EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRML   80 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~----G-------~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i   80 (158)
                      +..+|||+|||..+++++|+++|++|    |       .|..+.+..+      +|||||+|.+.++|+.|+ .||+..|
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~~~   77 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGIIF   77 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCCEE
Confidence            45899999999999999999999999    8       8999988755      689999999999999999 9999999


Q ss_pred             CCceEEEE
Q psy7051          81 DGRELRVQ   88 (158)
Q Consensus        81 ~g~~i~v~   88 (158)
                      .|+.|.|+
T Consensus        78 ~g~~l~V~   85 (87)
T 2hzc_A           78 QGQSLKIR   85 (87)
T ss_dssp             TTEECEEE
T ss_pred             CCeEEEEe
Confidence            99999986

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

Probab=99.77  E-value=2.9e-18  Score=117.64  Aligned_cols=79  Identities=27%  Similarity=0.433  Sum_probs=73.2

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeecC
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARYG   93 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~~   93 (158)
                      .+|||+|||..+++++|+++|++||.|..|.++.++ ++..+|||||+|.+.++|+.|++.|||..|.|+.|.|.++...
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~   79 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCC-C-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECC-CCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCC
Confidence            479999999999999999999999999999999886 5678999999999999999999999999999999999998744

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus}

Probab=99.77  E-value=2.3e-18  Score=107.60  Aligned_cols=73  Identities=30%  Similarity=0.468  Sum_probs=62.1

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcc--cCCceEEEE
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRM--LDGRELRVQ   88 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~--i~g~~i~v~   88 (158)
                      .+..+|||+|||+.+++++|+++|++||.|..|.|+.+     ++|||||+|.+.++|++    |++..  +.|..|.|.
T Consensus         9 ~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~   79 (89)
T 3d2w_A            9 HHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVHIS   79 (89)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEE
Confidence            45589999999999999999999999999999999875     58999999999999883    45554  468999999


Q ss_pred             eeec
Q psy7051          89 MARY   92 (158)
Q Consensus        89 ~a~~   92 (158)
                      ++..
T Consensus        80 ~a~~   83 (89)
T 3d2w_A           80 NAEP   83 (89)
T ss_dssp             ECC-
T ss_pred             EcCC
Confidence            8874

>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=99.77  E-value=8.3e-19  Score=109.20  Aligned_cols=76  Identities=30%  Similarity=0.486  Sum_probs=64.0

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      +..+|||+|||..+++++|+++|++||.|..|.++.+     ++|||||+|.+.++|++|+.  ....+.|..|.|.+++
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~--~~~~~~g~~l~v~~a~   76 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAE   76 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhc--CCceeCCEEEEEEecC
Confidence            4589999999999999999999999999999998765     57899999999999976432  1335589999999887


Q ss_pred             cCC
Q psy7051          92 YGR   94 (158)
Q Consensus        92 ~~~   94 (158)
                      ...
T Consensus        77 ~~~   79 (88)
T 1wf0_A           77 PKH   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            443

>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=99.76  E-value=4.7e-18  Score=117.62  Aligned_cols=79  Identities=27%  Similarity=0.352  Sum_probs=73.0

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccC---CceEEEE
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLD---GRELRVQ   88 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~---g~~i~v~   88 (158)
                      ...+|||+|||..+++++|+++|++||.|..|.++.+. ++.++|||||+|.+.++|+.|++.|||..+.   ++.|.|.
T Consensus        94 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~  172 (175)
T 3nmr_A           94 EDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVK  172 (175)
T ss_dssp             GGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEE
T ss_pred             CCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECC-CCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEE
Confidence            45799999999999999999999999999999998886 6889999999999999999999999998775   4899999


Q ss_pred             eee
Q psy7051          89 MAR   91 (158)
Q Consensus        89 ~a~   91 (158)
                      ||.
T Consensus       173 ~ad  175 (175)
T 3nmr_A          173 FAD  175 (175)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            874

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

Probab=99.76  E-value=8e-18  Score=108.24  Aligned_cols=80  Identities=18%  Similarity=0.194  Sum_probs=71.0

Q ss_pred             CCcEEEEeCCCC-----CCCHHHHHHHhhhcCceEEEEEccCCCC-CCcccEEEEEEcCHHHHHHHHHHhCCcccCCceE
Q psy7051          12 GMVSLKVDNLTY-----RTTPDDLRRVFERCGEVGDIYIPRDRFT-RESRGFAFVRFFDKRDAEDALDAMDGRMLDGREL   85 (158)
Q Consensus        12 ~~~~l~V~nl~~-----~~~~~~l~~~f~~~G~i~~v~~~~~~~~-~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i   85 (158)
                      +..+|+|.||..     ..++++|+++|++||.|..|.|+.++.+ +..+|||||+|.+.++|+.|++.|||..|.|+.|
T Consensus         7 ~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~i   86 (105)
T 2pe8_A            7 PTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVV   86 (105)
T ss_dssp             CCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcEE
Confidence            457899999963     2378999999999999999999887643 5789999999999999999999999999999999


Q ss_pred             EEEeee
Q psy7051          86 RVQMAR   91 (158)
Q Consensus        86 ~v~~a~   91 (158)
                      .|.++.
T Consensus        87 ~v~~a~   92 (105)
T 2pe8_A           87 KACFYN   92 (105)
T ss_dssp             EEEECC
T ss_pred             EEEEcC
Confidence            999986

>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=99.76  E-value=3.1e-18  Score=124.23  Aligned_cols=84  Identities=27%  Similarity=0.401  Sum_probs=75.7

Q ss_pred             CCCCCCCCCcEEEEeCCCC-CCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCc
Q psy7051           5 RPPPRIEGMVSLKVDNLTY-RTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGR   83 (158)
Q Consensus         5 ~p~~~~~~~~~l~V~nl~~-~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~   83 (158)
                      .|+...++..+|||+|||. .+++++|+++|++||.|..|.|+.+.     +|||||+|.+.++|+.|++.|||..|.|+
T Consensus        26 ~p~~~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~  100 (229)
T 2adc_A           26 IPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGK  100 (229)
T ss_dssp             CGGGGCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSS
T ss_pred             CCCCCCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCe
Confidence            3444456678999999999 99999999999999999999998774     68999999999999999999999999999


Q ss_pred             eEEEEeeecC
Q psy7051          84 ELRVQMARYG   93 (158)
Q Consensus        84 ~i~v~~a~~~   93 (158)
                      .|.|.+++..
T Consensus       101 ~l~v~~a~~~  110 (229)
T 2adc_A          101 PIRITLSKHQ  110 (229)
T ss_dssp             BCEEECCSCC
T ss_pred             EEEEEEecCc
Confidence            9999998744

>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=99.75  E-value=9.9e-18  Score=115.98  Aligned_cols=82  Identities=26%  Similarity=0.426  Sum_probs=73.4

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCC--CcccEEEEEEcCHHHHHHHHHHhCCcccC---CceEE
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTR--ESRGFAFVRFFDKRDAEDALDAMDGRMLD---GRELR   86 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~--~~~g~afV~f~~~~~a~~a~~~l~g~~i~---g~~i~   86 (158)
                      ...+|||+|||+.+++++|+++|++||+|..|.++.+..++  ..+|||||+|.+.++|+.|++.|++..+.   +..|.
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            35789999999999999999999999999999999988776  78999999999999999999999998875   57788


Q ss_pred             EEeeecC
Q psy7051          87 VQMARYG   93 (158)
Q Consensus        87 v~~a~~~   93 (158)
                      +.++...
T Consensus        82 ~~~~~~~   88 (175)
T 3nmr_A           82 MKPADSE   88 (175)
T ss_dssp             EEECGGG
T ss_pred             Ecccccc
Confidence            8777643

>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=99.75  E-value=1.2e-17  Score=124.21  Aligned_cols=83  Identities=29%  Similarity=0.499  Sum_probs=74.9

Q ss_pred             CCCCCCcEEEEeCCCCCCCHHHHH----HHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCc
Q psy7051           8 PRIEGMVSLKVDNLTYRTTPDDLR----RVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGR   83 (158)
Q Consensus         8 ~~~~~~~~l~V~nl~~~~~~~~l~----~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~   83 (158)
                      +...+..+|||+|||..+++++|+    ++|++||.|..|.++.   ++..+|||||+|.+.++|+.|++.|||..|.|+
T Consensus         4 ~~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   80 (282)
T 3pgw_A            4 PETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK   80 (282)
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCc
Confidence            345667899999999999999966    8999999999998875   677889999999999999999999999999999


Q ss_pred             eEEEEeeecC
Q psy7051          84 ELRVQMARYG   93 (158)
Q Consensus        84 ~i~v~~a~~~   93 (158)
                      .|.|.+++..
T Consensus        81 ~l~v~~a~~~   90 (282)
T 3pgw_A           81 PMRIQYAKTD   90 (282)
T ss_pred             EEEEEEeccC
Confidence            9999999643

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

Probab=99.74  E-value=6.3e-18  Score=123.13  Aligned_cols=79  Identities=27%  Similarity=0.331  Sum_probs=70.4

Q ss_pred             CCCCcEEEEeCCCCCC---------CHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCccc
Q psy7051          10 IEGMVSLKVDNLTYRT---------TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRML   80 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~---------~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i   80 (158)
                      .....+|||+||+..+         ++++|.++|++||+|..|.|+.+      +|||||+|.+.++|+.|++.|+|..|
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~------kG~AFV~F~~~~~Ae~A~~am~g~~l  204 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES------KNCGFVKFKYQANAEFAKEAMSNQTL  204 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHHHTTCCC
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC------CCEEEEEeCCHHHHHHHHHHhCCCEE
Confidence            3456899999999998         79999999999999999999764      78999999999999999999999999


Q ss_pred             ------------CCceEEEEeeecCC
Q psy7051          81 ------------DGRELRVQMARYGR   94 (158)
Q Consensus        81 ------------~g~~i~v~~a~~~~   94 (158)
                                  .|+.|.|.||+...
T Consensus       205 ~~~~~~e~~~~~~gr~L~V~wA~~~p  230 (240)
T 3u1l_A          205 LLPSDKEWDDRREGTGLLVKWANEDP  230 (240)
T ss_dssp             CCTTSTTGGGGGGSCCCEEEECC---
T ss_pred             eccccccccccCCCCEEEEEEccCCC
Confidence                        89999999998543

>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=1.6e-17  Score=115.25  Aligned_cols=77  Identities=29%  Similarity=0.509  Sum_probs=70.6

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      .....+|||+|||..+++++|+++|++||.|..+     ..++.++|||||+|.+.++|..|++.|||..|.|+.|.|.+
T Consensus        96 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  170 (175)
T 1fje_B           96 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY  170 (175)
T ss_dssp             TGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEE
T ss_pred             cccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEe
Confidence            3456899999999999999999999999998766     34777899999999999999999999999999999999999


Q ss_pred             ee
Q psy7051          90 AR   91 (158)
Q Consensus        90 a~   91 (158)
                      ++
T Consensus       171 a~  172 (175)
T 1fje_B          171 TG  172 (175)
T ss_dssp             CS
T ss_pred             cC
Confidence            87

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

Probab=99.73  E-value=9.7e-18  Score=115.38  Aligned_cols=78  Identities=29%  Similarity=0.507  Sum_probs=71.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      +..+|||+|||..+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|+.|++  ++..|.|+.|.|.++.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~~~   79 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK--TQHILDGKVIDPKRAI   79 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHH--SCCEETTEECCCEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHh--cccccCCeEccccccc
Confidence            35789999999999999999999999999999999998899999999999999999999997  4678899999888764

>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=3e-17  Score=122.14  Aligned_cols=76  Identities=22%  Similarity=0.293  Sum_probs=70.6

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccC-CceEEEEe
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLD-GRELRVQM   89 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~-g~~i~v~~   89 (158)
                      .+..+|||+|||..+++++|+++|++||.|..|.|+.+.     +|||||+|.+.++|+.|++.|||..|. |+.|+|.|
T Consensus       205 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~  279 (282)
T 3pgw_A          205 PPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISF  279 (282)
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEE
Confidence            345889999999999999999999999999999998653     589999999999999999999999999 99999999


Q ss_pred             ee
Q psy7051          90 AR   91 (158)
Q Consensus        90 a~   91 (158)
                      ++
T Consensus       280 ak  281 (282)
T 3pgw_A          280 AK  281 (282)
T ss_pred             ec
Confidence            86

>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=99.73  E-value=2e-17  Score=117.28  Aligned_cols=77  Identities=21%  Similarity=0.290  Sum_probs=70.7

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ..+|||+|||..+++++|+++|++||.|..|.|+.+. ++..+|||||+|.+.++|+.|++.+ +..|+|+.|.|.+++
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~  185 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKD  185 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETT
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhH
Confidence            3789999999999999999999999999999998876 5889999999999999999999755 569999999999875

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

Probab=99.71  E-value=4e-17  Score=121.99  Aligned_cols=81  Identities=30%  Similarity=0.377  Sum_probs=74.3

Q ss_pred             CCCcEEEEeCCCCC-CCHHHHHHHhhhcCceEEEEEccCCC-CCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEE
Q psy7051          11 EGMVSLKVDNLTYR-TTPDDLRRVFERCGEVGDIYIPRDRF-TRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ   88 (158)
Q Consensus        11 ~~~~~l~V~nl~~~-~~~~~l~~~f~~~G~i~~v~~~~~~~-~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~   88 (158)
                      ....+|||+|||.. +++++|.++|++||.|..|.++.+.. ++.++|||||+|.+.++|..|+ .|||..|.|+.|.|.
T Consensus       208 ~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V~  286 (292)
T 2ghp_A          208 LEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVS  286 (292)
T ss_dssp             CTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEEE
T ss_pred             CCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEEE
Confidence            44589999999999 99999999999999999999998875 5889999999999999999999 999999999999999


Q ss_pred             eeec
Q psy7051          89 MARY   92 (158)
Q Consensus        89 ~a~~   92 (158)
                      +++.
T Consensus       287 ~a~~  290 (292)
T 2ghp_A          287 LADK  290 (292)
T ss_dssp             ECCC
T ss_pred             EecC
Confidence            9973

>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=99.71  E-value=9e-17  Score=119.65  Aligned_cols=82  Identities=23%  Similarity=0.334  Sum_probs=77.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ...+|||+|||..+++++|.++|++||.|..|.++.+..++.++|||||+|.+.++|..|++.|+|..|.|+.|.|.++.
T Consensus        94 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~  173 (284)
T 3smz_A           94 TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTD  173 (284)
T ss_dssp             CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECC
Confidence            34789999999999999999999999999999999998899999999999999999999999999999999999999987


Q ss_pred             cC
Q psy7051          92 YG   93 (158)
Q Consensus        92 ~~   93 (158)
                      ..
T Consensus       174 ~~  175 (284)
T 3smz_A          174 AG  175 (284)
T ss_dssp             GG
T ss_pred             CC
Confidence            53

>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=99.71  E-value=6.7e-17  Score=120.37  Aligned_cols=83  Identities=25%  Similarity=0.274  Sum_probs=76.7

Q ss_pred             CCCCcEEEEeCCCCCC-CHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEE
Q psy7051          10 IEGMVSLKVDNLTYRT-TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ   88 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~-~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~   88 (158)
                      .....+|||+|||..+ ++++|.++|++||.|..|.|+.+. ++.++|+|||+|.+.++|..|++.|||..|.|+.|.|.
T Consensus       181 ~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~  259 (284)
T 3smz_A          181 LLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVS  259 (284)
T ss_dssp             TTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECS-SCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             cCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECC-CCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEE
Confidence            3456899999999995 999999999999999999998886 78899999999999999999999999999999999999


Q ss_pred             eeecC
Q psy7051          89 MARYG   93 (158)
Q Consensus        89 ~a~~~   93 (158)
                      ++...
T Consensus       260 ~a~~~  264 (284)
T 3smz_A          260 FCAPG  264 (284)
T ss_dssp             ECCSS
T ss_pred             EecCC
Confidence            99744

>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=99.70  E-value=5.2e-17  Score=116.15  Aligned_cols=78  Identities=12%  Similarity=0.171  Sum_probs=68.1

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCce--EEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCc----e
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEV--GDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGR----E   84 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i--~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~----~   84 (158)
                      ++..+|||+|||+.+++++|+++|++||.|  +.|.++.+.  +..+|+|||+|.+.++|..||..|||..|.|.    +
T Consensus       121 ~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p  198 (205)
T 3tyt_A          121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYP  198 (205)
T ss_dssp             CCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSC
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcc
Confidence            345789999999999999999999999999  889888764  44569999999999999999999999999886    4


Q ss_pred             EEEEee
Q psy7051          85 LRVQMA   90 (158)
Q Consensus        85 i~v~~a   90 (158)
                      +.|.++
T Consensus       199 ~~vk~~  204 (205)
T 3tyt_A          199 YTLKLC  204 (205)
T ss_dssp             EECEEE
T ss_pred             eEEEec
Confidence            666654

>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=99.69  E-value=1e-16  Score=118.43  Aligned_cols=75  Identities=40%  Similarity=0.664  Sum_probs=69.8

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      ....+|||+|||+.+++++|.++|++||.|..|.+..+      +|||||+|.+.++|+.|+..|||..|.|+.|.|.++
T Consensus        20 ~~~~~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           20 TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFA   93 (261)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeec
Confidence            44579999999999999999999999999999998654      689999999999999999999999999999999998


Q ss_pred             e
Q psy7051          91 R   91 (158)
Q Consensus        91 ~   91 (158)
                      .
T Consensus        94 ~   94 (261)
T 3sde_A           94 T   94 (261)
T ss_dssp             C
T ss_pred             c
Confidence            6

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

Probab=99.69  E-value=4.7e-17  Score=115.16  Aligned_cols=76  Identities=28%  Similarity=0.430  Sum_probs=71.1

Q ss_pred             CcEEEEeCCCC-CCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          13 MVSLKVDNLTY-RTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        13 ~~~l~V~nl~~-~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ..+|||+|||+ .+++++|+++|++||.|..|.++.+.     +|||||+|.+.++|+.|++.|||..|.|+.|.|.+++
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            47899999999 99999999999999999999998774     6899999999999999999999999999999999987


Q ss_pred             cC
Q psy7051          92 YG   93 (158)
Q Consensus        92 ~~   93 (158)
                      ..
T Consensus        78 ~~   79 (198)
T 1qm9_A           78 HQ   79 (198)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.69  E-value=3.9e-16  Score=101.35  Aligned_cols=80  Identities=25%  Similarity=0.411  Sum_probs=68.0

Q ss_pred             CCCCCcEEEEeCCCCCCC-----------HHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCC
Q psy7051           9 RIEGMVSLKVDNLTYRTT-----------PDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG   77 (158)
Q Consensus         9 ~~~~~~~l~V~nl~~~~~-----------~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g   77 (158)
                      ...+..+|+|.||.....           +++|+++|++||.|..|.| .+.   .++|||||+|.+.++|+.|++.|||
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng   86 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDG   86 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTT
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCC
Confidence            345568999999954332           5799999999999999966 433   2689999999999999999999999


Q ss_pred             cccCCceEEEEeeec
Q psy7051          78 RMLDGRELRVQMARY   92 (158)
Q Consensus        78 ~~i~g~~i~v~~a~~   92 (158)
                      ..|.|+.|.|.++..
T Consensus        87 ~~~~gr~l~v~~a~~  101 (112)
T 2dit_A           87 RWFGGRQITAQAWDG  101 (112)
T ss_dssp             CEETTEECEEEECCS
T ss_pred             CEECCcEEEEEEeCC
Confidence            999999999999874

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

Probab=99.69  E-value=1.5e-16  Score=112.58  Aligned_cols=77  Identities=21%  Similarity=0.314  Sum_probs=70.8

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcC-ceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccC-CceEEEE
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCG-EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLD-GRELRVQ   88 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G-~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~-g~~i~v~   88 (158)
                      ++..+|||+|||..+++++|+++|++|| .|..|.++.+.     +|+|||+|.+.++|+.|++.|||..|. |+.|.|.
T Consensus       118 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~  192 (198)
T 1qm9_A          118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD-----RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS  192 (198)
T ss_dssp             CCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTT-----SSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEE
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEE
Confidence            4468999999999999999999999999 99999986542     689999999999999999999999999 9999999


Q ss_pred             eeec
Q psy7051          89 MARY   92 (158)
Q Consensus        89 ~a~~   92 (158)
                      |++.
T Consensus       193 ~a~~  196 (198)
T 1qm9_A          193 FSKS  196 (198)
T ss_dssp             EECC
T ss_pred             eecc
Confidence            9873

>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=99.69  E-value=1.9e-16  Score=114.81  Aligned_cols=77  Identities=21%  Similarity=0.317  Sum_probs=70.5

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcC-ceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccC-CceEEEE
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCG-EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLD-GRELRVQ   88 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G-~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~-g~~i~v~   88 (158)
                      .+..+|||+|||..+++++|+++|++|| .|..|.++.+     .+|||||+|.+.++|+.|++.|||..|. |+.|.|.
T Consensus       149 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~  223 (229)
T 2adc_A          149 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS  223 (229)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEE
T ss_pred             CCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEE
Confidence            3468999999999999999999999999 9999998653     2689999999999999999999999999 9999999


Q ss_pred             eeec
Q psy7051          89 MARY   92 (158)
Q Consensus        89 ~a~~   92 (158)
                      |++.
T Consensus       224 ~a~~  227 (229)
T 2adc_A          224 FSKS  227 (229)
T ss_dssp             ECSS
T ss_pred             EecC
Confidence            9873

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

Probab=99.68  E-value=2.8e-17  Score=114.01  Aligned_cols=83  Identities=22%  Similarity=0.270  Sum_probs=71.3

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEE
Q psy7051           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ   88 (158)
Q Consensus         9 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~   88 (158)
                      ...+..+|||+|||..+++++|+++|..||.|..+ ++.+..++..+|||||+|.+.++|+.|+ .||+..|.|+.|.|.
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~-~~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~v~   86 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDL-AVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLE   86 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTC-CCCEEEEETTTTEEEEEESSHHHHHHHH-HGGGEEETTEEEEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceE-EEEECCCCccccEEEEEECCHHHHHHHH-hcCCCEeCCeEEEEe
Confidence            34556899999999999999999999999977652 3344456778999999999999999999 599999999999999


Q ss_pred             eeecC
Q psy7051          89 MARYG   93 (158)
Q Consensus        89 ~a~~~   93 (158)
                      ++...
T Consensus        87 ~~~~~   91 (175)
T 1fje_B           87 KPKGR   91 (175)
T ss_dssp             CCCCS
T ss_pred             cCCCc
Confidence            98743

>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=99.68  E-value=2.3e-16  Score=101.36  Aligned_cols=80  Identities=24%  Similarity=0.278  Sum_probs=68.9

Q ss_pred             CCcEEEEeCC--CCCCC--------HHHHHHHhhhcCceEEEEEccCCCC--CCcccEEEEEEcCHHHHHHHHHHhCCcc
Q psy7051          12 GMVSLKVDNL--TYRTT--------PDDLRRVFERCGEVGDIYIPRDRFT--RESRGFAFVRFFDKRDAEDALDAMDGRM   79 (158)
Q Consensus        12 ~~~~l~V~nl--~~~~~--------~~~l~~~f~~~G~i~~v~~~~~~~~--~~~~g~afV~f~~~~~a~~a~~~l~g~~   79 (158)
                      +..+|.|.|+  +..+.        +++|+++|++||.|..|.|+.+..+  +..+|+|||+|.+.++|++|++.|||..
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~   83 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   83 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCE
Confidence            4577999998  33332        3689999999999999999887654  3578999999999999999999999999


Q ss_pred             cCCceEEEEeee
Q psy7051          80 LDGRELRVQMAR   91 (158)
Q Consensus        80 i~g~~i~v~~a~   91 (158)
                      |+|+.|.|.++.
T Consensus        84 f~GR~i~v~~~~   95 (105)
T 3v4m_A           84 FANRVVVTKYCD   95 (105)
T ss_dssp             ETTEECEEEEEC
T ss_pred             eCCCEEEEEEeC
Confidence            999999999975

>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=99.66  E-value=5.1e-17  Score=104.32  Aligned_cols=72  Identities=21%  Similarity=0.432  Sum_probs=63.2

Q ss_pred             EeCCCCCCCHHHHHHHh------------hhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceE
Q psy7051          18 VDNLTYRTTPDDLRRVF------------ERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGREL   85 (158)
Q Consensus        18 V~nl~~~~~~~~l~~~f------------~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i   85 (158)
                      +.||+..+++++|+++|            ++||.|..|.|+.+. +++++|||||+|.+.++|++|++.|||..|+|+.|
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~-~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i   98 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCC-CCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            56677777777777666            999999999998876 47889999999999999999999999999999999


Q ss_pred             EEEee
Q psy7051          86 RVQMA   90 (158)
Q Consensus        86 ~v~~a   90 (158)
                      .|.++
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99986

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

Probab=99.65  E-value=4.2e-16  Score=115.07  Aligned_cols=80  Identities=25%  Similarity=0.251  Sum_probs=72.2

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCc-ccC---CceEEEE
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGR-MLD---GRELRVQ   88 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~-~i~---g~~i~v~   88 (158)
                      ..+|||+|||..+++++|+++|++||.|..|.++.+ .++.++|||||+|.+.++|..|+..||+. .+.   ++.|.|.
T Consensus        96 ~~~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           96 GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVE  174 (261)
T ss_dssp             SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE-TTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEE
T ss_pred             CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeC-CCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEe
Confidence            478999999999999999999999999999999988 48899999999999999999999999554 444   8999999


Q ss_pred             eeecC
Q psy7051          89 MARYG   93 (158)
Q Consensus        89 ~a~~~   93 (158)
                      ++...
T Consensus       175 ~~~~~  179 (261)
T 3sde_A          175 PMEQF  179 (261)
T ss_dssp             ECCCE
T ss_pred             ecccc
Confidence            98743

>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=5e-16  Score=116.05  Aligned_cols=81  Identities=22%  Similarity=0.345  Sum_probs=70.0

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcC-ceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCG-EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G-~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      ...+|||+|||..+++++|.++|.+|| .|..|.++.+.. +..+|||||+|.+.++|+.|++.|||..|.|+.|.|.++
T Consensus       116 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  194 (292)
T 2ghp_A          116 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS  194 (292)
T ss_dssp             CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            357899999999999999999999999 999999988764 778999999999999999999999999999999999998


Q ss_pred             ecC
Q psy7051          91 RYG   93 (158)
Q Consensus        91 ~~~   93 (158)
                      ...
T Consensus       195 ~~~  197 (292)
T 2ghp_A          195 NPL  197 (292)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            743

>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=1e-15  Score=105.70  Aligned_cols=75  Identities=25%  Similarity=0.456  Sum_probs=66.6

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhc----C-------ceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCccc
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERC----G-------EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRML   80 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~----G-------~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i   80 (158)
                      +..+|||+|||..+++++|+++|++|    |       .|..+.+..+      +|||||+|.+.++|+.|+ .||+..|
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~~------~g~afV~f~~~~~A~~A~-~~~~~~~   75 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGIIF   75 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEETT------TTEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecCC------CCEEEEEeCCHHHHHHHH-HhCCcEe
Confidence            45799999999999999999999999    6       6777766443      689999999999999999 8999999


Q ss_pred             CCceEEEEeeecC
Q psy7051          81 DGRELRVQMARYG   93 (158)
Q Consensus        81 ~g~~i~v~~a~~~   93 (158)
                      .|+.|.|.++...
T Consensus        76 ~g~~i~v~~~~~~   88 (172)
T 2g4b_A           76 QGQSLKIRRPHDY   88 (172)
T ss_dssp             TTEECEEECCSSC
T ss_pred             cCceeeecCCccc
Confidence            9999999987643

>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=99.65  E-value=6.5e-16  Score=101.21  Aligned_cols=80  Identities=18%  Similarity=0.278  Sum_probs=69.4

Q ss_pred             CCcEEEEeCCCC--CC---CHHHHHHHhhhcCceEEEEEccCCC----CCCcccEEEEEEcCHHHHHHHHHHhCCcccCC
Q psy7051          12 GMVSLKVDNLTY--RT---TPDDLRRVFERCGEVGDIYIPRDRF----TRESRGFAFVRFFDKRDAEDALDAMDGRMLDG   82 (158)
Q Consensus        12 ~~~~l~V~nl~~--~~---~~~~l~~~f~~~G~i~~v~~~~~~~----~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g   82 (158)
                      +..+|+|.|+-.  .+   .+++|+++|++||.|..|.|+.+..    ++..+|++||+|.+.++|.+|++.|||..|+|
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            457899999932  22   3689999999999999999988754    34567999999999999999999999999999


Q ss_pred             ceEEEEeee
Q psy7051          83 RELRVQMAR   91 (158)
Q Consensus        83 ~~i~v~~a~   91 (158)
                      +.|.|.++.
T Consensus        99 R~i~v~~~~  107 (118)
T 3ue2_A           99 RKVVAEVYD  107 (118)
T ss_dssp             EECEEEEEC
T ss_pred             cEEEEEEcC
Confidence            999999975

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

Probab=99.64  E-value=6e-15  Score=93.83  Aligned_cols=75  Identities=23%  Similarity=0.203  Sum_probs=62.2

Q ss_pred             CcEEEEeCCC-------CCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceE
Q psy7051          13 MVSLKVDNLT-------YRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGREL   85 (158)
Q Consensus        13 ~~~l~V~nl~-------~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i   85 (158)
                      ..+|.|.-..       ..+++++|+++|++||+|..|.|+.     ..+|||||+|.+.++|+.|++.++  .+.++.|
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~~-----~~rGfaFVeF~~~~~A~~Ai~~~~--~~~g~~l   82 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLSS-----KKPGTAVVEFATVKAAELAVQNEV--GLVDNPL   82 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEES-----SSSSEEEEEESCHHHHHHHHHTCC--BCSSSBC
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEcc-----CCCCEEEEEECCHHHHHHHHHhcC--CCCCCeE
Confidence            4567666543       4589999999999999999999873     468999999999999999998744  4689999


Q ss_pred             EEEeeecCC
Q psy7051          86 RVQMARYGR   94 (158)
Q Consensus        86 ~v~~a~~~~   94 (158)
                      .|.|++...
T Consensus        83 ~V~~a~~~~   91 (100)
T 2d9o_A           83 KISWLEGQP   91 (100)
T ss_dssp             EEECSSCCC
T ss_pred             EEEEccCCC
Confidence            999987543

>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=2e-15  Score=106.41  Aligned_cols=74  Identities=24%  Similarity=0.442  Sum_probs=65.3

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhc----C-------ceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccC
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERC----G-------EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLD   81 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~----G-------~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~   81 (158)
                      ..+|||+|||..+++++|.++|++|    |       .|..+.+.      ..+|||||+|.+.++|+.|+ .|||..|.
T Consensus         4 ~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~------~~~g~afV~F~~~~~A~~Al-~l~g~~~~   76 (198)
T 2yh0_A            4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRSVDETTQAM-AFDGIIFQ   76 (198)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEE------TTTTEEEEEESCSHHHHHHG-GGTTEEET
T ss_pred             eeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEec------CCCCEEEEEeCCHHHHHHHH-HhcCCEEc
Confidence            4789999999999999999999999    4       56666553      34789999999999999999 89999999


Q ss_pred             CceEEEEeeecC
Q psy7051          82 GRELRVQMARYG   93 (158)
Q Consensus        82 g~~i~v~~a~~~   93 (158)
                      |+.|.|.++...
T Consensus        77 g~~i~v~~~~~~   88 (198)
T 2yh0_A           77 GQSLKIRRPHDY   88 (198)
T ss_dssp             TEEEEEECCCCC
T ss_pred             CceEEEeCCCCC
Confidence            999999988744

>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=99.61  E-value=2e-15  Score=115.26  Aligned_cols=75  Identities=24%  Similarity=0.469  Sum_probs=64.2

Q ss_pred             CCCCcEEEEeC--CCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccC---Cc-
Q psy7051          10 IEGMVSLKVDN--LTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLD---GR-   83 (158)
Q Consensus        10 ~~~~~~l~V~n--l~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~---g~-   83 (158)
                      .++..+|||+|  |+..+++++|+++|++||+|..|.++.      .+|||||+|.+.++|++|++.|||.++.   |+ 
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~   88 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   88 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccccccCCc
Confidence            35668999999  578999999999999999999987754      3689999999999999999999999873   44 


Q ss_pred             -eEEEEee
Q psy7051          84 -ELRVQMA   90 (158)
Q Consensus        84 -~i~v~~a   90 (158)
                       .|.|.|+
T Consensus        89 ~~ly~~~~   96 (345)
T 3tht_A           89 ITLYLNFV   96 (345)
T ss_dssp             EECEEEEC
T ss_pred             eEEEEEEe
Confidence             5677775

>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=99.55  E-value=4.5e-14  Score=91.87  Aligned_cols=76  Identities=20%  Similarity=0.354  Sum_probs=64.5

Q ss_pred             CCcEEEEeCCCCCC----------CHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccC
Q psy7051          12 GMVSLKVDNLTYRT----------TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLD   81 (158)
Q Consensus        12 ~~~~l~V~nl~~~~----------~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~   81 (158)
                      +..+|.|.|+=...          .+++|+++|++||.|..|.|..+.    .+|+|||+|.+.++|+.|++.|||..|+
T Consensus         6 ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f~   81 (114)
T 3s6e_A            6 ATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWFA   81 (114)
T ss_dssp             CCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEET
T ss_pred             CCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEEC
Confidence            35678999983321          235789999999999999987653    4799999999999999999999999999


Q ss_pred             CceEEEEeee
Q psy7051          82 GRELRVQMAR   91 (158)
Q Consensus        82 g~~i~v~~a~   91 (158)
                      |+.|.|.++.
T Consensus        82 GR~i~v~~~~   91 (114)
T 3s6e_A           82 GKMITAAYVP   91 (114)
T ss_dssp             TEECEEEEEC
T ss_pred             CEEEEEEEEc
Confidence            9999999975

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

Probab=99.49  E-value=2.4e-13  Score=88.86  Aligned_cols=76  Identities=18%  Similarity=0.151  Sum_probs=67.1

Q ss_pred             CCCCcEEEEeCCCCC-CCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcC-HHHHHHHHHHhC--CcccCCceE
Q psy7051          10 IEGMVSLKVDNLTYR-TTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD-KRDAEDALDAMD--GRMLDGREL   85 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~-~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~-~~~a~~a~~~l~--g~~i~g~~i   85 (158)
                      .+....|+|+||+.. ++.++|+++|++||+|.+|.++.+..      .|||.|.+ .++|..|++.||  +..|+|..+
T Consensus        15 ~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~   88 (121)
T 1owx_A           15 EKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNKEV   88 (121)
T ss_dssp             CCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSE
T ss_pred             ccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCcEE
Confidence            455688999999999 99999999999999999999988753      59999999 899999999995  678999999


Q ss_pred             EEEeee
Q psy7051          86 RVQMAR   91 (158)
Q Consensus        86 ~v~~a~   91 (158)
                      +++...
T Consensus        89 ~~evL~   94 (121)
T 1owx_A           89 TWEVLE   94 (121)
T ss_dssp             EEEECC
T ss_pred             EEEECC
Confidence            988743

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

Probab=99.42  E-value=1.3e-12  Score=80.70  Aligned_cols=71  Identities=23%  Similarity=0.316  Sum_probs=60.2

Q ss_pred             cEEEEeCCCC----CCCH----HHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceE
Q psy7051          14 VSLKVDNLTY----RTTP----DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGREL   85 (158)
Q Consensus        14 ~~l~V~nl~~----~~~~----~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i   85 (158)
                      .||+|.-++.    ++-.    .+|.+.|.+||+|..++++.+.        +||+|.+.++|.+|++ |||..|+|+.|
T Consensus         8 ~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~-mnG~~v~Gr~L   78 (91)
T 2dnr_A            8 GTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLS-LNGKELLNRTI   78 (91)
T ss_dssp             CEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGG-GTTCEETTEEE
T ss_pred             CeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHh-cCCeEeCCeEE
Confidence            5688876652    3323    5789999999999999998773        8999999999999997 99999999999


Q ss_pred             EEEeeecC
Q psy7051          86 RVQMARYG   93 (158)
Q Consensus        86 ~v~~a~~~   93 (158)
                      +|++++..
T Consensus        79 kV~lkt~d   86 (91)
T 2dnr_A           79 TIALKSPS   86 (91)
T ss_dssp             EEEECCCS
T ss_pred             EEEeCCCC
Confidence            99998743

>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=99.27  E-value=1.3e-11  Score=76.55  Aligned_cols=70  Identities=20%  Similarity=0.316  Sum_probs=59.2

Q ss_pred             CcEEEEeCCCCC-----C-CH---HHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCc
Q psy7051          13 MVSLKVDNLTYR-----T-TP---DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGR   83 (158)
Q Consensus        13 ~~~l~V~nl~~~-----~-~~---~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~   83 (158)
                      ..||+|.-++..     + .+   .+|.+.|.+||+|..++++.+.        +||+|.+.++|.+||+ |||..|+|+
T Consensus        15 D~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG~~v~Gr   85 (95)
T 1ufw_A           15 DATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGMKVKGR   85 (95)
T ss_dssp             TCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGSEETTE
T ss_pred             CCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCCeeeCCe
Confidence            367999877643     2 21   5689999999999999998773        9999999999999997 999999999


Q ss_pred             eEEEEeee
Q psy7051          84 ELRVQMAR   91 (158)
Q Consensus        84 ~i~v~~a~   91 (158)
                      .|+|.+-.
T Consensus        86 ~L~V~~k~   93 (95)
T 1ufw_A           86 AVKISGPS   93 (95)
T ss_dssp             EEEEECCC
T ss_pred             EEEEeccC
Confidence            99998753

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

Probab=99.24  E-value=3.7e-11  Score=86.46  Aligned_cols=67  Identities=19%  Similarity=0.313  Sum_probs=59.7

Q ss_pred             CCHHHHHHHhhhcCceEEEEEccCC----CCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          25 TTPDDLRRVFERCGEVGDIYIPRDR----FTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        25 ~~~~~l~~~f~~~G~i~~v~~~~~~----~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      -.+++|.+.|++||.|..|.++.+.    .++..+|++||+|.+.++|++|++.|||..|+|+.|.|.+..
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~  211 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYD  211 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECC
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcC
Confidence            3567899999999999999998543    345889999999999999999999999999999999999975

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

Probab=98.95  E-value=6.4e-09  Score=65.85  Aligned_cols=72  Identities=17%  Similarity=0.218  Sum_probs=65.4

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhc-----CceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEE
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERC-----GEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR   86 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~-----G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~   86 (158)
                      ...+|-+-|||..++...|..+++++     |.|..|.+..+.      +-|+|+|.+...|.+|.-.|+|.+|.|++|+
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d~~~AgKasLaL~G~ef~gr~Lr   93 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKMLMILNGSQFQGKVIR   93 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHHHHHSSEEETTEEEE
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHHhhcCCeeecCeEEE
Confidence            35778889999999999999999999     999999998874      5799999999999998889999999999999


Q ss_pred             EEe
Q psy7051          87 VQM   89 (158)
Q Consensus        87 v~~   89 (158)
                      |.-
T Consensus        94 ~gT   96 (117)
T 2l9w_A           94 SGT   96 (117)
T ss_dssp             EEC
T ss_pred             ecC
Confidence            864

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

Probab=98.49  E-value=1.8e-06  Score=53.35  Aligned_cols=80  Identities=15%  Similarity=0.131  Sum_probs=63.7

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCC--cccEEEEEEcCHHHHHHHHHHhCCcccCCc-----eEE
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRE--SRGFAFVRFFDKRDAEDALDAMDGRMLDGR-----ELR   86 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~--~~g~afV~f~~~~~a~~a~~~l~g~~i~g~-----~i~   86 (158)
                      ++|.|.+||+.+||+++.+.+..+..+....++..+.+.+  ...-|||.|.+.+++....+.++|..+.+.     ...
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D~kg~~~~a~   81 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEcCCCCEeeeE
Confidence            5799999999999999999999998887777766554433  335799999999999999999999976332     346


Q ss_pred             EEeeecC
Q psy7051          87 VQMARYG   93 (158)
Q Consensus        87 v~~a~~~   93 (158)
                      |++|...
T Consensus        82 VE~AP~q   88 (91)
T 1uw4_A           82 VEFAPFQ   88 (91)
T ss_dssp             EEECSSC
T ss_pred             EEEcCCC
Confidence            7776543

>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=98.47  E-value=4.7e-07  Score=56.98  Aligned_cols=74  Identities=14%  Similarity=0.118  Sum_probs=62.6

Q ss_pred             CCcEEEEeCCCCCC-C----HHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEE
Q psy7051          12 GMVSLKVDNLTYRT-T----PDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR   86 (158)
Q Consensus        12 ~~~~l~V~nl~~~~-~----~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~   86 (158)
                      ..++|+|+||+..+ .    .+.++++|..|+++..+.+...-      .-..|.|.++++|.+|-..||+..|+|..|+
T Consensus         4 ~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF------RRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r   77 (104)
T 1wey_A            4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF------KRVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT------TEEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc------eEEEEEeCChHHHHHHHHHhccceecCceeE
Confidence            34789999998865 2    25789999999988887766542      3579999999999999999999999999999


Q ss_pred             EEeee
Q psy7051          87 VQMAR   91 (158)
Q Consensus        87 v~~a~   91 (158)
                      |.++.
T Consensus        78 ~YFgq   82 (104)
T 1wey_A           78 LYFAQ   82 (104)
T ss_dssp             EECCC
T ss_pred             EEecC
Confidence            99987

>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=98.33  E-value=2.8e-06  Score=52.67  Aligned_cols=55  Identities=22%  Similarity=0.270  Sum_probs=46.5

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhC
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD   76 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~   76 (158)
                      .+.++| ++|+++...||.++|+.||.| .|.++.|.       .|||.|.+++.|..|++.+.
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~WidDT-------sAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccCCE-EEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            356666 999999999999999999955 46676663       79999999999999998663

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

Probab=98.25  E-value=1.2e-05  Score=50.46  Aligned_cols=70  Identities=26%  Similarity=0.251  Sum_probs=58.0

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhh---c--CceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEE
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFER---C--GEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR   86 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~---~--G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~   86 (158)
                      ...+|.|.|||+.++++.|+-+|+.   -  |+|..++...        +-|+|+|.+.+.|+.+|+. ..+.|++..|.
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k-~~H~L~~~~Ls   77 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQ-ADHELHGAQLS   77 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTC-SCCBSSSSBCE
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcC-CcceecCeEEE
Confidence            3478999999999999999999987   2  4788887643        4699999999999999852 47889999999


Q ss_pred             EEee
Q psy7051          87 VQMA   90 (158)
Q Consensus        87 v~~a   90 (158)
                      |...
T Consensus        78 V~P~   81 (104)
T 2dhx_A           78 LRPA   81 (104)
T ss_dssp             EEEC
T ss_pred             EEcC
Confidence            8653

>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=98.23  E-value=3.4e-06  Score=52.46  Aligned_cols=54  Identities=22%  Similarity=0.290  Sum_probs=46.1

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhC
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD   76 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~   76 (158)
                      ..++| ++|+++...||.++|+.||.| .|.++.|.       .|||.|.+++.|..|+..+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fggv-~I~WidDT-------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSEEE-EEEEEETT-------EEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccCCE-EEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            45666 999999999999999999944 57777763       79999999999999998774

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

Probab=98.17  E-value=3.9e-06  Score=52.21  Aligned_cols=79  Identities=14%  Similarity=0.091  Sum_probs=58.3

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCC--cccEEEEEEcCHHHHHHHHHHhCCcccCCc-----eEE
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRE--SRGFAFVRFFDKRDAEDALDAMDGRMLDGR-----ELR   86 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~--~~g~afV~f~~~~~a~~a~~~l~g~~i~g~-----~i~   86 (158)
                      .+|.|..||+.+||+++.+.+..+-++....++..+.+.+  ...-|||.|.+.+++....+.++|..+.+.     ...
T Consensus        10 ~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~a~   89 (97)
T 2l08_A           10 HMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYPAV   89 (97)
T ss_dssp             CCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEEEE
T ss_pred             eeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEeeeE
Confidence            4689999999999999988888765554444444333332  224699999999999999999999976332     356


Q ss_pred             EEeeec
Q psy7051          87 VQMARY   92 (158)
Q Consensus        87 v~~a~~   92 (158)
                      |++|..
T Consensus        90 VE~APy   95 (97)
T 2l08_A           90 VEFAPF   95 (97)
T ss_dssp             EEECCC
T ss_pred             EEecCC
Confidence            777653

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=98.05  E-value=2.8e-05  Score=50.17  Aligned_cols=69  Identities=17%  Similarity=0.246  Sum_probs=55.5

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCC-ceEEEEe
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDG-RELRVQM   89 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g-~~i~v~~   89 (158)
                      ...|.|-++|+. ....|...|++||+|.......      ...+..|.|++..+|+.||. .||..|++ -.|-|..
T Consensus        24 ~~wVtVFGFp~~-~~~~VL~~F~~~G~Iv~~~~~~------~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p   93 (119)
T 1wwh_A           24 DTWVTVFGFPQA-SASYILLQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKP   93 (119)
T ss_dssp             GGEEEEECCCGG-GHHHHHHHHHTTSCEEEEEECS------SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEE
T ss_pred             CCEEEEECCCHH-HHHHHHHHHHhhCcEEEeccCC------CCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEE
Confidence            467888899988 4677889999999999887621      24699999999999999995 69999975 4556555

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=97.55  E-value=0.00018  Score=47.01  Aligned_cols=75  Identities=16%  Similarity=0.198  Sum_probs=53.5

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCceEE-EEEccC------------CCCC-CcccEEEEEEcCHHHHHHHHHHhCCcc
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGD-IYIPRD------------RFTR-ESRGFAFVRFFDKRDAEDALDAMDGRM   79 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~-v~~~~~------------~~~~-~~~g~afV~f~~~~~a~~a~~~l~g~~   79 (158)
                      .-|.|-++|+. ....+.+.|++||.|.+ +.+...            +... ....+..|+|++..+|..||. .||..
T Consensus         8 ~~VtVFGFp~~-~~~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~i   85 (132)
T 3p3d_A            8 LAILVFGYPET-MANQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGAV   85 (132)
T ss_dssp             CEEEEECCCGG-GHHHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTCE
T ss_pred             eEEEEEecCHH-HHHHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCeE
Confidence            45777799776 45567788999999866 222110            0000 024688999999999999995 69999


Q ss_pred             cCCceEEEEee
Q psy7051          80 LDGRELRVQMA   90 (158)
Q Consensus        80 i~g~~i~v~~a   90 (158)
                      |+|.-|-|...
T Consensus        86 i~G~mIGV~Py   96 (132)
T 3p3d_A           86 FNGVLLGVIPY   96 (132)
T ss_dssp             ETTEECEEEEC
T ss_pred             eCcEEEEEEEC
Confidence            99987777664

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=97.18  E-value=0.00025  Score=56.02  Aligned_cols=55  Identities=9%  Similarity=0.205  Sum_probs=41.6

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHH
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD   73 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~   73 (158)
                      ..+|+|. .+..+++.+|.++|++||+|..+.+-.+.     .-||.|||.+.+++.+++.
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~-----g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF-----GLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS-----SEEEEEECC---CCHHHHS
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC-----CeEEEEEeCCHHHHHHHHh
Confidence            4689996 79999999999999999999999886653     3699999999999987764

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

Probab=96.85  E-value=0.001  Score=44.55  Aligned_cols=36  Identities=11%  Similarity=0.093  Sum_probs=28.3

Q ss_pred             EEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcc
Q psy7051          42 DIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRM   79 (158)
Q Consensus        42 ~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~   79 (158)
                      .+.|+.+.  ...+|||||+|.+.++|+.|++.+++..
T Consensus         2 ~~kl~ln~--~~~~G~~fV~f~~~~~A~~al~~~~~~~   37 (158)
T 2kn4_A            2 QYKLILNG--KTLKGETTTEAVDAATAEKVFKQYANDN   37 (158)
T ss_dssp             EEEEEEEC--SSCEEEEEEECSSHHHHHHHHHHHHHHH
T ss_pred             cEEEEecC--ccccchhHHHHHHHHhHHHHHHhhcccC
Confidence            34555553  3578999999999999999998887643

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

Probab=96.72  E-value=0.00069  Score=45.15  Aligned_cols=40  Identities=20%  Similarity=0.233  Sum_probs=36.0

Q ss_pred             CCCcccEEEEEEcCHHHHHHHHHHh-CCcccCCceEEEEeee
Q psy7051          51 TRESRGFAFVRFFDKRDAEDALDAM-DGRMLDGRELRVQMAR   91 (158)
Q Consensus        51 ~~~~~g~afV~f~~~~~a~~a~~~l-~g~~i~g~~i~v~~a~   91 (158)
                      ....+|+++|+|.+.++|+.|++.| ||..|.| .|.+.++.
T Consensus         9 g~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~   49 (150)
T 2i2y_A            9 GKTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDAT   49 (150)
T ss_dssp             CSSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTT
T ss_pred             cccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceeccccc
Confidence            3456899999999999999999999 9999999 99998875

>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=96.36  E-value=0.018  Score=46.09  Aligned_cols=56  Identities=21%  Similarity=0.238  Sum_probs=46.4

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCC
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG   77 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g   77 (158)
                      ...++|+ +|..+...+|.++|+.||.+ .|.++.+.       .|||.|.+.+.|..+++.+..
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~widdt-------~a~V~~~~~~~a~~~l~~~~~  495 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVQIAVNTSKY  495 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEECSSS-------EEEEECSCHHHHHHHHHHHTT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEEcCC-------eEEEEECCHHHHHHHHHHHHh
Confidence            3567776 99999999999999999954 56666552       799999999999999998854

>2g0c_A ATP-dependent RNA helicase DBPA; RNA recognition motif, hydrolase; 1.70A {Bacillus subtilis} PDB: 3moj_B

Probab=93.50  E-value=0.41  Score=27.69  Aligned_cols=68  Identities=18%  Similarity=0.314  Sum_probs=42.0

Q ss_pred             EEEEeCC-CCCCCHHHHHHHhhhcC-----ceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEE
Q psy7051          15 SLKVDNL-TYRTTPDDLRRVFERCG-----EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ   88 (158)
Q Consensus        15 ~l~V~nl-~~~~~~~~l~~~f~~~G-----~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~   88 (158)
                      +|+|..- -..+...+|..++..-+     .|-.+.+..        .|.||+... +.+..+++.|++..+.|+.+.|+
T Consensus         2 ~~~i~~Grk~~~~p~~ivg~i~~~~gi~~~~IG~I~i~d--------~~s~v~v~~-~~~~~~~~~l~~~~i~g~~~~v~   72 (76)
T 2g0c_A            2 KLYFNGGKKKKIRAVDFVGTIAKIDGVSADDIGIITIMD--------NASYVEILN-GKGPHVLKVMKNTTVKGKQLKVN   72 (76)
T ss_dssp             EEEESCCCC----CHHHHHHHHTSTTCCGGGEEEEEECS--------SCEEEEECT-TCHHHHHHHHTTCCC---CCCEE
T ss_pred             EEEEeCCCccCCCHHHHHHHHHHccCCChhhccEEEEeC--------CcEEEEECH-HHHHHHHHHhccccCcCceEEEE
Confidence            4555311 34566777777776544     456666633        378998865 45777888999999999999988


Q ss_pred             eee
Q psy7051          89 MAR   91 (158)
Q Consensus        89 ~a~   91 (158)
                      .++
T Consensus        73 ~~~   75 (76)
T 2g0c_A           73 KAN   75 (76)
T ss_dssp             ECC
T ss_pred             ECC
Confidence            764

>3lpe_A Putative transcription antitermination protein NU; transcription regulation, SPT4, SPT5, NUSG, archaea, evoluti directed RNA polymerase; 1.90A {Methanocaldococcus jannaschii} PDB: 3ewg_A

Probab=84.97  E-value=2.6  Score=25.43  Aligned_cols=60  Identities=13%  Similarity=0.204  Sum_probs=37.6

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhh----cC-ceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCc
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDLRRVFER----CG-EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGR   78 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l~~~f~~----~G-~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~   78 (158)
                      ...+..|++.    .--|..+.+.+..    .| +|..+.++..     ..||.||++...++...+++.+.|.
T Consensus         9 d~~WYvv~~~----sG~E~~V~~~L~~~~~~~~l~i~~v~vP~~-----fPGYVfVe~~~~~~~~~~I~~t~gV   73 (92)
T 3lpe_A            9 AHMIFAVRTM----VGQEKNIAGLMASRAEKEQLDVYSILASES-----LKGYVLVEAETKGDVEELIKGMPRV   73 (92)
T ss_dssp             CCCEEEEEEC----TTCHHHHHHHHHHHHHHTTCCEEEEEECTT-----STTEEEEEESSHHHHHHHHTTCTTE
T ss_pred             CCeEEEEEEE----CChHHHHHHHHHHHHHhcCCcEEEEEEecc-----cCCEEEEEEecchhHHHHHHCCCCc
Confidence            3334555552    2345555554442    23 4666666543     5899999999999888888776664

>4eyt_A Telomerase associated protein P65; RNA, LA protein, LARP7, RRM, XRRM, RNA binding protein; 2.50A {Tetrahymena thermophila} PDB: 4erd_A

Probab=84.16  E-value=5.1  Score=24.21  Aligned_cols=58  Identities=16%  Similarity=0.099  Sum_probs=46.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCC
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG   77 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g   77 (158)
                      ...-|.|-|+|..+-..++.-.....|---.|..+.        |-|.|.|.+.++..-|+.+|-+
T Consensus        11 qnclikiinipqgtlkaevvlavrhlgyefycdyid--------gqamirfqnsdeqrlaiqklln   68 (129)
T 4eyt_A           11 QNCLIKIINIPQGTLKAEVVLAVRHLGYEFYCDYID--------GQAMIRFQNSDEQRLAIQKLLN   68 (129)
T ss_dssp             CSCEEEEECCCTTCCHHHHHHHHHTTCCCEEEEECS--------SCEEEEESSHHHHHHHHHHHEE
T ss_pred             hCcEEEEEecCCCceeeeeEEeehhcCeeEeeeeec--------CeeEEEecCChHHHHHHHHHHh
Confidence            345677889999999999888888888777777653        4699999999998888887643

---

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	158
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	2e-22
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	1e-19
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	3e-18
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	4e-18
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	1e-17
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	1e-17
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	5e-17
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	5e-17
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-16
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	3e-16
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	4e-16
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	4e-16
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	1e-15
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	1e-15
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-15
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	3e-15
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	4e-15
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	5e-15
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	7e-15
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	7e-15
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	7e-15
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	8e-15
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	1e-14
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-14
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	1e-14
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-14
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 9e-14
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	1e-13
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	1e-13
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-13
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	3e-13
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	3e-13
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	4e-13
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	4e-13
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	3e-07
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	5e-13
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	7e-13
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	8e-13
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	1e-12
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	1e-12
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	2e-12
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	2e-12
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	2e-12
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	3e-12
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	4e-12
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	6e-12
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	6e-12
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	7e-12
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	1e-11
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	2e-11
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	2e-11
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	2e-11
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	4e-11
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	5e-11
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	9e-11
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	1e-10
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	1e-10
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-10
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	2e-10
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	3e-10
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	6e-10
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	6e-10
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	7e-10
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	9e-10
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	1e-09
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	2e-09
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	3e-09
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	3e-09
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	1e-08
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-08
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	2e-08
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	2e-08
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	8e-08
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	8e-08
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-07
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	1e-07
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	6e-07
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	8e-07
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	1e-05
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	1e-05
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	2e-05
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-05
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	8e-05
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	4e-04
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	6e-04
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	0.001

>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 = 82.7 bits (204), Expect = 2e-22
 Identities = 27/77 (35%), Positives = 40/77 (51%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          SL V +L    T   L   F   G +  I + RD  TR S G+A+V F    DAE ALD 
Sbjct: 2  SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 75 MDGRMLDGRELRVQMAR 91
          M+  ++ G+ +R+  ++
Sbjct: 62 MNFDVIKGKPVRIMWSQ 78

>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 = 75.8 bits (186), Expect = 1e-19
 Identities = 26/78 (33%), Positives = 44/78 (56%), Gaps = 2/78 (2%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          +L V NL    T D L  +F + G +    I RD+ T   RG AFVR+  + +A++A+ A
Sbjct: 8  NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 67

Query: 75 MDGRMLDG--RELRVQMA 90
          ++  + +G  + L V++A
Sbjct: 68 LNNVIPEGGSQPLSVRLA 85

>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 = 72.3 bits (177), Expect = 3e-18
 Identities = 25/79 (31%), Positives = 40/79 (50%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          +L V+ L    T  +L  +F   G +    I RD  T  S G+AFV F  + D++ A+  
Sbjct: 4  NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 75 MDGRMLDGRELRVQMARYG 93
          ++G  +  + L+V  AR G
Sbjct: 64 LNGITVRNKRLKVSYARPG 82

>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 = 72.3 bits (177), Expect = 4e-18
 Identities = 25/85 (29%), Positives = 44/85 (51%), Gaps = 2/85 (2%)

Query: 8  PRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDR-FTRESRGFAFVRFFDKR 66
          P+ +    + V N+ ++    ++R +F   GE+  + +P+    T   RGF FV F  K+
Sbjct: 3  PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQ 62

Query: 67 DAEDALDAM-DGRMLDGRELRVQMA 90
          DA+ A +A+     L GR L ++ A
Sbjct: 63 DAKKAFNALCHSTHLYGRRLVLEWA 87

>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 = 70.4 bits (172), Expect = 1e-17
 Identities = 25/73 (34%), Positives = 40/73 (54%), Gaps = 1/73 (1%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          +  L+++TT + LR  F + GEV +  + RD  T+ SRGF FV F D+   +  L A   
Sbjct: 5  IGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQSR 63

Query: 78 RMLDGRELRVQMA 90
            LD + +  ++A
Sbjct: 64 HELDSKTIDPKVA 76

>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 = 70.3 bits (172), Expect = 1e-17
 Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 1/75 (1%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V NL +  +  D++ +F   G +    +     +  S G A V F  K DA  A+   
Sbjct: 3  LLVSNLDFGVSDADIQELFAEFGTLKKAAVHY-DRSGRSLGTADVHFERKADALKAMKQY 61

Query: 76 DGRMLDGRELRVQMA 90
          +G  LDGR + +Q+ 
Sbjct: 62 NGVPLDGRPMNIQLV 76

>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 = 69.2 bits (169), Expect = 5e-17
 Identities = 18/73 (24%), Positives = 34/73 (46%), Gaps = 1/73 (1%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V  L+  T  + +R  F   GEV  I +P D  T + RGF F+ F ++   +  ++    
Sbjct: 4  VGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKY 62

Query: 78 RMLDGRELRVQMA 90
            +   +  +++A
Sbjct: 63 HNVGLSKCEIKVA 75

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 69.3 bits (169), Expect = 5e-17
 Identities = 22/83 (26%), Positives = 37/83 (44%), Gaps = 3/83 (3%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGD---IYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          + NL + TT + L+ VF + G +                S GF FV +     A+ AL  
Sbjct: 3  IKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQ 62

Query: 75 MDGRMLDGRELRVQMARYGRPPS 97
          + G  +DG +L V+++     P+
Sbjct: 63 LQGHTVDGHKLEVRISERATKPA 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 = 67.7 bits (165), Expect = 2e-16
 Identities = 18/76 (23%), Positives = 34/76 (44%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          +  L      D ++ +    G +    + +D  T  S+G+AF  + D    + A+  ++G
Sbjct: 6  IGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNG 65

Query: 78 RMLDGRELRVQMARYG 93
            L  ++L VQ A  G
Sbjct: 66 MQLGDKKLLVQRASVG 81

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 68.1 bits (166), Expect = 3e-16
 Identities = 29/117 (24%), Positives = 53/117 (45%), Gaps = 11/117 (9%)

Query: 5   RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
           R PP  E    L + NL Y+ T +++  +F + G +  I +     TR   G A+V + D
Sbjct: 1   RLPP--EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETR---GTAYVVYED 55

Query: 65  KRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRDRRY 121
             DA++A D + G  +  R L V          ++R+    D  ++ ++ +    +Y
Sbjct: 56  IFDAKNACDHLSGFNVCNRYLVVLYYN------ANRAFQKMDTKKKEEQLKLLKEKY 106

>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 = 67.3 bits (164), Expect = 4e-16
 Identities = 23/82 (28%), Positives = 45/82 (54%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          +L V NL++ TT + +  +F + G++  I +  D+  + + GF FV ++ + DAE+A+  
Sbjct: 9  TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 68

Query: 75 MDGRMLDGRELRVQMARYGRPP 96
          ++G  LD R +R       +  
Sbjct: 69 INGTRLDDRIIRTDWDAGFKEG 90

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

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

 Score = 67.0 bits (163), Expect = 4e-16
 Identities = 18/89 (20%), Positives = 38/89 (42%), Gaps = 5/89 (5%)

Query: 2  SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          S G+P P I     +KV N+ +  + D++   F     +      +        G A V 
Sbjct: 3  SSGKPGPTI-----IKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVA 57

Query: 62 FFDKRDAEDALDAMDGRMLDGRELRVQMA 90
          F  + +A  A+  ++ R +  R++++ + 
Sbjct: 58 FESRDEATAAVIDLNDRPIGSRKVKLVLG 86

>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 = 65.9 bits (160), Expect = 1e-15
 Identities = 25/77 (32%), Positives = 44/77 (57%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          +L V+ L    T ++ R +F   GE+    + RD+ T +S G+ FV + D +DAE A++ 
Sbjct: 4  NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 75 MDGRMLDGRELRVQMAR 91
          ++G  L  + ++V  AR
Sbjct: 64 LNGLRLQTKTIKVSYAR 80

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 65.9 bits (160), Expect = 1e-15
 Identities = 23/86 (26%), Positives = 45/86 (52%), Gaps = 1/86 (1%)

Query: 6  PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
          P   +EG + L V ++      D+++  F   GE+ +I++  DR T  S+G+A V +   
Sbjct: 1  PQRSVEGWI-LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETH 59

Query: 66 RDAEDALDAMDGRMLDGRELRVQMAR 91
          + A  A +A++G  + G+ ++V    
Sbjct: 60 KQALAAKEALNGAEIMGQTIQVDWCF 85

>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 = 65.0 bits (158), Expect = 2e-15
 Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          +  L++ TT  DL+  F + GEV D  +  D  T  SRGF FV F +    +  +D    
Sbjct: 4  IGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKE 62

Query: 78 RMLDGRELRVQMA 90
            L+G+ +  + A
Sbjct: 63 HKLNGKVIDPKRA 75

>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 = 64.7 bits (157), Expect = 3e-15
 Identities = 28/86 (32%), Positives = 47/86 (54%)

Query: 6  PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
          P  R +   +++V NL+  T   DL+ +F   G +  IY+ +D+ T +S+GFAF+ F  +
Sbjct: 1  PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRR 60

Query: 66 RDAEDALDAMDGRMLDGRELRVQMAR 91
           DA  A+  + G   D   L V+ A+
Sbjct: 61 EDAARAIAGVSGFGYDHLILNVEWAK 86

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

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

 Score = 64.3 bits (156), Expect = 4e-15
 Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 2/75 (2%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V  L    T  +L ++F + G +    I  D+ T  SRG  F+RF  + +AE+A+  ++G
Sbjct: 11 VSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNG 70

Query: 78 RMLDGRE--LRVQMA 90
          +   G    + V+ A
Sbjct: 71 QKPSGATEPITVKFA 85

>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 = 63.9 bits (155), Expect = 5e-15
 Identities = 33/73 (45%), Positives = 45/73 (61%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
           L V  L+  TT  DLR VF + G + D+ I  D+ +R SRGFAFV F +  DA++A + 
Sbjct: 11 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 70

Query: 75 MDGRMLDGRELRV 87
           +G  LDGR +RV
Sbjct: 71 ANGMELDGRRIRV 83

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.1 bits (156), Expect = 7e-15
 Identities = 28/103 (27%), Positives = 49/103 (47%), Gaps = 10/103 (9%)

Query: 2   SYGRPPPRIEGMVSLKVDNL-TYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
           S G+  PR      + + NL T      D+  +F + G++    + +        GFAFV
Sbjct: 5   SSGKTDPRSMN-SRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK--------GFAFV 55

Query: 61  RFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRG 103
           ++ ++R+A  A+   DGRM+ G+ L + +A   +   S  S G
Sbjct: 56  QYVNERNARAAVAGEDGRMIAGQVLDINLAAEPKVNRSGPSSG 98

>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 = 63.9 bits (155), Expect = 7e-15
 Identities = 24/77 (31%), Positives = 42/77 (54%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          ++ V  L  + +   L  +F + G V + ++P+DR T + +G+ FV F  + DA+ A+  
Sbjct: 11 TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI 70

Query: 75 MDGRMLDGRELRVQMAR 91
          MD   L G+ +RV  A 
Sbjct: 71 MDMIKLYGKPIRVNKAS 87

>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 = 63.9 bits (155), Expect = 7e-15
 Identities = 30/78 (38%), Positives = 38/78 (48%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V  L        L   F   G++ DI IP D  T + RGFAFV F    DA  A+D M+ 
Sbjct: 10 VGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNE 69

Query: 78 RMLDGRELRVQMARYGRP 95
            L GR +RV +A+  R 
Sbjct: 70 SELFGRTIRVNLAKPMRI 87

>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 = 63.6 bits (154), Expect = 8e-15
 Identities = 22/75 (29%), Positives = 34/75 (45%), Gaps = 1/75 (1%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIY-IPRDRFTRESRGFAFVRFFDKRDAEDALDAMD 76
          + NL        L   F   G +     I RD  T  S+G+AF+ F     ++ A++AM+
Sbjct: 3  IGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMN 62

Query: 77 GRMLDGRELRVQMAR 91
          G+ L  R + V  A 
Sbjct: 63 GQYLCNRPITVSYAF 77

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.5 bits (154), Expect = 1e-14
 Identities = 24/82 (29%), Positives = 38/82 (46%), Gaps = 2/82 (2%)

Query: 10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAE 69
          ++    L V  L ++TT  DL+  F   GEV  + + +D  T  S+GF FVRF +     
Sbjct: 5  VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQV 64

Query: 70 DALDAMDGRMLDGRELRVQMAR 91
            +      M+DGR    ++  
Sbjct: 65 KVMSQRH--MIDGRWCDCKLPN 84

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.9 bits (155), Expect = 1e-14
 Identities = 23/93 (24%), Positives = 35/93 (37%), Gaps = 7/93 (7%)

Query: 6  PPPR---IEGMVSLK--VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRE--SRGFA 58
           P     +  MV  +  +D+  Y    +D+R    + G V  I IPR     E    G  
Sbjct: 2  HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKI 61

Query: 59 FVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR 91
          FV F    D + A+  + GR    R +  +   
Sbjct: 62 FVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCD 94

>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 = 63.6 bits (154), Expect = 1e-14
 Identities = 16/80 (20%), Positives = 28/80 (35%), Gaps = 4/80 (5%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGD--IYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
          L +  +      +++     +  E     I         ++RGFAFV +   R A  A  
Sbjct: 4  LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 63

Query: 74 AMDGR--MLDGRELRVQMAR 91
           +      L G ++ V  A 
Sbjct: 64 KLMPGRIQLWGHQIAVDWAE 83

>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 = 62.7 bits (152), Expect = 2e-14
 Identities = 13/77 (16%), Positives = 35/77 (45%), Gaps = 6/77 (7%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          ++    +    T   +R+ F   G++ +I +  ++       ++FVRF     A  A+ +
Sbjct: 20 TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG------YSFVRFSTHESAAHAIVS 73

Query: 75 MDGRMLDGRELRVQMAR 91
          ++G  ++G  ++    +
Sbjct: 74 VNGTTIEGHVVKCYWGK 90

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.6 bits (149), Expect = 9e-14
 Identities = 13/75 (17%), Positives = 34/75 (45%), Gaps = 1/75 (1%)

Query: 15  SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
            +++         +    + E+ GEV ++ +  +       G  +V+F  + DAE A+  
Sbjct: 29  DVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVID 87

Query: 75  MDGRMLDGRELRVQM 89
           ++ R  +G+ +  ++
Sbjct: 88  LNNRWFNGQPIHAEL 102

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

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

 Score = 60.8 bits (147), Expect = 1e-13
 Identities = 24/76 (31%), Positives = 43/76 (56%), Gaps = 6/76 (7%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V NL    T +++R++FE+ G+ G+++I +D+       F F+R   +  AE A   +D 
Sbjct: 13 VGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG------FGFIRLETRTLAEIAKVELDN 66

Query: 78 RMLDGRELRVQMARYG 93
            L G++LRV+ A + 
Sbjct: 67 MPLRGKQLRVRFACHS 82

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 60.6 bits (146), Expect = 1e-13
 Identities = 15/76 (19%), Positives = 31/76 (40%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L + N     T  ++R + +    V             SR FA++    K DA   ++ +
Sbjct: 4  LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 63

Query: 76 DGRMLDGRELRVQMAR 91
          +G  ++G  L  +++ 
Sbjct: 64 NGLKIEGYTLVTKVSN 79

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 60.5 bits (146), Expect = 2e-13
 Identities = 28/87 (32%), Positives = 46/87 (52%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
           V NL+Y ++ +DL ++F   G + +++ P D  T++ +GFAFV F     A  A   +DG
Sbjct: 13  VRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDG 72

Query: 78  RMLDGRELRVQMARYGRPPSSSRSRGG 104
           ++  GR L V  +   +  S S    G
Sbjct: 73  QVFQGRMLHVLPSTIKKEASQSGPSSG 99

>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 = 59.9 bits (145), Expect = 3e-13
 Identities = 18/76 (23%), Positives = 31/76 (40%), Gaps = 4/76 (5%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
           + D L      +DLR    + G++  + +          G A V F D  +A+  +  +
Sbjct: 22 FEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHP----DGVASVSFRDPEEADYCIQTL 77

Query: 76 DGRMLDGRELRVQMAR 91
          DGR   GR++  Q   
Sbjct: 78 DGRWFGGRQITAQAWD 93

>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 = 59.0 bits (142), Expect = 3e-13
 Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 1/73 (1%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V  L+  TT +D++  FE+ G+V D  +  D+ T   RGF FV F  +   E     +  
Sbjct: 4  VGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EIHF 62

Query: 78 RMLDGRELRVQMA 90
            ++ + +  + A
Sbjct: 63 HEINNKMVECKKA 75

>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 = 59.8 bits (144), Expect = 4e-13
 Identities = 28/93 (30%), Positives = 45/93 (48%), Gaps = 9/93 (9%)

Query: 15  SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIP--------RDRFTRESRGFAFVRFFDKR 66
           ++ V  L    T DDL   F++CG V               D+ T + +G A V + D  
Sbjct: 10  AIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPP 69

Query: 67  DAEDALDAMDGRMLDGRELRVQMARYGRPPSSS 99
            A+ A++  DG+   G +L+V +AR  +PP +S
Sbjct: 70  TAKAAVEWFDGKDFQGSKLKVSLAR-KKPPMNS 101

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.6 bits (148), Expect = 4e-13
 Identities = 22/76 (28%), Positives = 34/76 (44%), Gaps = 1/76 (1%)

Query: 16  LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
           + V  +   T    LR  FE+ G++  I I  DR + + RGFAFV F D    +  +   
Sbjct: 100 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQ 158

Query: 76  DGRMLDGRELRVQMAR 91
               ++G    V+ A 
Sbjct: 159 KYHTVNGHNCEVRKAL 174

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.8 bits (107), Expect = 3e-07
 Identities = 20/62 (32%), Positives = 35/62 (56%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          +  L++ TT + LR  FE+ G + D  + RD  T+ SRGF FV +    + + A++A   
Sbjct: 11 IGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPH 70

Query: 78 RM 79
          ++
Sbjct: 71 KV 72

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.3 bits (143), Expect = 5e-13
 Identities = 24/92 (26%), Positives = 42/92 (45%), Gaps = 2/92 (2%)

Query: 2  SYGRPPPRIEGMVSLK--VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAF 59
          S G    + EG       + +L       DL ++F   G V    +  D+ T  S+ F F
Sbjct: 5  SIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGF 64

Query: 60 VRFFDKRDAEDALDAMDGRMLDGRELRVQMAR 91
          V + +   A+ A+ +M+G  +  + L+VQ+ R
Sbjct: 65 VSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKR 96

>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 = 58.5 bits (141), Expect = 7e-13
 Identities = 22/86 (25%), Positives = 39/86 (45%), Gaps = 2/86 (2%)

Query: 6  PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
          P  R  G+ ++ + NL        L   F   G +    +  D     S+G+ FV F  +
Sbjct: 1  PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQ 58

Query: 66 RDAEDALDAMDGRMLDGRELRVQMAR 91
            AE A++ M+G +L+ R++ V   +
Sbjct: 59 EAAERAIEKMNGMLLNDRKVFVGRFK 84

>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 = 58.9 bits (142), Expect = 8e-13
 Identities = 26/87 (29%), Positives = 43/87 (49%), Gaps = 1/87 (1%)

Query: 5  RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
          R     E    L +  L++ TT + LR  +E+ G++ D  + RD  ++ SRGF FV F  
Sbjct: 12 RKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSS 71

Query: 65 KRDAEDALDAMDGRMLDGRELRVQMAR 91
            + + A+ A     +DGR +  + A 
Sbjct: 72 MAEVDAAM-AARPHSIDGRVVEPKRAV 97

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 59.5 bits (143), Expect = 1e-12
 Identities = 29/104 (27%), Positives = 53/104 (50%), Gaps = 1/104 (0%)

Query: 4   GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFF 63
            +  P  + + +L V+ +        LR++FER G +  + I  DR TR+SRG+ FV+F 
Sbjct: 33  TQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQ 92

Query: 64  DKRDAEDALDAMDGRMLDGRELRVQMARYGRP-PSSSRSRGGRD 106
               A+ A+  ++G  +  + L+V +A  G   P  + + G  +
Sbjct: 93  SGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAGAVGDGN 136

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.2 bits (140), Expect = 1e-12
 Identities = 30/84 (35%), Positives = 45/84 (53%), Gaps = 1/84 (1%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
           V  L Y TT   LR+ FE  G++ +  +  DR T +SRG+ FV   D+  AE A    + 
Sbjct: 15  VGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP 74

Query: 78  RMLDGRELRVQMARYGRPPSSSRS 101
            ++DGR+  V +A  G  P S ++
Sbjct: 75  -IIDGRKANVNLAYLGAKPRSLQT 97

>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 = 57.7 bits (139), Expect = 2e-12
 Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          +  L++ TT + LR  FE+ G + D  + RD  T+ SRGF FV +    + + A++    
Sbjct: 11 IGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARP 69

Query: 78 RMLDGRELRVQMA 90
            +DGR +  + A
Sbjct: 70 HKVDGRVVEPKRA 82

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.8 bits (139), Expect = 2e-12
 Identities = 33/88 (37%), Positives = 40/88 (45%), Gaps = 3/88 (3%)

Query: 8  PRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRD 67
          P       + V NL       D+  VF + G + DI +   R       FAFV F D RD
Sbjct: 9  PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGP---PFAFVEFEDPRD 65

Query: 68 AEDALDAMDGRMLDGRELRVQMARYGRP 95
          AEDA+   DG   DG  LRV+  R GR 
Sbjct: 66 AEDAVYGRDGYDYDGYRLRVEFPRSGRG 93

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

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

 Score = 58.1 bits (140), Expect = 2e-12
 Identities = 27/109 (24%), Positives = 49/109 (44%), Gaps = 20/109 (18%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
           V+NL Y  T D L ++F + G V  I      FT+ ++  A +++ D   A+ A  ++DG
Sbjct: 12  VENLFYPVTLDVLHQIFSKFGTVLKIIT----FTKNNQFQALLQYADPVSAQHAKLSLDG 67

Query: 78  RML--DGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRDRRYTRS 124
           + +      LR+  ++                + + +  +SRD  YTR 
Sbjct: 68  QNIYNACCTLRIDFSKL------------TSLNVKYNNDKSRD--YTRP 102

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.7 bits (136), Expect = 3e-12
 Identities = 15/69 (21%), Positives = 31/69 (44%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          +  L   TT  DL ++ +  G++       D+ T + +G+ FV F     A+ A+ A+  
Sbjct: 3  IRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKA 62

Query: 78 RMLDGRELR 86
            +  +  +
Sbjct: 63 SGVQAQMAK 71

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

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

 Score = 56.6 bits (136), Expect = 4e-12
 Identities = 26/86 (30%), Positives = 44/86 (51%), Gaps = 5/86 (5%)

Query: 15  SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
           +L V NL+   T   + ++F + G      +  +  +     + FV F++ RDA  AL A
Sbjct: 10  TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAA 67

Query: 75  MDGRMLDGRELRVQMARYGRPPSSSR 100
           M+GR + G+E++V  A     PSS +
Sbjct: 68  MNGRKILGKEVKVNWA---TTPSSQK 90

>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 = 55.9 bits (134), Expect = 6e-12
 Identities = 24/73 (32%), Positives = 35/73 (47%), Gaps = 1/73 (1%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V  +   T    LR  FE+ G++  I I  DR + + RGFAFV F D  D+ D +     
Sbjct: 7  VGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDKIVIQKY 65

Query: 78 RMLDGRELRVQMA 90
            ++G    V+ A
Sbjct: 66 HTVNGHNCEVRKA 78

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.2 bits (135), Expect = 6e-12
 Identities = 20/78 (25%), Positives = 38/78 (48%), Gaps = 1/78 (1%)

Query: 15 SLKVDNLTYRTTPDDLRR-VFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
          ++ ++NL  +   D+L++ +       G I       + + RG AFV F +   A +AL 
Sbjct: 5  TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALR 64

Query: 74 AMDGRMLDGRELRVQMAR 91
          +M G     + +R+Q A+
Sbjct: 65 SMQGFPFYDKPMRIQYAK 82

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

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

 Score = 55.9 bits (134), Expect = 7e-12
 Identities = 33/84 (39%), Positives = 53/84 (63%), Gaps = 3/84 (3%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
           V  L++ T    L +VF + G++ ++ + +DR T+ SRGF FV F +  DA+DA+ AM+G
Sbjct: 10  VGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNG 69

Query: 78  RMLDGRELRVQMARYGRPPSSSRS 101
           + +DGR++RV  A      S +RS
Sbjct: 70  KSVDGRQIRVDQA---GKSSDNRS 90

>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 = 55.8 bits (134), Expect = 1e-11
 Identities = 25/76 (32%), Positives = 44/76 (57%), Gaps = 2/76 (2%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V N+ +R    DLR++F + G++ D+ I  +     S+GF FV F +  DA+ A + +
Sbjct: 14 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKL 71

Query: 76 DGRMLDGRELRVQMAR 91
           G +++GR++ V  A 
Sbjct: 72 HGTVVEGRKIEVNNAT 87

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 55.0 bits (132), Expect = 2e-11
 Identities = 22/86 (25%), Positives = 39/86 (45%), Gaps = 5/86 (5%)

Query: 6  PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
             ++    +L   NL++  T D+L+ VFE       + I       +S+G A++ F  +
Sbjct: 9  TSKKVRAARTLLAKNLSFNITEDELKEVFEDA-----LEIRLVSQDGKSKGIAYIEFKSE 63

Query: 66 RDAEDALDAMDGRMLDGRELRVQMAR 91
           DAE  L+   G  +DGR + +    
Sbjct: 64 ADAEKNLEEKQGAEIDGRSVSLYYTG 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 = 54.6 bits (131), Expect = 2e-11
 Identities = 21/76 (27%), Positives = 39/76 (51%), Gaps = 6/76 (7%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L V NL   T+ + + + F                 ++ R +AFV F ++ DA +A+ A+
Sbjct: 11 LYVRNLMLSTSEEMIEKEFNNIKPG------AVERVKKIRDYAFVHFSNREDAVEAMKAL 64

Query: 76 DGRMLDGRELRVQMAR 91
          +G++LDG  + V +A+
Sbjct: 65 NGKVLDGSPIEVTLAK 80

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.1 bits (132), Expect = 2e-11
 Identities = 27/90 (30%), Positives = 43/90 (47%)

Query: 15  SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
           S+ V N+ Y  T + L+ +F   G V    +  DR T + +G+ F  + D+  A  A+  
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 75  MDGRMLDGRELRVQMARYGRPPSSSRSRGG 104
           ++GR   GR LRV  A   +     +S G 
Sbjct: 70  LNGREFSGRALRVDNAASEKNKEELKSLGT 99

>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 = 54.3 bits (130), Expect = 4e-11
 Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 1/77 (1%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          ++    L  R  P DL   F   G+V D+ I  DR +R S+G A+V F + +    A+  
Sbjct: 20 TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-G 78

Query: 75 MDGRMLDGRELRVQMAR 91
          + G+ L G  + VQ ++
Sbjct: 79 LTGQRLLGVPIIVQASQ 95

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 54.0 bits (129), Expect = 5e-11
 Identities = 23/91 (25%), Positives = 44/91 (48%), Gaps = 6/91 (6%)

Query: 7  PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKR 66
          P  +    ++ + NL++ +  + L  V ++ G++  + +     T  S+G AF +F  + 
Sbjct: 2  PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQE 61

Query: 67 DAEDALDAM------DGRMLDGRELRVQMAR 91
           A+  L A        G  LDGR+L+V +A 
Sbjct: 62 AAQKCLAAASLEAEGGGLKLDGRQLKVDLAV 92

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

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

 Score = 53.6 bits (128), Expect = 9e-11
 Identities = 28/116 (24%), Positives = 49/116 (42%), Gaps = 8/116 (6%)

Query: 12  GMVSLKVDNL-TYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
           G   L V NL   R TP  L  +F   G+V  + I  ++        A V+  D   A+ 
Sbjct: 1   GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE-----NALVQMADGNQAQL 55

Query: 71  ALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRDRRYTRSRS 126
           A+  ++G  L G+ +R+ ++++          G  D+   +D   S   R+ +  S
Sbjct: 56  AMSHLNGHKLHGKPIRITLSKHQNVQLP--REGQEDQGLTKDYGNSPLHRFKKPGS 109

>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 = 53.1 bits (127), Expect = 1e-10
 Identities = 23/89 (25%), Positives = 37/89 (41%), Gaps = 7/89 (7%)

Query: 15  SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
            + V   T   T D+LR  F + G+V D+        +  R FAFV F D + A+     
Sbjct: 7   GVFVGRCTGDMTEDELREFFSQYGDVMDV-----FIPKPFRAFAFVTFADDQIAQSLC-- 59

Query: 75  MDGRMLDGRELRVQMARYGRPPSSSRSRG 103
            +  ++ G  + +  A      +S  S G
Sbjct: 60  GEDLIIKGISVHISNAEPKHNSNSGPSSG 88

>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 = 52.8 bits (126), Expect = 1e-10
 Identities = 23/90 (25%), Positives = 39/90 (43%), Gaps = 11/90 (12%)

Query: 13  MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDAL 72
           M  L + NL+   T DDLR++F          +          G+AFV + D+  A  A+
Sbjct: 1   MNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKS------GYAFVDYPDQNWAIRAI 54

Query: 73  DAMDGRM-LDGRELRVQMARYGRPPSSSRS 101
           + + G++ L G+ + V  +         RS
Sbjct: 55  ETLSGKVELHGKIMEVDYSV----SKKLRS 80

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.8 bits (126), Expect = 1e-10
 Identities = 15/84 (17%), Positives = 32/84 (38%), Gaps = 6/84 (7%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPR-----DRFTRESRGFAFVRFFDKRDAEDAL 72
          V N+ +  T + +   F     +G +              + + FAF+ F    +   A+
Sbjct: 6  VGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM 65

Query: 73 DAMDGRMLDGRELRVQMARYGRPP 96
             DG +  G+ L+++     +P 
Sbjct: 66 A-FDGIIFQGQSLKIRRPHDYQPL 88

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.3 bits (125), Expect = 2e-10
 Identities = 18/69 (26%), Positives = 31/69 (44%), Gaps = 6/69 (8%)

Query: 23 YRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDG 82
             TP  LR  F   G + D+ +   R        AFV +     A+ A+  ++G  ++ 
Sbjct: 13 EDMTPTLLRGAFSPFGNIIDLSMDPPR------NCAFVTYEKMESADQAVAELNGTQVES 66

Query: 83 RELRVQMAR 91
           +L+V +AR
Sbjct: 67 VQLKVNIAR 75

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.0 bits (124), Expect = 3e-10
 Identities = 13/69 (18%), Positives = 33/69 (47%), Gaps = 7/69 (10%)

Query: 20 NLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGR- 78
           L    + + L  V E+CG V  + +P ++       ++F R+    +++ A   ++G+ 
Sbjct: 27 GLGNGVSRNQLLPVLEKCGLVDALLMPPNKP------YSFARYRTTEESKRAYVTLNGKE 80

Query: 79 MLDGRELRV 87
          ++D    ++
Sbjct: 81 VVDDLGQKI 89

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.7 bits (123), Expect = 6e-10
 Identities = 18/86 (20%), Positives = 31/86 (36%), Gaps = 1/86 (1%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
           + NL Y  T + ++  F                    +GF +  F D      AL +++ 
Sbjct: 20  LGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNE 78

Query: 78  RMLDGRELRVQMARYGRPPSSSRSRG 103
             L  + +RV +A   +   S  S G
Sbjct: 79  ESLGNKRIRVDVADQAQDKDSGPSSG 104

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 50.6 bits (120), Expect = 6e-10
 Identities = 13/76 (17%), Positives = 28/76 (36%), Gaps = 3/76 (3%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          ++ V NL      + + + F+ CG +  + +           FA + F     A  A+  
Sbjct: 2  TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKN--FRFARIEFARYDGALAAI-T 58

Query: 75 MDGRMLDGRELRVQMA 90
             +++   E+ V   
Sbjct: 59 KTHKVVGQNEIIVSHL 74

>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 = 50.9 bits (121), Expect = 7e-10
 Identities = 16/92 (17%), Positives = 33/92 (35%), Gaps = 7/92 (7%)

Query: 12  GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDA 71
           G   + V NL   +   ++  + +           +  +   ++  AFV   +   A++A
Sbjct: 4   GSSGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNA 56

Query: 72  LDAMDGRMLDGRELRVQMARYGRPPSSSRSRG 103
           +         G++L VQ+        S  S G
Sbjct: 57  IQMFHQYSFRGKDLIVQLQPTDALLCSGPSSG 88

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.9 bits (121), Expect = 9e-10
 Identities = 25/76 (32%), Positives = 36/76 (47%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
          L + NL+ R T  DL  +F R  E     I     T   RG AF+ F +K  A  AL  +
Sbjct: 21 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 80

Query: 76 DGRMLDGRELRVQMAR 91
          +G  L G+ L ++  +
Sbjct: 81 NGYKLYGKILVIEFGK 96

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 50.2 bits (119), Expect = 1e-09
 Identities = 17/76 (22%), Positives = 31/76 (40%), Gaps = 6/76 (7%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVG---DIYIPRDRFTRES---RGFAFVRFFDKRDAEDA 71
          V  L+ R    ++ +  E  G+ G    + I        S      A+V +    DA  A
Sbjct: 13 VVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRA 72

Query: 72 LDAMDGRMLDGRELRV 87
          +  ++  ++DGR L+ 
Sbjct: 73 IQCVNNVVVDGRTLKA 88

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.2 bits (119), Expect = 2e-09
 Identities = 13/77 (16%), Positives = 24/77 (31%), Gaps = 1/77 (1%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          +L + NL       +L  + +  G+V          +  SRG  F R       E  +  
Sbjct: 20 NLYISNLPLSMDEQELENMLKPFGQV-ISTRILRDSSGTSRGVGFARMESTEKCEAVIGH 78

Query: 75 MDGRMLDGRELRVQMAR 91
           +G+ +           
Sbjct: 79 FNGKFIKTPPGVSAPTE 95

>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 = 49.8 bits (118), Expect = 3e-09
 Identities = 13/93 (13%), Positives = 28/93 (30%), Gaps = 13/93 (13%)

Query: 16  LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
              D  +   T      +F    +       +            + F +   A DA   +
Sbjct: 13  ANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF------KRVRINFSNPLSAADARLRL 66

Query: 76  DGRMLDGRELRVQMAR-------YGRPPSSSRS 101
                 G+E+++  A+       +  PP+  +S
Sbjct: 67  HKTEFLGKEMKLYFAQTLHIGSSHLAPPNPDKS 99

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 49.3 bits (117), Expect = 3e-09
 Identities = 24/99 (24%), Positives = 41/99 (41%), Gaps = 11/99 (11%)

Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          + YG+  P       L V  L   T+   L R F+R G +  I   +         FA++
Sbjct: 9  IGYGKANPT----TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS------FAYI 58

Query: 61 RFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSS 99
          ++     A+ A   M G  L G + R+++  + +   SS
Sbjct: 59 QYESLDAAQAACAKMRGFPLGGPDRRLRV-DFAKSGPSS 96

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

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

 Score = 47.4 bits (112), Expect = 1e-08
 Identities = 15/76 (19%), Positives = 28/76 (36%), Gaps = 2/76 (2%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          S+ +       T DD++   E  G+V +    R    +  +G  FV F     A+  +  
Sbjct: 8  SVYIKGFPTDATLDDIKEWLEDKGQVLN-IQMRRTLHKAFKGSIFVVFDSIESAKKFV-E 65

Query: 75 MDGRMLDGRELRVQMA 90
            G+     +L +   
Sbjct: 66 TPGQKYKETDLLILFK 81

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.9 bits (113), Expect = 1e-08
 Identities = 21/102 (20%), Positives = 38/102 (37%), Gaps = 2/102 (1%)

Query: 2   SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
           S G  P        +++  L +  + +++ + F     V +       F   S G AFV+
Sbjct: 5   SSGNSPDTANDGF-VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQ 63

Query: 62  FFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRG 103
           F  +  AE AL       +  R + +  +      +S  S G
Sbjct: 64  FASQEIAEKALK-KHKERIGHRYIEIFKSSRAEVRTSGPSSG 104

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 47.0 bits (111), Expect = 2e-08
 Identities = 18/79 (22%), Positives = 31/79 (39%), Gaps = 3/79 (3%)

Query: 15 SLKVDNLTYRTTPDDLRRVF--ERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDAL 72
           + + NL+     ++L R                  +    +   AF+ F +K  AE AL
Sbjct: 6  EIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL 65

Query: 73 DAMDGRMLDGRELRVQMAR 91
            M+  +L  RE+ V +A 
Sbjct: 66 -QMNRSLLGNREISVSLAD 83

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.5 bits (112), Expect = 2e-08
 Identities = 19/96 (19%), Positives = 35/96 (36%), Gaps = 7/96 (7%)

Query: 14  VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
           V   + N+ +  T  D+ +  E      +          +  G A V+F ++ DA  +  
Sbjct: 9   VCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSE- 67

Query: 74  AMDGRMLDGRELRV------QMARYGRPPSSSRSRG 103
            +  + L+GRE  V       M    + P +    G
Sbjct: 68  RLHRKKLNGREAFVHVVTLEDMREIEKNPPAQGKSG 103

>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 = 45.7 bits (107), Expect = 8e-08
 Identities = 18/77 (23%), Positives = 35/77 (45%), Gaps = 2/77 (2%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
          +L + NL    +  +L+          D+ +   R T  +R F +V F    D E AL+ 
Sbjct: 15 NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAEDLEKALE- 72

Query: 75 MDGRMLDGRELRVQMAR 91
          + G  + G E++++  +
Sbjct: 73 LTGLKVFGNEIKLEKPK 89

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

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

 Score = 45.5 bits (107), Expect = 8e-08
 Identities = 19/87 (21%), Positives = 36/87 (41%), Gaps = 10/87 (11%)

Query: 6  PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
          PP        L + N+    + +DL+ +F   G V    +   +F ++ R  A ++    
Sbjct: 8  PPSAT-----LHLSNIPPSVSEEDLKVLFSSNGGV----VKGFKFFQKDRKMALIQMGSV 58

Query: 66 RDAEDALDAMDGRML-DGRELRVQMAR 91
           +A  AL  +    L +   LRV  ++
Sbjct: 59 EEAVQALIDLHNHDLGENHHLRVSFSK 85

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

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

 Score = 45.6 bits (107), Expect = 1e-07
 Identities = 16/91 (17%), Positives = 30/91 (32%), Gaps = 11/91 (12%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD- 76
           V  L       DL    E+ G +  + +   +        A V F +   A++ +     
Sbjct: 20  VRGLCESVVEADLVEALEKFGTICYVMMMPFKR------QALVEFENIDSAKECVTFAAD 73

Query: 77  -GRMLDGRELRVQMARY---GRPPSSSRSRG 103
               + G++     +      RP +S  S G
Sbjct: 74  VPVYIAGQQAFFNYSTSKRITRPGNSGPSSG 104

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.2 bits (106), Expect = 1e-07
 Identities = 25/102 (24%), Positives = 33/102 (32%), Gaps = 8/102 (7%)

Query: 2   SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
           S G PP R      + V  L    +  DL+      G+V    + +D           V 
Sbjct: 5   SSGGPPTRRSDF-RVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDGM-------GMVE 56

Query: 62  FFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRG 103
           +  K D E AL  +D       E      R     SS  S G
Sbjct: 57  YLRKEDMEYALRKLDDTKFRSHEGETSYIRVYPERSSGPSSG 98

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 42.9 bits (100), Expect = 6e-07
 Identities = 18/87 (20%), Positives = 35/87 (40%), Gaps = 11/87 (12%)

Query: 6  PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
          PP +I     L + NL   T    L  +F +     ++ +  +R        AFV F  +
Sbjct: 6  PPNQI-----LFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFTTE 55

Query: 66 RDAEDALDAMDGRMLD-GRELRVQMAR 91
            +  A +A+ G  +     +++  A+
Sbjct: 56 LQSNAAKEALQGFKITPTHAMKITFAK 82

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.6 bits (99), Expect = 8e-07
 Identities = 16/74 (21%), Positives = 27/74 (36%), Gaps = 7/74 (9%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          +  L    T  ++  +             +  F  + +G AFV   +   AE A++    
Sbjct: 3  IRGLPGDVTNQEVHDLLSDY-------ELKYCFVDKYKGTAFVTLLNGEQAEAAINTFHQ 55

Query: 78 RMLDGRELRVQMAR 91
            L  REL VQ+  
Sbjct: 56 SRLRERELSVQLQP 69

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.8 bits (92), Expect = 1e-05
 Identities = 10/89 (11%), Positives = 27/89 (30%), Gaps = 13/89 (14%)

Query: 6  PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
           P R+     L +  L    T  ++  +              +    + +  AF+    +
Sbjct: 6  APSRV-----LHIRKLPGEVTETEVIALGLPF------GKVTNILMLKGKNQAFLELATE 54

Query: 66 RDAEDALDAM--DGRMLDGRELRVQMARY 92
            A   ++        L  + + +Q + +
Sbjct: 55 EAAITMVNYYSAVTPHLRNQPIYIQYSNH 83

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.5 bits (92), Expect = 1e-05
 Identities = 11/66 (16%), Positives = 21/66 (31%), Gaps = 8/66 (12%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
          V      +    +   F + G +    +           +  +R+  K  A  AL + DG
Sbjct: 9  VFGFPQASA-SYILLQFAQYGNILKHVMSNTG------NWMHIRYQSKLQARKAL-SKDG 60

Query: 78 RMLDGR 83
          R+    
Sbjct: 61 RIFGES 66

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

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

 Score = 39.8 bits (92), Expect = 2e-05
 Identities = 20/111 (18%), Positives = 37/111 (33%), Gaps = 8/111 (7%)

Query: 11  EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKR-DAE 69
            G +     +L  +T  +DL  +F   GE+  I   R            + F +K  +A 
Sbjct: 9   IGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEAL 62

Query: 70  DALDAMDGRMLDGRELRVQ-MARYGRPPSSSRSRGGRDRDRRRDRSRSRDR 119
                 +   L  R   V      G     +  +   D+    ++ +S+ R
Sbjct: 63  GKAKDANNGNLQLRNKEVTWEVLEGEVEKEALKKIIEDQQESLNKWKSKGR 113

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.0 bits (90), Expect = 3e-05
 Identities = 19/89 (21%), Positives = 29/89 (32%), Gaps = 3/89 (3%)

Query: 15  SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
            + +  L YR T +D+   F     +               G A V F    DA  A+ A
Sbjct: 17  CVHMRGLPYRATENDIYNFFSPLNPMRVHIE--IGPDGRVTGEADVEFATHEDAVAAM-A 73

Query: 75  MDGRMLDGRELRVQMARYGRPPSSSRSRG 103
            D   +  R + + +        S  S G
Sbjct: 74  KDKANMQHRYVELFLNSTAGTSGSGPSSG 102

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.6 bits (86), Expect = 8e-05
 Identities = 16/96 (16%), Positives = 32/96 (33%), Gaps = 6/96 (6%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
             NL   T   +++  F R G +G + +P           A V F +  +A  A   +  
Sbjct: 15  AKNLPAGTLAAEIQETFSRFGSLGRVLLPEGG------ITAIVEFLEPLEARKAFRHLAY 68

Query: 78  RMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDR 113
                  L ++ A  G   ++ + +  +        
Sbjct: 69  SKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEKA 104

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.4 bits (81), Expect = 4e-04
 Identities = 13/69 (18%), Positives = 27/69 (39%), Gaps = 8/69 (11%)

Query: 25 TTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA--MDGRMLDG 82
               L ++ E  G + +  I            AF+      DA+ A+D       ++ G
Sbjct: 21 NLRYQLLQLVEPFGVISNHLILNKIN------EAFIEMATTEDAQAAVDYYTTTPALVFG 74

Query: 83 RELRVQMAR 91
          + +RV +++
Sbjct: 75 KPVRVHLSQ 83

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.2 bits (80), Expect = 6e-04
 Identities = 15/87 (17%), Positives = 30/87 (34%), Gaps = 1/87 (1%)

Query: 4  GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFF 63
           R     E    + +  L +      +   F++   V D          ++ G  FV F 
Sbjct: 9  SRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFR 68

Query: 64 DKRDAEDALDAMDGRMLDGRELRVQMA 90
          ++ D + AL     + +  R ++V   
Sbjct: 69 NEADYKAAL-CRHKQYMGNRFIQVHPI 94

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.5 bits (78), Expect = 0.001
 Identities = 22/91 (24%), Positives = 29/91 (31%), Gaps = 11/91 (12%)

Query: 16  LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
           + V  L    +  DL+      G+V    + RD           V F  K D   A+  +
Sbjct: 3   VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGTG-------VVEFVRKEDMTYAVRKL 55

Query: 76  DGRMLDGRELRVQMAR----YGRPPSSSRSR 102
           D       E      R      R PS  RSR
Sbjct: 56  DNTKFRSHEGETAYIRVKVDGPRSPSYGRSR 86

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	158
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.92
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.92
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.92
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.92
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.92
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.92
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.92
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.92
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.92
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.91
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.91
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.91
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.91
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.91
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.91
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.9
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.9
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.9
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.9
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.9
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.9
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.9
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.9
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.89
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.89
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.89
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.89
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.89
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.89
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.89
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.89
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.89
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.88
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.88
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.88
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.88
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.88
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.88
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.88
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.87
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.87
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.87
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.87
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.87
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.87
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.87
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.86
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.86
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.86
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.86
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.86
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.86
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.86
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.85
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.85
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.85
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.85
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.85
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.85
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.85
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.85
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.85
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.85
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.85
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.84
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.84
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.84
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.83
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.83
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.83
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.83
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.82
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.82
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.82
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.81
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.8
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.79
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.77
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.76
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.76
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	99.71
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.71
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.71
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.64
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.63
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.59
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.59
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	98.59
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	98.34
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	98.17
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	97.55

>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=99.92  E-value=4.1e-25  Score=138.12  Aligned_cols=88  Identities=28%  Similarity=0.439  Sum_probs=81.6

Q ss_pred             CCCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceE
Q psy7051           6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGREL   85 (158)
Q Consensus         6 p~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i   85 (158)
                      |........+|||+|||..+++++|+++|++||+|..|.|+.++.++.++|||||+|.+.++|+.|++.|||..|.|+.|
T Consensus         2 P~~~~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l   81 (93)
T d1x5ua1           2 PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPI   81 (93)
T ss_dssp             CCCCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBC
T ss_pred             CCCcCCCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            44455566899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEeeecC
Q psy7051          86 RVQMARYG   93 (158)
Q Consensus        86 ~v~~a~~~   93 (158)
                      +|.+|+..
T Consensus        82 ~V~~A~~~   89 (93)
T d1x5ua1          82 RVNKASAH   89 (93)
T ss_dssp             EEEETTTT
T ss_pred             EEEEcCCC
Confidence            99999743

>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=99.92  E-value=7e-25  Score=135.71  Aligned_cols=84  Identities=25%  Similarity=0.344  Sum_probs=78.6

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEE
Q psy7051           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ   88 (158)
Q Consensus         9 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~   88 (158)
                      ...+..+|||+|||..+++++|.++|++||+|..|.|+.++.++.++|||||+|.+.++|+.|++.|||..|.|+.|.|+
T Consensus         3 ~s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~   82 (88)
T d1rk8a_           3 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD   82 (88)
T ss_dssp             CCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34456789999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             eeec
Q psy7051          89 MARY   92 (158)
Q Consensus        89 ~a~~   92 (158)
                      ||..
T Consensus        83 ~a~~   86 (88)
T d1rk8a_          83 WCFV   86 (88)
T ss_dssp             ESEE
T ss_pred             EecC
Confidence            9974

>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=99.92  E-value=1.4e-24  Score=137.21  Aligned_cols=84  Identities=32%  Similarity=0.585  Sum_probs=79.1

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      .+..+|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|+.||+.||+..|.|+.|+|.++
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            44578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCC
Q psy7051          91 RYGR   94 (158)
Q Consensus        91 ~~~~   94 (158)
                      +...
T Consensus        86 ~~~~   89 (99)
T d1whwa_          86 TIKK   89 (99)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            8543

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.92  E-value=2.7e-25  Score=135.81  Aligned_cols=79  Identities=30%  Similarity=0.437  Sum_probs=76.3

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeec
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARY   92 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~   92 (158)
                      ++|||+|||+.+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|+.|++.|||..|.|+.|.|++|++
T Consensus         3 t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1           3 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             SEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            6799999999999999999999999999999999988999999999999999999999999999999999999999974

>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=99.92  E-value=4e-25  Score=137.39  Aligned_cols=86  Identities=33%  Similarity=0.580  Sum_probs=81.3

Q ss_pred             CCCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceE
Q psy7051           6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGREL   85 (158)
Q Consensus         6 p~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i   85 (158)
                      |....++..+|||+|||..+++++|.++|++||+|..|.|+.+..++.++|||||+|.+.++|+.|++.|||..|.|+.|
T Consensus         1 P~~~~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i   80 (90)
T d2cq0a1           1 PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLIL   80 (90)
T ss_dssp             SCCCCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEEC
T ss_pred             CCCCCCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            45556677899999999999999999999999999999999998899999999999999999999999999999999999


Q ss_pred             EEEeee
Q psy7051          86 RVQMAR   91 (158)
Q Consensus        86 ~v~~a~   91 (158)
                      .|++|+
T Consensus        81 ~v~~ak   86 (90)
T d2cq0a1          81 NVEWAK   86 (90)
T ss_dssp             EEEESS
T ss_pred             EEEeee
Confidence            999997

>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=99.92  E-value=1.7e-24  Score=135.24  Aligned_cols=82  Identities=28%  Similarity=0.569  Sum_probs=78.2

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      ....+|||+|||+.+++++|.++|++||+|..|.++.++.++.++|||||+|.+.++|+.|++.|||..|.|+.|.|+|+
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            45679999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ec
Q psy7051          91 RY   92 (158)
Q Consensus        91 ~~   92 (158)
                      ..
T Consensus        85 ~~   86 (93)
T d1h2vz_          85 AG   86 (93)
T ss_dssp             SC
T ss_pred             CC
Confidence            64

>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=99.92  E-value=1.1e-24  Score=133.06  Aligned_cols=79  Identities=32%  Similarity=0.587  Sum_probs=76.0

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeec
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARY   92 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~   92 (158)
                      ++|||+|||..+++++|+++|++||+|..|.++.+..++..+|||||+|.+.++|+.|++.|||..|.|+.|.|++|++
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            5799999999999999999999999999999999988999999999999999999999999999999999999999873

>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=99.92  E-value=3.3e-24  Score=143.28  Aligned_cols=84  Identities=31%  Similarity=0.514  Sum_probs=78.8

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ..++|||+|||+++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|+.||+.|||..|+|+.|+|.+++
T Consensus        41 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~  120 (139)
T d1u6fa1          41 VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAA  120 (139)
T ss_dssp             TTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            34689999999999999999999999999999999998899999999999999999999999999999999999999998


Q ss_pred             cCCC
Q psy7051          92 YGRP   95 (158)
Q Consensus        92 ~~~~   95 (158)
                      ....
T Consensus       121 ~~~~  124 (139)
T d1u6fa1         121 SGHQ  124 (139)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            5543

>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=99.92  E-value=1.5e-24  Score=137.75  Aligned_cols=85  Identities=25%  Similarity=0.293  Sum_probs=79.2

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEE
Q psy7051           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ   88 (158)
Q Consensus         9 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~   88 (158)
                      ..++..+|||+|||+.+++++|+++|++||.|..+.++.+..++..+|||||+|.+.++|+.||+.|||..|.|+.|.|+
T Consensus        14 ~~p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~   93 (102)
T d2cpza1          14 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQ   93 (102)
T ss_dssp             CCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            33455789999999999999999999999999999999999899999999999999999999999999999999999999


Q ss_pred             eeecC
Q psy7051          89 MARYG   93 (158)
Q Consensus        89 ~a~~~   93 (158)
                      +++..
T Consensus        94 ~a~~k   98 (102)
T d2cpza1          94 LKRSK   98 (102)
T ss_dssp             CCCCS
T ss_pred             EeCCC
Confidence            99743

>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=99.91  E-value=1.3e-24  Score=132.14  Aligned_cols=77  Identities=35%  Similarity=0.496  Sum_probs=75.1

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        15 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      +|||+|||+.+++++|.++|++||+|..|.|+.++.++.++|||||+|.++++|+.|++.|||..|.|+.|+|.+|+
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999986

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.91  E-value=9.4e-25  Score=135.40  Aligned_cols=83  Identities=37%  Similarity=0.465  Sum_probs=78.2

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ...+|||+|||+.+++++|+++|++||+|..|.++.++.++.++|||||+|.+.++|+.|++.||+..|.|+.|.|.+|+
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~   83 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   83 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            34789999999999999999999999999999999999899999999999999999999999999999999999999997


Q ss_pred             cCC
Q psy7051          92 YGR   94 (158)
Q Consensus        92 ~~~   94 (158)
                      ..+
T Consensus        84 p~~   86 (89)
T d2cqba1          84 PMR   86 (89)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            443

>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=99.91  E-value=2.3e-24  Score=132.48  Aligned_cols=80  Identities=24%  Similarity=0.409  Sum_probs=76.7

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeecC
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARYG   93 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~~   93 (158)
                      .+|||+|||+.+++++|+++|++||+|..|.|+.++.++.++|||||+|.++++|+.|++.||+..|.|+.|.|++|+..
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            46999999999999999999999999999999999999999999999999999999999999999999999999999743

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.91  E-value=3.8e-24  Score=130.95  Aligned_cols=77  Identities=43%  Similarity=0.632  Sum_probs=73.5

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEE
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV   87 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v   87 (158)
                      ++..+|||+|||..+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|+.|++.|||..|.|+.|+|
T Consensus         7 ~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           7 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            34578999999999999999999999999999999999889999999999999999999999999999999999987

>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=99.91  E-value=1e-23  Score=134.05  Aligned_cols=82  Identities=34%  Similarity=0.562  Sum_probs=76.0

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      ...++|||+|||+.+++++|+++|++||+|..|.|+.++.++.++|||||+|.+.++|+.||+.+|+ .|.|+.|.|.++
T Consensus         8 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a   86 (103)
T d2cqda1           8 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLA   86 (103)
T ss_dssp             CSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEES
T ss_pred             CCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEc
Confidence            3457899999999999999999999999999999999998999999999999999999999988775 799999999998


Q ss_pred             ecC
Q psy7051          91 RYG   93 (158)
Q Consensus        91 ~~~   93 (158)
                      ...
T Consensus        87 ~~~   89 (103)
T d2cqda1          87 YLG   89 (103)
T ss_dssp             TTT
T ss_pred             CCC
Confidence            754

>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=99.91  E-value=8.7e-24  Score=129.88  Aligned_cols=78  Identities=29%  Similarity=0.480  Sum_probs=73.6

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCC--ceEEEEee
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDG--RELRVQMA   90 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g--~~i~v~~a   90 (158)
                      .++|||+|||+.+++++|+++|++||+|..|.++.++.++.++|||||+|.+.++|+.|++.|||..|.|  .+|.|.||
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            4679999999999999999999999999999999998899999999999999999999999999999987  55999886

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.90  E-value=9.3e-24  Score=129.76  Aligned_cols=79  Identities=33%  Similarity=0.557  Sum_probs=74.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCC--ceEEEEe
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDG--RELRVQM   89 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g--~~i~v~~   89 (158)
                      ..++|||+|||..+++++|+++|++||+|..|.++.++.++.++|||||+|.+.++|+.|++.|||..+.|  ++|.|.|
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            34679999999999999999999999999999999998899999999999999999999999999999876  7899998


Q ss_pred             e
Q psy7051          90 A   90 (158)
Q Consensus        90 a   90 (158)
                      |
T Consensus        85 A   85 (85)
T d1b7fa2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.90  E-value=1.2e-23  Score=130.54  Aligned_cols=82  Identities=38%  Similarity=0.646  Sum_probs=77.4

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ...+|||+|||+.+++++|+++|++||.|..|.++.+..++.++|||||+|.+.++|+.|++.|||..|.|+.|.|++|.
T Consensus         4 ~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~   83 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAG   83 (90)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEE
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            45679999999999999999999999999999999988899999999999999999999999999999999999999997


Q ss_pred             cC
Q psy7051          92 YG   93 (158)
Q Consensus        92 ~~   93 (158)
                      ..
T Consensus        84 ~~   85 (90)
T d1x5sa1          84 KS   85 (90)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.90  E-value=1.5e-23  Score=131.18  Aligned_cols=83  Identities=29%  Similarity=0.538  Sum_probs=76.4

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCC-CCCCcccEEEEEEcCHHHHHHHHHHh-CCcccCCceEEEE
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDR-FTRESRGFAFVRFFDKRDAEDALDAM-DGRMLDGRELRVQ   88 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~-~~~~~~g~afV~f~~~~~a~~a~~~l-~g~~i~g~~i~v~   88 (158)
                      ....+|||+|||..+++++|+++|++||.|..|.|+.+. .+|.++|||||+|.+.++|+.||+.| |+..|.|+.|.|+
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            456789999999999999999999999999999998774 47889999999999999999999998 8999999999999


Q ss_pred             eeecC
Q psy7051          89 MARYG   93 (158)
Q Consensus        89 ~a~~~   93 (158)
                      ||+..
T Consensus        86 ~A~~~   90 (94)
T d2cpha1          86 WADSE   90 (94)
T ss_dssp             ECCCC
T ss_pred             EcCCC
Confidence            99843

>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=99.90  E-value=1.2e-23  Score=127.29  Aligned_cols=76  Identities=32%  Similarity=0.477  Sum_probs=73.1

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        15 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      +|||+|||+.+++++|+++|++||.|..|.|+.++ +++++|||||+|.+.++|+.|++.|||..|+|+.|.|+++.
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            59999999999999999999999999999999886 88899999999999999999999999999999999999986

>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=99.90  E-value=3.8e-23  Score=128.27  Aligned_cols=79  Identities=29%  Similarity=0.446  Sum_probs=73.3

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeec
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARY   92 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~   92 (158)
                      ..+|||+|||..+++++|+++|++||+|..|.++.+..++  ++||||+|.+.++|+.|++.|||..|.|+.|+|.||+.
T Consensus         8 ~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~   85 (90)
T d2cqia1           8 PRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATT   85 (90)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCC
Confidence            4689999999999999999999999999999998886554  78999999999999999999999999999999999974


Q ss_pred             C
Q psy7051          93 G   93 (158)
Q Consensus        93 ~   93 (158)
                      .
T Consensus        86 ~   86 (90)
T d2cqia1          86 P   86 (90)
T ss_dssp             T
T ss_pred             C
Confidence            3

>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=99.90  E-value=2.2e-23  Score=127.80  Aligned_cols=80  Identities=31%  Similarity=0.516  Sum_probs=75.1

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      +...+|||+|||..+++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|+.|++ +++..|.|+.|.|..|
T Consensus         4 e~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A   82 (84)
T d1l3ka1           4 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRA   82 (84)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEEC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEee
Confidence            345789999999999999999999999999999999999999999999999999999999996 6999999999999877


Q ss_pred             e
Q psy7051          91 R   91 (158)
Q Consensus        91 ~   91 (158)
                      .
T Consensus        83 ~   83 (84)
T d1l3ka1          83 V   83 (84)
T ss_dssp             C
T ss_pred             e
Confidence            4

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.90  E-value=2.6e-23  Score=128.95  Aligned_cols=82  Identities=29%  Similarity=0.454  Sum_probs=75.4

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      .+...+|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|+.||+.  ...|+|+.|.|.+
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 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKL   82 (90)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEEC
T ss_pred             CcCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEEe
Confidence            45568899999999999999999999999999999999999999999999999999999999974  4589999999999


Q ss_pred             eecC
Q psy7051          90 ARYG   93 (158)
Q Consensus        90 a~~~   93 (158)
                      +...
T Consensus        83 a~~k   86 (90)
T d2cqga1          83 PNSK   86 (90)
T ss_dssp             CCTT
T ss_pred             CCCC
Confidence            8743

>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=99.90  E-value=1.1e-23  Score=128.30  Aligned_cols=78  Identities=19%  Similarity=0.268  Sum_probs=68.5

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      .||||+|||+++++++|.++|++||.|..+.++.+..++.++|||||+|.+.++|+.|++.|||..|.|+.|.|++++
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~   79 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSN   79 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcc
Confidence            589999999999999999999999999988888887789999999999999999999999999999999999999986

>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=99.89  E-value=4.1e-24  Score=132.47  Aligned_cols=81  Identities=25%  Similarity=0.388  Sum_probs=74.1

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      .+..+|||+|||+.+++++|+++|++||.|..|.|+.+..  ..+|||||+|.+.++|+.|++.|||..|+|+.|.|.++
T Consensus         6 s~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~--~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a   83 (89)
T d1cvja2           6 SGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN--GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRF   83 (89)
T ss_dssp             TTTTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTT--BCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecC--CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            4557899999999999999999999999999999988853  35799999999999999999999999999999999999


Q ss_pred             ecC
Q psy7051          91 RYG   93 (158)
Q Consensus        91 ~~~   93 (158)
                      +..
T Consensus        84 ~~~   86 (89)
T d1cvja2          84 KSR   86 (89)
T ss_dssp             CCT
T ss_pred             CCC
Confidence            743

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.89  E-value=4.9e-24  Score=135.75  Aligned_cols=80  Identities=31%  Similarity=0.550  Sum_probs=76.5

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeec
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARY   92 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~   92 (158)
                      ..+|||+|||..+++++|+++|++||+|..|.|+.++.++.++|||||+|.+.++|+.|++.||+..|.|+.|+|+++..
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~   87 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            46899999999999999999999999999999999988999999999999999999999999999999999999999864

>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=99.89  E-value=1.4e-23  Score=132.87  Aligned_cols=78  Identities=31%  Similarity=0.469  Sum_probs=74.7

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ..+|||+|||..+++++|+++|+.||.|..|.|+.+..++.++|||||+|.+.++|++|++ |||..|.|+.|.|.+++
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~   95 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQ   95 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECC
Confidence            3689999999999999999999999999999999999899999999999999999999995 99999999999999876

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.89  E-value=2.3e-23  Score=127.39  Aligned_cols=78  Identities=28%  Similarity=0.372  Sum_probs=73.0

Q ss_pred             EEEeCCCCCCCHHHHHHHhhhcCceEEE-EEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeecC
Q psy7051          16 LKVDNLTYRTTPDDLRRVFERCGEVGDI-YIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARYG   93 (158)
Q Consensus        16 l~V~nl~~~~~~~~l~~~f~~~G~i~~v-~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~~   93 (158)
                      |||+|||+++++++|+++|++||.|..+ .++.+..+++++|||||+|.+.++|+.|++.|||..|.|+.|.|.+|...
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k   79 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKK   79 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCC
Confidence            7999999999999999999999998665 78888889999999999999999999999999999999999999998743

>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=99.89  E-value=2.5e-23  Score=124.91  Aligned_cols=75  Identities=31%  Similarity=0.521  Sum_probs=70.9

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        15 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      .|||+|||+++++++|.++|++||+|..|.|+.++.+++++|||||+|.+.++|+.||+ +++..|.|+.|.|..|
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            48999999999999999999999999999999999999999999999999999999996 7999999999998643

>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=99.89  E-value=3e-23  Score=127.41  Aligned_cols=77  Identities=30%  Similarity=0.564  Sum_probs=71.4

Q ss_pred             EEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCC---CcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeec
Q psy7051          16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTR---ESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARY   92 (158)
Q Consensus        16 l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~---~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~   92 (158)
                      |||+|||+++++++|+++|++||+|..|.|+.++.++   .++|||||+|.+.++|+.|++.|||..|.|+.|.|++++.
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            7999999999999999999999999999998876555   3579999999999999999999999999999999999863

>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=99.89  E-value=1.3e-22  Score=127.72  Aligned_cols=84  Identities=26%  Similarity=0.453  Sum_probs=77.2

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhC------CcccCC
Q psy7051           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD------GRMLDG   82 (158)
Q Consensus         9 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~------g~~i~g   82 (158)
                      ..+...+|||+|||+.+++++|+++|++||+|..+.++.+..++.++|||||+|.+.++|..|++.||      |..|.|
T Consensus         4 ~~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~g   83 (98)
T d1x4ha1           4 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   83 (98)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             CCCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECC
Confidence            45566789999999999999999999999999999999998899999999999999999999999887      567899


Q ss_pred             ceEEEEeeec
Q psy7051          83 RELRVQMARY   92 (158)
Q Consensus        83 ~~i~v~~a~~   92 (158)
                      +.|.|++|..
T Consensus        84 r~l~v~~a~~   93 (98)
T d1x4ha1          84 RQLKVDLAVT   93 (98)
T ss_dssp             CEEEEECCCC
T ss_pred             EEEEEEECCC
Confidence            9999999874

>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=99.89  E-value=1.2e-23  Score=126.94  Aligned_cols=75  Identities=32%  Similarity=0.602  Sum_probs=72.1

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        15 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      +|||+|||+.+++++|+++|++||+|..+.|+.++.++.++|||||+|.+.++|++|++ ++++.|+|+.|.|..|
T Consensus         2 klfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            69999999999999999999999999999999999999999999999999999999996 7999999999999876

>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=99.89  E-value=6.6e-23  Score=129.73  Aligned_cols=86  Identities=31%  Similarity=0.410  Sum_probs=77.3

Q ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceE--------EEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcc
Q psy7051           8 PRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVG--------DIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRM   79 (158)
Q Consensus         8 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~--------~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~   79 (158)
                      .......+|||+|||..+++++|+++|++||.|.        .+.+..+..++..+|||||+|.+.++|..|++.|||..
T Consensus         3 ~~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~   82 (101)
T d2cpea1           3 DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKD   82 (101)
T ss_dssp             CCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCE
T ss_pred             CCCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCE
Confidence            3445678999999999999999999999999874        56667777889999999999999999999999999999


Q ss_pred             cCCceEEEEeeecC
Q psy7051          80 LDGRELRVQMARYG   93 (158)
Q Consensus        80 i~g~~i~v~~a~~~   93 (158)
                      |.|+.|.|.+|+..
T Consensus        83 ~~gr~i~V~~a~~~   96 (101)
T d2cpea1          83 FQGSKLKVSLARKK   96 (101)
T ss_dssp             ETTEECEEECSSCC
T ss_pred             ECCEEEEEEEcCCC
Confidence            99999999999853

>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=99.88  E-value=3.4e-23  Score=124.19  Aligned_cols=75  Identities=24%  Similarity=0.414  Sum_probs=70.9

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        15 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      +|||+|||+++++++|+++|++||+|..|.|+.++.++.++|||||+|.+.++|++||+ ++++.|+|+.|.|..|
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            59999999999999999999999999999999999999999999999999999999996 5788999999999865

>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=99.88  E-value=3e-23  Score=131.72  Aligned_cols=79  Identities=29%  Similarity=0.500  Sum_probs=74.6

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeec
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARY   92 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~   92 (158)
                      ..+|||+|||+.+++++|+++|.+||.|..+.|+.++.++.++|||||+|.+.++|++||+ +++..|.|+.|.|.+|..
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~   98 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVA   98 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECcc
Confidence            3689999999999999999999999999999999999899999999999999999999995 799999999999998873

>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=2.1e-22  Score=125.64  Aligned_cols=80  Identities=31%  Similarity=0.530  Sum_probs=73.7

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      ....+|||+|||+.+++++|+++|++||+|..|.++.+..  .++|||||+|.+.++|+.|++.||+..|.|+.|.|++|
T Consensus         9 ~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~--~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A   86 (93)
T d2cq3a1           9 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   86 (93)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcceeeecccccccc--CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            3457899999999999999999999999999999988753  36899999999999999999999999999999999999


Q ss_pred             ec
Q psy7051          91 RY   92 (158)
Q Consensus        91 ~~   92 (158)
                      +.
T Consensus        87 ~~   88 (93)
T d2cq3a1          87 TA   88 (93)
T ss_dssp             CS
T ss_pred             Cc
Confidence            74

>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=99.88  E-value=1.4e-22  Score=122.76  Aligned_cols=77  Identities=29%  Similarity=0.402  Sum_probs=72.8

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      ..+|||+|||+++|+++|+++|++||.|..+.++.++.++..+|||||+|.++++|++|++ |||..|+|+.|+|..|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            3689999999999999999999999999999999999999999999999999999999995 8999999999999865

>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=3.2e-22  Score=125.23  Aligned_cols=81  Identities=38%  Similarity=0.525  Sum_probs=72.7

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      .....+|||+|||+.+++++|+++|++||.|..+.+..+   ...++||||+|.+.++|+.||+.||+..|.|+.|+|++
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~   87 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF   87 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            345578999999999999999999999999999987654   34579999999999999999999999999999999999


Q ss_pred             eecC
Q psy7051          90 ARYG   93 (158)
Q Consensus        90 a~~~   93 (158)
                      |+..
T Consensus        88 a~~~   91 (95)
T d1x4aa1          88 PRSG   91 (95)
T ss_dssp             CCCC
T ss_pred             ccCC
Confidence            9844

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=3.2e-23  Score=131.44  Aligned_cols=83  Identities=31%  Similarity=0.334  Sum_probs=77.2

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      ++..+|||+|||..+++++|.++|.+||.|..+.++.+..++.++|||||+|.+.++|+.|++.|||..|.|+.|.|+||
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   95 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG   95 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            45689999999999999999999999999998888877778889999999999999999999999999999999999999


Q ss_pred             ecC
Q psy7051          91 RYG   93 (158)
Q Consensus        91 ~~~   93 (158)
                      +..
T Consensus        96 k~k   98 (102)
T d2cpxa1          96 KNK   98 (102)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            853

>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=99.88  E-value=7e-23  Score=122.84  Aligned_cols=75  Identities=27%  Similarity=0.431  Sum_probs=71.6

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        15 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      .|||+|||.++++++|+++|++||.|..+.++.++.++.+++||||+|.+.++|+.|++ ||+..|+|+.|.|..|
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            48999999999999999999999999999999998899999999999999999999996 9999999999999875

>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=5.7e-22  Score=128.02  Aligned_cols=77  Identities=29%  Similarity=0.404  Sum_probs=71.4

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeec
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARY   92 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~   92 (158)
                      ..+|||+|||..+++++|.++|++||.|..|.+..+   +..+|||||+|.+.++|..||+.|||..|.|+.|.|.++..
T Consensus         7 ~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~   83 (114)
T d2f9da1           7 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNA   83 (114)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            478999999999999999999999999999998754   45689999999999999999999999999999999999863

>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=99.87  E-value=5.3e-22  Score=124.43  Aligned_cols=74  Identities=19%  Similarity=0.411  Sum_probs=70.1

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeec
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARY   92 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~   92 (158)
                      ..+|||+|||..+++++|+++|++||.|..|.++.+      +|||||+|.+.++|+.|+..|||..|.|+.|+|.|++.
T Consensus        18 ~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~   91 (96)
T d1x4ga1          18 NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKE   91 (96)
T ss_dssp             CCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            478999999999999999999999999999999876      68999999999999999999999999999999999874

>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=99.87  E-value=6.8e-22  Score=120.76  Aligned_cols=76  Identities=20%  Similarity=0.293  Sum_probs=69.1

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCccc-CCceEEEEe
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRML-DGRELRVQM   89 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i-~g~~i~v~~   89 (158)
                      ++..+|||+|||..+++++|.++|++||+|..|.++.+.     +|||||+|.+.++|+.|++.|||..| +|+.|+|.|
T Consensus         6 pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~   80 (83)
T d2b0ga1           6 PPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITF   80 (83)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT-----CSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc-----ceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEE
Confidence            345799999999999999999999999999999997653     68999999999999999999999988 568999999


Q ss_pred             ee
Q psy7051          90 AR   91 (158)
Q Consensus        90 a~   91 (158)
                      |+
T Consensus        81 ak   82 (83)
T d2b0ga1          81 AK   82 (83)
T ss_dssp             CC
T ss_pred             ec
Confidence            86

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=9e-22  Score=125.10  Aligned_cols=82  Identities=21%  Similarity=0.415  Sum_probs=71.8

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCC-CCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDR-FTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~-~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      ++..+|||+|||+.+++++|+++|++|| |..+.++.+. .++.++|||||+|.+.++|++|+ .||+..|.|+.|+|.+
T Consensus        13 ~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l~V~~   90 (104)
T d1wi8a_          13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEEEEE
Confidence            4568999999999999999999999998 7677766654 46788999999999999998777 6999999999999999


Q ss_pred             eecCC
Q psy7051          90 ARYGR   94 (158)
Q Consensus        90 a~~~~   94 (158)
                      |....
T Consensus        91 a~~~~   95 (104)
T d1wi8a_          91 ADQAQ   95 (104)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            98543

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.87  E-value=3.1e-22  Score=123.08  Aligned_cols=80  Identities=30%  Similarity=0.395  Sum_probs=69.6

Q ss_pred             CCcEEEEeCCCCCCC-HHHHHHHhhhcCceEEEEEccC-CCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          12 GMVSLKVDNLTYRTT-PDDLRRVFERCGEVGDIYIPRD-RFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~-~~~l~~~f~~~G~i~~v~~~~~-~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      ...+|||+|||..++ +++|+++|++||.|..|.|+.+ ..++.++|||||+|.+.++|+.|++ ||+..|+|+.|.|.+
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            457899999999875 6679999999999999998764 5678899999999999999999995 999999999999999


Q ss_pred             eec
Q psy7051          90 ARY   92 (158)
Q Consensus        90 a~~   92 (158)
                      |+.
T Consensus        82 a~~   84 (86)
T d2ghpa3          82 ADK   84 (86)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            973

>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=99.87  E-value=9.1e-22  Score=123.76  Aligned_cols=78  Identities=21%  Similarity=0.255  Sum_probs=70.9

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      .....+|||+|||+.+++++|+++|++||+|+.|.+..       .|||||+|.+.++|+.||+.|||..|.|+.|.|.+
T Consensus        12 ~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~   84 (98)
T d1wg4a_          12 RRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSY   84 (98)
T ss_dssp             CSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEE
Confidence            34567899999999999999999999999999998854       47999999999999999999999999999999999


Q ss_pred             eecCC
Q psy7051          90 ARYGR   94 (158)
Q Consensus        90 a~~~~   94 (158)
                      ++...
T Consensus        85 ~~~~~   89 (98)
T d1wg4a_          85 IRVYP   89 (98)
T ss_dssp             EEEEC
T ss_pred             EecCC
Confidence            87543

>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=99.87  E-value=5.7e-22  Score=124.72  Aligned_cols=74  Identities=27%  Similarity=0.520  Sum_probs=67.2

Q ss_pred             CCcEEEEeCCC-CCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          12 GMVSLKVDNLT-YRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        12 ~~~~l~V~nl~-~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      ...+|||+||+ ..+++++|+++|++||.|..|.|        .+|||||+|.+.++|+.||+.|||..|.|+.|+|+++
T Consensus        14 ~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a   85 (98)
T d1wf2a_          14 MNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLA   85 (98)
T ss_dssp             CCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEET
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            34679999997 56889999999999999999988        3689999999999999999999999999999999999


Q ss_pred             ecC
Q psy7051          91 RYG   93 (158)
Q Consensus        91 ~~~   93 (158)
                      +..
T Consensus        86 ~~~   88 (98)
T d1wf2a_          86 AEP   88 (98)
T ss_dssp             TSC
T ss_pred             CCC
Confidence            754

>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=99.86  E-value=2.2e-22  Score=123.99  Aligned_cols=72  Identities=24%  Similarity=0.283  Sum_probs=66.8

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeecC
Q psy7051          15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARYG   93 (158)
Q Consensus        15 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~~   93 (158)
                      +|||+|||+.+++++|+++|++||+|..+.+..+       |||||+|.+.++|+.||+.|||..|.|+.|.|.+++..
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~   73 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            6999999999999999999999999999998654       79999999999999999999999999999999887643

>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=99.86  E-value=1.2e-21  Score=120.32  Aligned_cols=76  Identities=34%  Similarity=0.579  Sum_probs=70.6

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      +..+|||+|||..+++++|.++|++||+|..|.+..+      ++||||+|.+.++|+.|++.|||..|.|+.|+|++|.
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~   80 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFAC   80 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            3467999999999999999999999999999999765      5799999999999999999999999999999999997


Q ss_pred             cC
Q psy7051          92 YG   93 (158)
Q Consensus        92 ~~   93 (158)
                      ..
T Consensus        81 ~~   82 (86)
T d2cpja1          81 HS   82 (86)
T ss_dssp             CC
T ss_pred             Cc
Confidence            54

>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=7.8e-23  Score=127.07  Aligned_cols=80  Identities=21%  Similarity=0.292  Sum_probs=72.6

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      ....+|||+|||..+++++|+++|++||.|..+.|+.+ .++.++|||||+|.+.++|+.||+ ||+..|.|+.|.|++|
T Consensus        11 ~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~a   88 (91)
T d1fjeb1          11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   88 (91)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECC
T ss_pred             CCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEec
Confidence            34578999999999999999999999999988877654 588899999999999999999995 9999999999999998


Q ss_pred             ec
Q psy7051          91 RY   92 (158)
Q Consensus        91 ~~   92 (158)
                      +.
T Consensus        89 k~   90 (91)
T d1fjeb1          89 KG   90 (91)
T ss_dssp             CC
T ss_pred             CC
Confidence            73

>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=99.86  E-value=7.8e-22  Score=123.67  Aligned_cols=81  Identities=27%  Similarity=0.473  Sum_probs=72.3

Q ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEE
Q psy7051           8 PRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV   87 (158)
Q Consensus         8 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v   87 (158)
                      ....+..+|||+|||..+++++|+++|.+||.|..+..     ++..++||||+|.+.++|+.|++.||+..|.|+.|.|
T Consensus        11 ~~~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~-----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V   85 (96)
T d1fjca_          11 KKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSL   85 (96)
T ss_dssp             STTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE-----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEE
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee-----cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEE
Confidence            34455689999999999999999999999998876654     5667899999999999999999999999999999999


Q ss_pred             EeeecC
Q psy7051          88 QMARYG   93 (158)
Q Consensus        88 ~~a~~~   93 (158)
                      .|+...
T Consensus        86 ~~a~~k   91 (96)
T d1fjca_          86 YYTGEK   91 (96)
T ss_dssp             EECSSS
T ss_pred             EEeCCC
Confidence            999843

>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=99.86  E-value=2.4e-21  Score=121.64  Aligned_cols=76  Identities=32%  Similarity=0.437  Sum_probs=69.1

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCC--ceEEEEe
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDG--RELRVQM   89 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g--~~i~v~~   89 (158)
                      +..+|||+|||.++++++|+++|++||+|..|.+..+      ++||||+|.+.++|+.|++.||+..|.|  .+|+|+|
T Consensus        16 Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~   89 (97)
T d1whya_          16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDF   89 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEe
Confidence            3578999999999999999999999999999998765      5799999999999999999999999976  4799999


Q ss_pred             eecC
Q psy7051          90 ARYG   93 (158)
Q Consensus        90 a~~~   93 (158)
                      ++..
T Consensus        90 ak~~   93 (97)
T d1whya_          90 AKSG   93 (97)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            9843

>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=99.86  E-value=2.7e-21  Score=123.80  Aligned_cols=76  Identities=28%  Similarity=0.430  Sum_probs=69.9

Q ss_pred             CcEEEEeCCCC-CCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          13 MVSLKVDNLTY-RTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        13 ~~~l~V~nl~~-~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ..+|||+||++ .+++++|.++|+.||+|..|.|+.++     +|||||+|++.++|+.|++.|||..|.|+.|+|++++
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~   76 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   76 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            47899999965 59999999999999999999998774     6899999999999999999999999999999999987


Q ss_pred             cC
Q psy7051          92 YG   93 (158)
Q Consensus        92 ~~   93 (158)
                      ..
T Consensus        77 ~~   78 (109)
T d2adca1          77 HQ   78 (109)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.86  E-value=9e-22  Score=126.43  Aligned_cols=75  Identities=21%  Similarity=0.347  Sum_probs=69.3

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeec
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARY   92 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~   92 (158)
                      .++|||+|||+.+++++|+++|++||+|..|.|..      .++||||+|.+.++|+.|++.|||..|.|+.|.|+|+..
T Consensus        10 ~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~------~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~   83 (111)
T d1whxa_          10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPI   83 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEET
T ss_pred             CCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec------cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCC
Confidence            47899999999999999999999999999998853      368999999999999999999999999999999999974


Q ss_pred             C
Q psy7051          93 G   93 (158)
Q Consensus        93 ~   93 (158)
                      .
T Consensus        84 ~   84 (111)
T d1whxa_          84 G   84 (111)
T ss_dssp             T
T ss_pred             C
Confidence            3

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

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

Probab=99.85  E-value=7.3e-22  Score=121.38  Aligned_cols=80  Identities=18%  Similarity=0.270  Sum_probs=70.2

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      +..++|||+|||..+++++|+++|..||.|....++....++.++|+|||+|.+.++|+.|++.||+..|.|++|+|.++
T Consensus         7 p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           7 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            34578999999999999999999999998865433333458889999999999999999999999999999999999875

>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=99.85  E-value=6.1e-21  Score=121.22  Aligned_cols=83  Identities=18%  Similarity=0.211  Sum_probs=74.1

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      ....+|||+|||+.+++++|+++|..+|.|..+.++.+..++.++|||||+|.++++|++|++ +|+..|.|+.|.|.++
T Consensus        13 ~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~~   91 (104)
T d1wg5a_          13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKS   91 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEEC
Confidence            445679999999999999999999999998887666666788999999999999999999995 8999999999999999


Q ss_pred             ecCC
Q psy7051          91 RYGR   94 (158)
Q Consensus        91 ~~~~   94 (158)
                      +...
T Consensus        92 ~~~~   95 (104)
T d1wg5a_          92 SRAE   95 (104)
T ss_dssp             CTTT
T ss_pred             CHHH
Confidence            7543

>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=99.85  E-value=2.8e-21  Score=119.22  Aligned_cols=77  Identities=21%  Similarity=0.314  Sum_probs=68.7

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCccc-CCceEEEEee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRML-DGRELRVQMA   90 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i-~g~~i~v~~a   90 (158)
                      +..+|||+|||..+++++|+++|++||.|..+.+....    .++||||+|.+.++|..|+..|||..| +|+.|+|.|+
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~~----~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~s   84 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS   84 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeeec----ccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeC
Confidence            35789999999999999999999999999888765432    468999999999999999999999988 5899999999


Q ss_pred             ec
Q psy7051          91 RY   92 (158)
Q Consensus        91 ~~   92 (158)
                      +.
T Consensus        85 k~   86 (88)
T d2adca2          85 KS   86 (88)
T ss_dssp             SS
T ss_pred             CC
Confidence            74

>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=99.85  E-value=7e-22  Score=122.22  Aligned_cols=79  Identities=20%  Similarity=0.325  Sum_probs=70.5

Q ss_pred             CCCCcEEEEeCCCCCCCHHHH---HHHhhhcCceEEEEEccCCCCCCc---ccEEEEEEcCHHHHHHHHHHhCCcccCCc
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDL---RRVFERCGEVGDIYIPRDRFTRES---RGFAFVRFFDKRDAEDALDAMDGRMLDGR   83 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l---~~~f~~~G~i~~v~~~~~~~~~~~---~g~afV~f~~~~~a~~a~~~l~g~~i~g~   83 (158)
                      +....+|||+|||+.+++++|   .++|++||+|..|.++.++.++..   .|||||+|.+.++|+.|++.|||..|.|+
T Consensus         5 viq~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr   84 (89)
T d2cpia1           5 VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGR   84 (89)
T ss_dssp             CCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             EEecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCE
Confidence            344578999999999999999   778999999999999988766544   48999999999999999999999999999


Q ss_pred             eEEEE
Q psy7051          84 ELRVQ   88 (158)
Q Consensus        84 ~i~v~   88 (158)
                      .|+|.
T Consensus        85 ~lkvS   89 (89)
T d2cpia1          85 TLKAS   89 (89)
T ss_dssp             EEEEE
T ss_pred             EEEEC
Confidence            99984

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=8.2e-22  Score=124.67  Aligned_cols=80  Identities=20%  Similarity=0.326  Sum_probs=72.8

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      ...++|||+|||.++++++|+++|++||.|..+.+..+. ++..+|||||+|.+.++|+.|++.|||..|.|+++.|.++
T Consensus        16 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~   94 (101)
T d1x5oa1          16 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT   94 (101)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCC
Confidence            345789999999999999999999999999999888774 7889999999999999999999999999999999887665


Q ss_pred             e
Q psy7051          91 R   91 (158)
Q Consensus        91 ~   91 (158)
                      +
T Consensus        95 ~   95 (101)
T d1x5oa1          95 E   95 (101)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.85  E-value=4.2e-22  Score=118.53  Aligned_cols=71  Identities=23%  Similarity=0.341  Sum_probs=68.2

Q ss_pred             EEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEE
Q psy7051          16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR   86 (158)
Q Consensus        16 l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~   86 (158)
                      |||+|||..+++++|.++|++||.|..+.++.++.++..+|||||+|.+.++|+.|++.|||..|.|+.|+
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            79999999999999999999999999999999988999999999999999999999999999999998764

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=6e-21  Score=117.23  Aligned_cols=76  Identities=28%  Similarity=0.472  Sum_probs=68.7

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      ...++|||+|||..+++++|.++|++||.|..+.+..      .+|||||+|.+.++|..|++.|||..|.|+.|.|.||
T Consensus         6 ~~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~------~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~a   79 (86)
T d2cpda1           6 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA   79 (86)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE------CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECC
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc------ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            3457899999999999999999999999987776643      3689999999999999999999999999999999998


Q ss_pred             ec
Q psy7051          91 RY   92 (158)
Q Consensus        91 ~~   92 (158)
                      ++
T Consensus        80 kP   81 (86)
T d2cpda1          80 KP   81 (86)
T ss_dssp             CC
T ss_pred             cC
Confidence            73

>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=99.85  E-value=4e-21  Score=117.79  Aligned_cols=77  Identities=21%  Similarity=0.292  Sum_probs=71.7

Q ss_pred             CcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        13 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ..+|||+|||..+++++|.++|+.||+|..|.|+.+. ++.++|||||+|.+.++|++||+ +++..|.|+.|.|.+..
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            3689999999999999999999999999999998775 78899999999999999999995 79999999999999864

>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=8.4e-22  Score=119.52  Aligned_cols=75  Identities=27%  Similarity=0.360  Sum_probs=66.9

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCc-ccCCceEEEEeeec
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGR-MLDGRELRVQMARY   92 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~-~i~g~~i~v~~a~~   92 (158)
                      .+|||+|||..+++++|+++|++||.|..+.+..      .+|||||+|.+.++|+.|++.|||. .|.|+.|.|++|..
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~------~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~   75 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec------ccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            5799999999999999999999999987665554      3689999999999999999999996 69999999999985


Q ss_pred             CC
Q psy7051          93 GR   94 (158)
Q Consensus        93 ~~   94 (158)
                      ..
T Consensus        76 k~   77 (80)
T d2cqha1          76 KK   77 (80)
T ss_dssp             CC
T ss_pred             cC
Confidence            43

>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=99.85  E-value=4.3e-21  Score=121.51  Aligned_cols=81  Identities=20%  Similarity=0.200  Sum_probs=71.2

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEe
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM   89 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~   89 (158)
                      .....+|||+|||+.+|+++|+++|..|| |..|.++.+. ++..+|||||+|.+.++|+.|++ ||+..|+|+.|.|.+
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~   88 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFL   88 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEec-CCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            34457899999999999999999999997 4567777765 67889999999999999999995 899999999999999


Q ss_pred             eecC
Q psy7051          90 ARYG   93 (158)
Q Consensus        90 a~~~   93 (158)
                      +...
T Consensus        89 s~~~   92 (102)
T d1weza_          89 NSTA   92 (102)
T ss_dssp             ECCC
T ss_pred             cCCC
Confidence            8743

>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=99.85  E-value=4.4e-21  Score=114.88  Aligned_cols=74  Identities=18%  Similarity=0.266  Sum_probs=67.7

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      ++|||+|||+++++++|+++|+.||.|..|.++.++..  ..+||||+|.+.++|++|+ .+|+..|+|+.|.|+.+
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 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAI-TKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccc--cceEEEEEEcchHHhHHHH-HhcCcEECCEEEEEEEC
Confidence            58999999999999999999999999999999888643  3579999999999999999 58999999999999865

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=4.1e-21  Score=118.46  Aligned_cols=75  Identities=19%  Similarity=0.366  Sum_probs=65.0

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      +..+|||+|||+.+++++|+++|++|| +..+.+      +..++||||+|.+.++|+.|++.||+..|.|+.|.|++++
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~   76 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            457899999999999999999999999 222333      2247899999999999999999999999999999999997


Q ss_pred             cC
Q psy7051          92 YG   93 (158)
Q Consensus        92 ~~   93 (158)
                      ..
T Consensus        77 ~~   78 (88)
T d1wg1a_          77 TD   78 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.84  E-value=5.8e-21  Score=115.48  Aligned_cols=72  Identities=28%  Similarity=0.413  Sum_probs=66.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ...+|||+||+  +|+++|+++|++||+|..|.+..+      ++||||+|.+.++|..|++.|||..|.|+.|+|.|++
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~   75 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIAR   75 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECC
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            35789999996  899999999999999999988654      5799999999999999999999999999999999997

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=3e-21  Score=119.11  Aligned_cols=74  Identities=31%  Similarity=0.501  Sum_probs=66.8

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      +..+|||+|||+.+++++|+++|++||.|..|.+..+     .++||||+|.+.++|+.|+.  ++..|+|+.|.|.+++
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~-----~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~   76 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAE   76 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeec-----cCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCC
Confidence            4579999999999999999999999999999987543     47899999999999999984  7889999999999987


Q ss_pred             c
Q psy7051          92 Y   92 (158)
Q Consensus        92 ~   92 (158)
                      .
T Consensus        77 ~   77 (88)
T d1wf0a_          77 P   77 (88)
T ss_dssp             C
T ss_pred             C
Confidence            4

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

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

Probab=99.83  E-value=1.3e-19  Score=114.94  Aligned_cols=82  Identities=13%  Similarity=0.146  Sum_probs=71.9

Q ss_pred             CCCCCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHh--CCcccCCc
Q psy7051           6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM--DGRMLDGR   83 (158)
Q Consensus         6 p~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l--~g~~i~g~   83 (158)
                      .....++..+|||+|||..+++++|.++|++||.|+.|.+..+      +++|||+|.+.++|+.|++.|  ++..+.|+
T Consensus         8 ~~~~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~   81 (104)
T d1wexa_           8 SHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQ   81 (104)
T ss_dssp             SCCCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSS
T ss_pred             CCCcCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeE
Confidence            3445567789999999999999999999999999999988654      579999999999999999977  45678999


Q ss_pred             eEEEEeeecC
Q psy7051          84 ELRVQMARYG   93 (158)
Q Consensus        84 ~i~v~~a~~~   93 (158)
                      +|+|.|++..
T Consensus        82 ~l~v~~s~~~   91 (104)
T d1wexa_          82 QAFFNYSTSK   91 (104)
T ss_dssp             BCEEEECSSS
T ss_pred             EEEEEEcCCC
Confidence            9999999753

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=3.4e-20  Score=114.29  Aligned_cols=78  Identities=14%  Similarity=0.135  Sum_probs=70.1

Q ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHh--CCcccCCceEE
Q psy7051           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM--DGRMLDGRELR   86 (158)
Q Consensus         9 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l--~g~~i~g~~i~   86 (158)
                      +.++..+|||+|||..+++++|+++|++||.|..+.+..+      ++||||+|.+.++|+.|++.+  ++..|.|+.|.
T Consensus         4 ~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~   77 (88)
T d2cq1a1           4 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIY   77 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEE
Confidence            4567789999999999999999999999999999988765      479999999999999999865  56789999999


Q ss_pred             EEeeec
Q psy7051          87 VQMARY   92 (158)
Q Consensus        87 v~~a~~   92 (158)
                      |.|++.
T Consensus        78 v~~sk~   83 (88)
T d2cq1a1          78 IQYSNH   83 (88)
T ss_dssp             EEECSC
T ss_pred             EEECCC
Confidence            999974

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=7.2e-21  Score=118.08  Aligned_cols=78  Identities=31%  Similarity=0.525  Sum_probs=69.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHH----HhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEE
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV   87 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~----~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v   87 (158)
                      |..+|||+|||+.+++++|++    +|++||+|..|.+..   ++..+|||||+|.+.++|..|++.|||..|.|+.|.|
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v   78 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   78 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            357899999999999998864    589999999998754   4556899999999999999999999999999999999


Q ss_pred             Eeeec
Q psy7051          88 QMARY   92 (158)
Q Consensus        88 ~~a~~   92 (158)
                      .+|+.
T Consensus        79 ~~ak~   83 (91)
T d1nu4a_          79 QYAKT   83 (91)
T ss_dssp             EECSS
T ss_pred             EEeCC
Confidence            99974

>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=3.4e-20  Score=116.08  Aligned_cols=81  Identities=21%  Similarity=0.239  Sum_probs=71.7

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCc-eEEEEEccCC-CCCCcccEEEEEEcCHHHHHHHHHHhCCc--ccCCceEEEEe
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGE-VGDIYIPRDR-FTRESRGFAFVRFFDKRDAEDALDAMDGR--MLDGRELRVQM   89 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~-i~~v~~~~~~-~~~~~~g~afV~f~~~~~a~~a~~~l~g~--~i~g~~i~v~~   89 (158)
                      .+|||+|||..+++++|.++|++||+ |..|.|+.+. .++..+|||||+|.+.++|..|++.|++.  .+.|+.|.|.|
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~   81 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDW   81 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEE
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEE
Confidence            47999999999999999999999995 8999998874 46788999999999999999999999754  45799999999


Q ss_pred             eecCC
Q psy7051          90 ARYGR   94 (158)
Q Consensus        90 a~~~~   94 (158)
                      |+...
T Consensus        82 A~p~~   86 (96)
T d2disa1          82 AEPEI   86 (96)
T ss_dssp             SCSSC
T ss_pred             cCCCC
Confidence            97543

>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=99.82  E-value=4.9e-20  Score=110.23  Aligned_cols=70  Identities=21%  Similarity=0.367  Sum_probs=63.1

Q ss_pred             EEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeeec
Q psy7051          16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARY   92 (158)
Q Consensus        16 l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~~   92 (158)
                      |||+|||+++++++|+++|++|| +..+.+.      ..+|||||+|.+.++|+.|++.|||..|.|+.|.|++++.
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~~------~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~   70 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVD------KYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPT   70 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEE------TTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCS
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeec------ccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCC
Confidence            79999999999999999999999 5555443      3578999999999999999999999999999999999974

>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=99.82  E-value=1.6e-20  Score=120.08  Aligned_cols=78  Identities=24%  Similarity=0.370  Sum_probs=70.0

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCccc--CCceEEEE
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRML--DGRELRVQ   88 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i--~g~~i~v~   88 (158)
                      .+..+|||+|||..+|+++|+++|++||.|..|.+..++    .+|||||+|.+.++|+.|++.|||..|  .+..|.|.
T Consensus         5 s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~   80 (108)
T d2adba1           5 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID   80 (108)
T ss_dssp             CCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEE
T ss_pred             CCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEE
Confidence            345789999999999999999999999999999887664    478999999999999999999999988  57889999


Q ss_pred             eeec
Q psy7051          89 MARY   92 (158)
Q Consensus        89 ~a~~   92 (158)
                      +++.
T Consensus        81 ~s~~   84 (108)
T d2adba1          81 FSKL   84 (108)
T ss_dssp             ECSS
T ss_pred             ecCC
Confidence            8874

>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=99.82  E-value=1.1e-20  Score=119.80  Aligned_cols=79  Identities=20%  Similarity=0.241  Sum_probs=70.4

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ...+|||+|||+.+++++|.++|..||.|..+.++....++.++|||||+|.+.++|+.||+ ||+..|+|+.|.|.++.
T Consensus         7 ~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~~   85 (103)
T d2cpya1           7 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVT   85 (103)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEEC
T ss_pred             CceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEECC
Confidence            34689999999999999999999999988765444555588999999999999999999995 89999999999999875

>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=99.81  E-value=2.2e-20  Score=120.07  Aligned_cols=80  Identities=18%  Similarity=0.210  Sum_probs=71.3

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      ....+|||+|||+.+++++|.++|+.||.|..+.++.+..+|..+|||||+|.+.++|++|++ ||+..|+|+.|.|..+
T Consensus        16 ~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~~   94 (112)
T d1wela1          16 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPI   94 (112)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEE
T ss_pred             CCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEEc
Confidence            445789999999999999999999999988765555555689999999999999999999995 8999999999999887


Q ss_pred             e
Q psy7051          91 R   91 (158)
Q Consensus        91 ~   91 (158)
                      .
T Consensus        95 ~   95 (112)
T d1wela1          95 T   95 (112)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.80  E-value=1.4e-19  Score=111.71  Aligned_cols=78  Identities=19%  Similarity=0.286  Sum_probs=69.3

Q ss_pred             CCCCCcEEEEeCCCCC-CCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHh--CCcccCCceE
Q psy7051           9 RIEGMVSLKVDNLTYR-TTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM--DGRMLDGREL   85 (158)
Q Consensus         9 ~~~~~~~l~V~nl~~~-~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l--~g~~i~g~~i   85 (158)
                      ..++..+|||+|||.. +|++||.++|++||.|..|.++.+      +++|||+|++.++|+.|++.|  ++..+.|++|
T Consensus         4 ~~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~------k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l   77 (89)
T d1x4da1           4 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPV   77 (89)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             CCCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc------ceEEEEEEcchhhHHHHHHHHhhCCCccCCceE
Confidence            3466789999999986 789999999999999999999765      468999999999999999966  6778999999


Q ss_pred             EEEeeec
Q psy7051          86 RVQMARY   92 (158)
Q Consensus        86 ~v~~a~~   92 (158)
                      .|.||+.
T Consensus        78 ~V~~s~~   84 (89)
T d1x4da1          78 RVHLSQK   84 (89)
T ss_dssp             EEEEECC
T ss_pred             EEEECCC
Confidence            9999973

>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=99.79  E-value=2.9e-19  Score=112.33  Aligned_cols=76  Identities=18%  Similarity=0.273  Sum_probs=68.0

Q ss_pred             CCCcEEEEeCCCCC-CCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHH--HhCCcccCCceEEE
Q psy7051          11 EGMVSLKVDNLTYR-TTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD--AMDGRMLDGRELRV   87 (158)
Q Consensus        11 ~~~~~l~V~nl~~~-~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~--~l~g~~i~g~~i~v   87 (158)
                      ....+|||+|||.. +++++|.++|++||.|..|.++.+      +++|||+|.+.++|..|++  .+++..|.|+.|.|
T Consensus        16 ~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V   89 (99)
T d1x4fa1          16 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKV   89 (99)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEE
T ss_pred             CCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEEEE
Confidence            44578999999975 899999999999999999998765      5799999999999999997  47788999999999


Q ss_pred             Eeeec
Q psy7051          88 QMARY   92 (158)
Q Consensus        88 ~~a~~   92 (158)
                      .+|+.
T Consensus        90 ~~s~~   94 (99)
T d1x4fa1          90 DLSEK   94 (99)
T ss_dssp             EEECS
T ss_pred             EEcCC
Confidence            99963

>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=99.77  E-value=7.7e-19  Score=111.25  Aligned_cols=77  Identities=13%  Similarity=0.089  Sum_probs=67.9

Q ss_pred             CCCcEEEEeCCCCCC-CH----HHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceE
Q psy7051          11 EGMVSLKVDNLTYRT-TP----DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGREL   85 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~-~~----~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i   85 (158)
                      .+..+|||+||+..+ ++    ++|+++|++||.|+.|.+...      ++||||+|.+.++|+.|++.|||..|.|+.|
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l   76 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAADARLRLHKTEFLGKEM   76 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT------TTEEEEECSSTTHHHHHHHTSTTSEETTEEC
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecC------CCEEEEEECCHHHHHHHHHHhcccccCCCEe
Confidence            345789999999876 33    569999999999999988754      5799999999999999999999999999999


Q ss_pred             EEEeeecC
Q psy7051          86 RVQMARYG   93 (158)
Q Consensus        86 ~v~~a~~~   93 (158)
                      +|.|++..
T Consensus        77 ~v~~a~~~   84 (104)
T d1weya_          77 KLYFAQTL   84 (104)
T ss_dssp             EEECCCCS
T ss_pred             EEeecccC
Confidence            99999743

>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=99.76  E-value=1.2e-20  Score=116.76  Aligned_cols=77  Identities=21%  Similarity=0.406  Sum_probs=66.1

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEc-----cCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEE
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIP-----RDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ   88 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~-----~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~   88 (158)
                      .+|||+|||..+++++|+++|++||.|..+.+.     .+..++..+|||||+|.+.++|+.|+ .|||..|.|+.|+|.
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            579999999999999999999999987655443     23456678899999999999999999 599999999999997


Q ss_pred             eee
Q psy7051          89 MAR   91 (158)
Q Consensus        89 ~a~   91 (158)
                      .++
T Consensus        81 r~k   83 (90)
T d1u2fa_          81 RPH   83 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            544

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=3.8e-18  Score=117.93  Aligned_cols=80  Identities=28%  Similarity=0.362  Sum_probs=75.0

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        11 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      ....+|||+|||..+++++|.++|..||.|..+.++.+..++.++|||||+|.+.++|..|++ +++..|.|+.|.|.+|
T Consensus        95 ~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~A  173 (183)
T d1u1qa_          95 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA  173 (183)
T ss_dssp             CCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEEC
T ss_pred             cccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEec
Confidence            445789999999999999999999999999999999998889999999999999999999996 7899999999999988


Q ss_pred             e
Q psy7051          91 R   91 (158)
Q Consensus        91 ~   91 (158)
                      .
T Consensus       174 ~  174 (183)
T d1u1qa_         174 L  174 (183)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.71  E-value=5.4e-19  Score=111.98  Aligned_cols=75  Identities=17%  Similarity=0.348  Sum_probs=69.4

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEee
Q psy7051          15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA   90 (158)
Q Consensus        15 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a   90 (158)
                      .++|.++...+++++|+++|++||+|..|.|+.+ .++..+|+|||+|.+.++|..|++.|||.+|+|+.|.|+++
T Consensus        29 ~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~-~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          29 DVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCS-SSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             hHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecC-CCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            4777788888899999999999999999999876 48889999999999999999999999999999999999986

>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=99.71  E-value=1.8e-17  Score=106.43  Aligned_cols=76  Identities=21%  Similarity=0.194  Sum_probs=66.1

Q ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCH-HHHHHHHHHhCCcccCCceEEEE
Q psy7051          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK-RDAEDALDAMDGRMLDGRELRVQ   88 (158)
Q Consensus        10 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~-~~a~~a~~~l~g~~i~g~~i~v~   88 (158)
                      ..+...+||+|||..+|+++|+++|++||+|..|.|+.+      ++||||.|.+. ++|.+|+..||+..|.+..+.|.
T Consensus         8 ~~g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~   81 (113)
T d1owxa_           8 KIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVT   81 (113)
T ss_dssp             CCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEE
T ss_pred             CCCCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEE
Confidence            445678899999999999999999999999999999765      68999999986 68999999999998887777776


Q ss_pred             eee
Q psy7051          89 MAR   91 (158)
Q Consensus        89 ~a~   91 (158)
                      ++.
T Consensus        82 ~~~   84 (113)
T d1owxa_          82 WEV   84 (113)
T ss_dssp             EEE
T ss_pred             Eee
Confidence            653

>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=99.71  E-value=2.5e-17  Score=103.61  Aligned_cols=65  Identities=25%  Similarity=0.489  Sum_probs=58.4

Q ss_pred             CCCCcEEEEeC--CCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCccc
Q psy7051          10 IEGMVSLKVDN--LTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRML   80 (158)
Q Consensus        10 ~~~~~~l~V~n--l~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i   80 (158)
                      .++..+|+|.|  ||..+|+++|+++|++||.|+.|.++.+      ++||||+|.+.++|+.|++.|||..|
T Consensus        15 ~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            35567888855  9999999999999999999999988765      47999999999999999999999987

>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=99.64  E-value=3.7e-16  Score=107.72  Aligned_cols=79  Identities=30%  Similarity=0.508  Sum_probs=71.1

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      ...+|||+|||+.+++++|.++|++||.|..+.++.+..++..+|||||+|.+.++|+.|+. +++..+.+..+.+....
T Consensus         5 ~~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~~~~~   83 (183)
T d1u1qa_           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (183)
T ss_dssp             HHHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcccccchhhhhhh
Confidence            34799999999999999999999999999999999998899999999999999999999996 56777888887776654

>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=99.63  E-value=6.4e-16  Score=96.74  Aligned_cols=81  Identities=23%  Similarity=0.423  Sum_probs=68.3

Q ss_pred             CCCCCCCcEEEEeCC--CCCC---------CHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHh
Q psy7051           7 PPRIEGMVSLKVDNL--TYRT---------TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM   75 (158)
Q Consensus         7 ~~~~~~~~~l~V~nl--~~~~---------~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l   75 (158)
                      |.......+|+|.||  |..+         .+++|.+.|++||.|..|.+..+.    ..|+|||+|.+.++|..|+..|
T Consensus         2 p~~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~----~~G~~fV~f~~~e~A~~A~~~l   77 (99)
T d2dita1           2 PSRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRH----PDGVASVSFRDPEEADYCIQTL   77 (99)
T ss_dssp             CCCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTC----TTCEEEEECSCHHHHHHHHHHS
T ss_pred             CCCCCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCC----CccEEEEEECCHHHHHHHHHHh
Confidence            344556789999999  5432         136788999999999999886653    5689999999999999999999


Q ss_pred             CCcccCCceEEEEeee
Q psy7051          76 DGRMLDGRELRVQMAR   91 (158)
Q Consensus        76 ~g~~i~g~~i~v~~a~   91 (158)
                      ||..|+|+.|.|+++.
T Consensus        78 ng~~~~gr~i~v~~~~   93 (99)
T d2dita1          78 DGRWFGGRQITAQAWD   93 (99)
T ss_dssp             TTCEETTEECEEEECC
T ss_pred             CCcEECCEEEEEEEeC
Confidence            9999999999999986

>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=99.59  E-value=2.2e-15  Score=90.76  Aligned_cols=70  Identities=19%  Similarity=0.247  Sum_probs=59.0

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCce-EEEEeee
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRE-LRVQMAR   91 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~-i~v~~a~   91 (158)
                      +.|+|+|||++++++.| ++|++||+|..+.+..+      ++||||+|.+.++|+.||+ +||..|+|+. |.|....
T Consensus         5 ~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~~------~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~   75 (81)
T d1wwha1           5 TWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNT------GNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCI   75 (81)
T ss_dssp             GEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECSS------SSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECC
T ss_pred             cEEEEECCChHHHHHHH-HHHHhhhhhheEEecCC------CCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCC
Confidence            56999999999886655 57999999999987543      5899999999999999995 9999999974 5676553

>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=99.59  E-value=1.5e-15  Score=95.84  Aligned_cols=80  Identities=24%  Similarity=0.278  Sum_probs=67.1

Q ss_pred             CCcEEEEeCC--CCCCC--------HHHHHHHhhhcCceEEEEEccCCCCC--CcccEEEEEEcCHHHHHHHHHHhCCcc
Q psy7051          12 GMVSLKVDNL--TYRTT--------PDDLRRVFERCGEVGDIYIPRDRFTR--ESRGFAFVRFFDKRDAEDALDAMDGRM   79 (158)
Q Consensus        12 ~~~~l~V~nl--~~~~~--------~~~l~~~f~~~G~i~~v~~~~~~~~~--~~~g~afV~f~~~~~a~~a~~~l~g~~   79 (158)
                      |..+|.|.||  +..+.        .++|++.|++||.|..|.|+.+..+.  ...|++||+|.+.++|..|+..|||..
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~   82 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   82 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCC
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCE
Confidence            4578999999  44432        35688999999999999998765443  345899999999999999999999999


Q ss_pred             cCCceEEEEeee
Q psy7051          80 LDGRELRVQMAR   91 (158)
Q Consensus        80 i~g~~i~v~~a~   91 (158)
                      |+|+.|.|.+..
T Consensus        83 f~gR~v~v~f~~   94 (104)
T d1o0pa_          83 FANRVVVTKYCD   94 (104)
T ss_dssp             SSSSCCEEEEEC
T ss_pred             ECCeEEEEEEcC
Confidence            999999999975

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.59  E-value=2.4e-07  Score=55.67  Aligned_cols=79  Identities=15%  Similarity=0.144  Sum_probs=64.7

Q ss_pred             cEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCc--ccEEEEEEcCHHHHHHHHHHhCCcccCCc-----eEE
Q psy7051          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRES--RGFAFVRFFDKRDAEDALDAMDGRMLDGR-----ELR   86 (158)
Q Consensus        14 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~--~g~afV~f~~~~~a~~a~~~l~g~~i~g~-----~i~   86 (158)
                      ++|.|..||+.+||+++.+.+...|.+..+.....+.+.++  ..-|||.|.+.+++....+.++|..+.+.     .-.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~g~~~~a~   81 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcCCCCEeeeE
Confidence            67999999999999999999999999988877766555443  35799999999999999999999976332     346


Q ss_pred             EEeeec
Q psy7051          87 VQMARY   92 (158)
Q Consensus        87 v~~a~~   92 (158)
                      |++|..
T Consensus        82 VE~AP~   87 (91)
T d1uw4a_          82 VEFAPF   87 (91)
T ss_dssp             EEECSS
T ss_pred             EEEcCc
Confidence            777754

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.34  E-value=8.2e-07  Score=52.64  Aligned_cols=67  Identities=19%  Similarity=0.292  Sum_probs=53.6

Q ss_pred             cEEEEeCCCCCCCH---------HHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCce
Q psy7051          14 VSLKVDNLTYRTTP---------DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRE   84 (158)
Q Consensus        14 ~~l~V~nl~~~~~~---------~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~   84 (158)
                      -||.|.-..+...+         .+|.+.|..||+|.-|+++.+        ..+|+|.+-+.|.+|+ .++|.+++|+.
T Consensus        16 gTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al-~l~g~~v~G~~   86 (95)
T d1ufwa_          16 ATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVL-DVDGMKVKGRA   86 (95)
T ss_dssp             CEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHH-HGGGSEETTEE
T ss_pred             cEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHh-ccCCeEEcceE
Confidence            56767444433222         367888899999999999776        5899999999999999 58999999999


Q ss_pred             EEEEe
Q psy7051          85 LRVQM   89 (158)
Q Consensus        85 i~v~~   89 (158)
                      |+|..
T Consensus        87 l~It~   91 (95)
T d1ufwa_          87 VKISG   91 (95)
T ss_dssp             EEEEC
T ss_pred             EEEec
Confidence            99874

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.17  E-value=9.7e-06  Score=45.61  Aligned_cols=61  Identities=20%  Similarity=0.291  Sum_probs=52.0

Q ss_pred             HHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhCCcccCCceEEEEeee
Q psy7051          28 DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR   91 (158)
Q Consensus        28 ~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~i~g~~i~v~~a~   91 (158)
                      +.|.+.|.++|.|..+.+.... .+  ...|-|...+.++|..|+..|+...|+++.|.|.++.
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~-dg--~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHT-DY--QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCC-ST--TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHhheeEEEEEEEecc-CC--cEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            4466778999999999886543 22  3479999999999999999999999999999999986

>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=97.55  E-value=0.00018  Score=43.04  Aligned_cols=57  Identities=18%  Similarity=0.173  Sum_probs=46.0

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHHhhhcCceEEEEEccCCCCCCcccEEEEEEcCHHHHHHHHHHhC
Q psy7051          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD   76 (158)
Q Consensus        12 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~   76 (158)
                      ...-||.-.+|..+...||.++|++||.|. |.++.+.       -|||...+.++|+.+++.+.
T Consensus        14 ~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIddT-------Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          14 KRDHVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCSEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             CcceeEEEeCCcccchhHHHHHhcCCCceE-EEEecCc-------eEEEEecCHHHHHHHHHHhc
Confidence            345588889999999999999999999875 4444442       69999999999999887544