Citrus Sinensis ID: 043443

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------30
Protein Sequence
AKSSLLSSLVFLVQEGSAMRRYSPPYYSPPRRGYGGRGRSPPRRGYGGGGGGYGRRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAESRKRPEEMRQRHRFRGGSSYGGPRSSYYGRYRSRSLSRSRSPHHPQGSRSRYRSRSYTPVPRQHEDYSISPRRRHIEHPGSPRGPPQERGAEYSRRSYSPGYDDSADRRNPNGNGYGEKSGYEETQAHWRSPPPRGVSRSPSGSRSRSRSADLSPRHTR
Secondary Structure (PSIPRED)
ccccccccEEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccEEEEcccccccHHHHHHHHcccccEEEEEEccccccccccccEEEEEccHHHHHHHHHHHcccEEcccEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHHHHccHHcccccccccccccccccccccccccccccccccccccccccccEEEEEcccccccHHHHHHHHHHccccEEEEEcccccccccccEEEEEEccHHHHHHHHHHHcccEEccEEEEEEEEccccccccHHcHccccccccccccccccHcccccccccccccccccccccccccccccccccccccccccccccHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
AKSSLLSSLVFLVQEgsamrrysppyyspprrgyggrgrspprrgyggggggygrrkeqnhgsllvrnipldcrpeelrapferfgvvrdvylpkdyytgeprgfafvqfvdpyeAAEAQHhmngkrfagREISVVLAAESRKRPEEMRQRhrfrggssyggprssyygryrsrslsrsrsphhpqgsrsryrsrsytpvprqhedysisprrrhiehpgsprgppqergaeysrrsyspgyddsadrrnpngngygeksgyeetqahwrsppprgvsrspsgsrsrsrsadlsprhtr
Flexible Loop (DISEMBL)
AKSSLLSSLVFLVQegsamrrysppyyspprrgyggrgrspprrgYGGGGGGYGRRKEQNHGSLLVRNIPLDCRPEElrapferfgvvrDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHmngkrfagrEISVVLaaesrkrpeemrqrhrfrggssyggprssyYGRYrsrslsrsrsphhpqgsrsryrsrsytpvprqhedysisprrrhiehpgsprgppqergaeYSRRSyspgyddsadrrnpNGNGYGEKSGYeetqahwrsppprgvsrspsgsrsrsrsadlsprhtr
Low Complexity Region (SEG)
AKssllsslvflvQEGSAMrrysppyyspprrgyggrgrspprrgyggggggygrrKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAESRKRPEEMRQRHRFrggssyggprssyygryrsrslsrsrsPHHPQGsrsryrsrsyTPVPRQHEDYSISPRRRHIEHPGSPRGPPQERGAEYSRRSYSPGYDDSADRRNPNGNGYGEKSGYEETQAHWrsppprgvsrspsgsrsrsrsADLSPRHTR
Disordered region (IsUnstruct)
********LVFLV**************************************************LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL******************************************************************************************************************************************************************
Disordered Region (DISOPRED)
*****LS*********************************************************LVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV********************************************************************************************************************************************************************
Disordered Region (DISEMBL)
AKSSLLSSLVFLVQEGSAMRRYSPPYYSPPR********SPPRRGYGGGGGGYGRRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAE******************SYGGPRSSYYGRY**********************************DYSISPRRRH****************************DSADRRNPNGNGYGEKSGY*************************************
Disordered Region (DISPRO)
****LLSSLVFLVQEGSAMRRYSPPYY********************************NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAE***************************************************************************************************************************************************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
AKSSLLSSLVFLVQEGSAMRRYSPPYYSPPRRGYGGRGRSPPRRGYGGGGGGYGRRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAESRKRPEEMRQRHRFRGGSSYGGPRSSYYGRYRSRSLSRSRSPHHPQGSRSRYRSRSYTPVPRQHEDYSISPRRRHIEHPGSPRGPPQERGAEYSRRSYSPGYDDSADRRNPNGNGYGEKSGYEETQAHWRSPPPRGVSRSPSGSRSRSRSADLSPRHTR
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	299	2.2.26 [Sep-21-2011]
Q9SEU4	287	Serine/arginine-rich spli	no	no	0.397	0.414	0.581	2e-32
Q8WXF0	261	Serine/arginine-rich spli	yes	no	0.311	0.356	0.440	6e-18
Q9R0U0	262	Serine/arginine-rich spli	yes	no	0.304	0.347	0.450	6e-18
O75494	262	Serine/arginine-rich spli	no	no	0.304	0.347	0.450	6e-18
P30352	221	Serine/arginine-rich spli	yes	no	0.254	0.343	0.473	2e-12
Q5R1W5	221	Serine/arginine-rich spli	no	no	0.267	0.361	0.45	8e-12
Q06A98	221	Serine/arginine-rich spli	no	no	0.254	0.343	0.473	2e-11
Q6PDU1	221	Serine/arginine-rich spli	no	no	0.254	0.343	0.473	2e-11
Q62093	221	Serine/arginine-rich spli	no	no	0.254	0.343	0.473	2e-11
Q01130	221	Serine/arginine-rich spli	no	no	0.254	0.343	0.473	2e-11

>sp|Q9SEU4|SR33_ARATH Serine/arginine-rich splicing factor 33 OS=Arabidopsis thaliana GN=SR33 PE=1 SV=1

 Score =  139 bits (351), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 75/129 (58%), Positives = 92/129 (71%), Gaps = 10/129 (7%)

Query: 20  RRYSPPYYSPPRRGYGGRGRSPPRRGYGGGGGGYGRRKEQNHGSLLVRNIPLDCRPEELR 79
           R Y+P   SPPR GYG RGRSP  RG       YG R      SLLVRN+  DCR E+LR
Sbjct: 4   RSYTP---SPPR-GYGRRGRSPSPRGR------YGGRSRDLPTSLLVRNLRHDCRQEDLR 53

Query: 80  APFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA 139
             FE+FG V+D+YLP+DYYTG+PRGF FVQF+DP +AA+A+HHM+G    GRE++VV A 
Sbjct: 54  KSFEQFGPVKDIYLPRDYYTGDPRGFGFVQFMDPADAADAKHHMDGYLLLGRELTVVFAE 113

Query: 140 ESRKRPEEM 148
           E+RK+P EM
Sbjct: 114 ENRKKPTEM 122

Involved in intron recognition and spliceosome assembly during the alternative splicing process.
Arabidopsis thaliana (taxid: 3702)

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

 Score = 91.7 bits (226), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 41/93 (44%), Positives = 60/93 (64%)

Query: 61  HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQ 120
           + SL +RN+    RPE+LR  F R+G + DVY+P D+YT  PRGFA+VQF D  +A +A 
Sbjct: 9   NTSLFIRNVADATRPEDLRREFGRYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDAL 68

Query: 121 HHMNGKRFAGREISVVLAAESRKRPEEMRQRHR 153
           +++N K   GR+I +  A   RK P +M+ + R
Sbjct: 69  YNLNRKWVCGRQIEIQFAQGDRKTPGQMKSKER 101

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

Homo sapiens (taxid: 9606)

>sp|Q9R0U0|SRS10_MOUSE Serine/arginine-rich splicing factor 10 OS=Mus musculus GN=Srsf10 PE=1 SV=2

 Score = 91.7 bits (226), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 41/91 (45%), Positives = 59/91 (64%)

Query: 61  HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQ 120
           + SL VRN+  D R E+LR  F R+G + DVY+P D+YT  PRGFA+VQF D  +A +A 
Sbjct: 9   NTSLFVRNVADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDAL 68

Query: 121 HHMNGKRFAGREISVVLAAESRKRPEEMRQR 151
           H+++ K   GR+I +  A   RK P +M+ +
Sbjct: 69  HNLDRKWICGRQIEIQFAQGDRKTPNQMKAK 99

Splicing factor that in its dephosphorylated form acts as a general repressor of pre-mRNA splicing. Seems to interfere with the U1 snRNP 5'-splice recognition of SNRNP70. Required for splicing repression in M-phase cells and after heat shock (By similarity). May be involved in regulation of alternative splicing in neurons, with isoform 1 acting as a positive and isoform 3 as a negative regulator.

Mus musculus (taxid: 10090)

>sp|O75494|SRS10_HUMAN Serine/arginine-rich splicing factor 10 OS=Homo sapiens GN=SRSF10 PE=1 SV=1

 Score = 91.7 bits (226), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 41/91 (45%), Positives = 59/91 (64%)

Query: 61  HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQ 120
           + SL VRN+  D R E+LR  F R+G + DVY+P D+YT  PRGFA+VQF D  +A +A 
Sbjct: 9   NTSLFVRNVADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDAL 68

Query: 121 HHMNGKRFAGREISVVLAAESRKRPEEMRQR 151
           H+++ K   GR+I +  A   RK P +M+ +
Sbjct: 69  HNLDRKWICGRQIEIQFAQGDRKTPNQMKAK 99

Splicing factor that in its dephosphorylated form acts as a general repressor of pre-mRNA splicing. Seems to interfere with the U1 snRNP 5'-splice recognition of SNRNP70. Required for splicing repression in M-phase cells and after heat shock. May be involved in regulation of alternative splicing in neurons, with isoform 1 acting as a positive and isoform 3 as a negative regulator.

Homo sapiens (taxid: 9606)

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

 Score = 73.2 bits (178), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 36/76 (47%), Positives = 48/76 (63%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           SL V N+     P+ LR  FE++G V DVY+P+D YT E RGFAFV+F D  +A +A   
Sbjct: 15  SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 74

Query: 123 MNGKRFAGREISVVLA 138
           M+G    GRE+ V +A
Sbjct: 75  MDGAVLDGRELRVQMA 90

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 = 71.2 bits (173), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 36/80 (45%), Positives = 49/80 (61%)

Query: 59  QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAE 118
           +   SL V N+     P+ LR  FE++G V DVY+P+D YT E RGFAFV+F D  +A +
Sbjct: 11  EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAED 70

Query: 119 AQHHMNGKRFAGREISVVLA 138
           A   M+G    GRE+ V +A
Sbjct: 71  AMDAMDGAVLDGRELRVQMA 90

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 = 70.1 bits (170), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 36/76 (47%), Positives = 48/76 (63%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           SL V N+     P+ LR  FE++G V DVY+P+D YT E RGFAFV+F D  +A +A   
Sbjct: 15  SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 74

Query: 123 MNGKRFAGREISVVLA 138
           M+G    GRE+ V +A
Sbjct: 75  MDGAVLDGRELRVQMA 90

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 = 69.7 bits (169), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 36/76 (47%), Positives = 48/76 (63%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           SL V N+     P+ LR  FE++G V DVY+P+D YT E RGFAFV+F D  +A +A   
Sbjct: 15  SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 74

Query: 123 MNGKRFAGREISVVLA 138
           M+G    GRE+ V +A
Sbjct: 75  MDGAVLDGRELRVQMA 90

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 = 69.7 bits (169), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 36/76 (47%), Positives = 48/76 (63%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           SL V N+     P+ LR  FE++G V DVY+P+D YT E RGFAFV+F D  +A +A   
Sbjct: 15  SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 74

Query: 123 MNGKRFAGREISVVLA 138
           M+G    GRE+ V +A
Sbjct: 75  MDGAVLDGRELRVQMA 90

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 = 69.7 bits (169), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 36/76 (47%), Positives = 48/76 (63%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           SL V N+     P+ LR  FE++G V DVY+P+D YT E RGFAFV+F D  +A +A   
Sbjct: 15  SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 74

Query: 123 MNGKRFAGREISVVLA 138
           M+G    GRE+ V +A
Sbjct: 75  MDGAVLDGRELRVQMA 90

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)

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	299
296086246	353	unnamed protein product [Vitis vinifera]	0.953	0.807	0.717	1e-80
225449547	276	PREDICTED: uncharacterized protein LOC10	0.923	1.0	0.733	9e-79
449524006	305	PREDICTED: uncharacterized protein LOC10	0.876	0.859	0.727	1e-70
449459926	286	PREDICTED: uncharacterized protein LOC10	0.919	0.961	0.719	8e-69
356553842	271	PREDICTED: uncharacterized protein LOC10	0.819	0.904	0.645	7e-64
224112763	232	predicted protein [Populus trichocarpa]	0.709	0.913	0.733	9e-63
356499101	276	PREDICTED: uncharacterized protein LOC10	0.695	0.753	0.672	1e-60
255584869	265	serine/arginine rich splicing factor, pu	0.732	0.826	0.781	2e-58
222622536	304	hypothetical protein OsJ_06104 [Oryza sa	0.819	0.805	0.626	4e-58
218190416	289	hypothetical protein OsI_06591 [Oryza sa	0.802	0.830	0.635	7e-58

>gi|296086246|emb|CBI31687.3| unnamed protein product [Vitis vinifera]

 Score =  306 bits (783), Expect = 1e-80,   Method: Compositional matrix adjust.
 Identities = 208/290 (71%), Positives = 230/290 (79%), Gaps = 5/290 (1%)

Query: 10  VFLVQEGSAMRRYSPPYYSPPRRGYGGRGRSPPRRGYGGGGGGYGRRKEQNHGSLLVRNI 69
           +F     S MRRYSPPYYS PRRGYGGR RSPPRRGYGG G    RRKEQNHGSLLVRNI
Sbjct: 69  IFQKNFKSIMRRYSPPYYSAPRRGYGGRERSPPRRGYGGYG----RRKEQNHGSLLVRNI 124

Query: 70  PLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFA 129
           PL+CRPE+LR PFERFG+VRDVYLPKDYYTGEPRGFAFVQFVDPYEA+EAQ+HMNG+ FA
Sbjct: 125 PLNCRPEDLRVPFERFGLVRDVYLPKDYYTGEPRGFAFVQFVDPYEASEAQYHMNGQIFA 184

Query: 130 GREISVVLAAESRKRPEEMRQRHRFRGGSSYGGPRSSYYGRYRSRSLSRSRSPHHPQGSR 189
           GREISVV+AAE+RKRPEEMR R R RG SSYGG RSSYYG  RSRS+SRSRSP       
Sbjct: 185 GREISVVVAAETRKRPEEMRTRARVRGPSSYGGRRSSYYGGSRSRSVSRSRSPPRLLSGS 244

Query: 190 SRYRSRSYTPVPRQHEDYSISPRRRHIEHPGSPRGPPQERGAEYSRRSYSPGYDDSADRR 249
            RYRSRSY+PVPR+  DYS+SPRRR +EHP SPR  P ER  ++ RRSYSPGYDD+AD+ 
Sbjct: 245 RRYRSRSYSPVPRRRGDYSVSPRRR-VEHPRSPRDHPPERDGDHIRRSYSPGYDDAADQN 303

Query: 250 NPNGNGYGEKSGYEETQAHWRSPPPRGVSRSPSGSRSRSRSADLSPRHTR 299
           +  GNGY EKS YE  +A  R   P     S S S SRSRSAD+SPRH+R
Sbjct: 304 HHTGNGYLEKSAYEPDEARDRRRSPPPRRVSRSLSGSRSRSADVSPRHSR 353

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225449547|ref|XP_002283722.1| PREDICTED: uncharacterized protein LOC100258210 [Vitis vinifera]

 Score =  299 bits (766), Expect = 9e-79,   Method: Compositional matrix adjust.
 Identities = 206/281 (73%), Positives = 227/281 (80%), Gaps = 5/281 (1%)

Query: 19  MRRYSPPYYSPPRRGYGGRGRSPPRRGYGGGGGGYGRRKEQNHGSLLVRNIPLDCRPEEL 78
           MRRYSPPYYS PRRGYGGR RSPPRRGYGG G    RRKEQNHGSLLVRNIPL+CRPE+L
Sbjct: 1   MRRYSPPYYSAPRRGYGGRERSPPRRGYGGYG----RRKEQNHGSLLVRNIPLNCRPEDL 56

Query: 79  RAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA 138
           R PFERFG+VRDVYLPKDYYTGEPRGFAFVQFVDPYEA+EAQ+HMNG+ FAGREISVV+A
Sbjct: 57  RVPFERFGLVRDVYLPKDYYTGEPRGFAFVQFVDPYEASEAQYHMNGQIFAGREISVVVA 116

Query: 139 AESRKRPEEMRQRHRFRGGSSYGGPRSSYYGRYRSRSLSRSRSPHHPQGSRSRYRSRSYT 198
           AE+RKRPEEMR R R RG SSYGG RSSYYG  RSRS+SRSRSP        RYRSRSY+
Sbjct: 117 AETRKRPEEMRTRARVRGPSSYGGRRSSYYGGSRSRSVSRSRSPPRLLSGSRRYRSRSYS 176

Query: 199 PVPRQHEDYSISPRRRHIEHPGSPRGPPQERGAEYSRRSYSPGYDDSADRRNPNGNGYGE 258
           PVPR+  DYS+SPRRR +EHP SPR  P ER  ++ RRSYSPGYDD+AD+ +  GNGY E
Sbjct: 177 PVPRRRGDYSVSPRRR-VEHPRSPRDHPPERDGDHIRRSYSPGYDDAADQNHHTGNGYLE 235

Query: 259 KSGYEETQAHWRSPPPRGVSRSPSGSRSRSRSADLSPRHTR 299
           KS YE  +A  R   P     S S S SRSRSAD+SPRH+R
Sbjct: 236 KSAYEPDEARDRRRSPPPRRVSRSLSGSRSRSADVSPRHSR 276

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449524006|ref|XP_004169014.1| PREDICTED: uncharacterized protein LOC101227075 [Cucumis sativus]

 Score =  272 bits (696), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 203/279 (72%), Positives = 224/279 (80%), Gaps = 17/279 (6%)

Query: 19  MRRYSPPYYSPPRRGYGGRGRSPPRRGYGGGGGGYGRRK---------EQNHGSLLVRNI 69
           MRRYSPPY+SPPRRGYGGRGRSPP RGYGGGGGG G            EQ HGSLLVRNI
Sbjct: 1   MRRYSPPYHSPPRRGYGGRGRSPPGRGYGGGGGGGGGGGGGGGYGRRREQPHGSLLVRNI 60

Query: 70  PLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFA 129
           P+DCRPEELRAPFERFG+VRDVY+PKDYYTGEPRGFAFV+FVDPYEA+EAQ+HMNGK+FA
Sbjct: 61  PMDCRPEELRAPFERFGLVRDVYIPKDYYTGEPRGFAFVEFVDPYEASEAQYHMNGKKFA 120

Query: 130 GREISVVLAAESRKRPEEMRQRHRFRGGSSYGGPRSSYYGRYRSRSLSRSRSPHHPQGSR 189
           GREI+VVLAAESRKRPE+MRQR R RG S YGG R S+YGR RSRS+SRSRSP HP GSR
Sbjct: 121 GREITVVLAAESRKRPEQMRQRSR-RGPSGYGG-RRSHYGRSRSRSVSRSRSPRHPSGSR 178

Query: 190 SRYRSRSYTPVPRQHEDYSISPRRRHIEHPGSPRGPPQERGAEYSRRSYSPGYDDSADRR 249
           SRYRSRSY+P PR   DYS+SP RRH ++P SPRG P+ER  E SR+ YSPGYD+ AD  
Sbjct: 179 SRYRSRSYSPAPRWRGDYSVSPGRRHTDYPESPRGAPRERDVERSRQVYSPGYDN-ADEH 237

Query: 250 NPNGNGYGEKSGYEETQAH----WRSPPPRGVSRSPSGS 284
             NGNGY +KS   E Q H    WR+ P R  SRSPSGS
Sbjct: 238 GQNGNGYHDKSPSVEHQDHLRVNWRASPGR-TSRSPSGS 275

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449459926|ref|XP_004147697.1| PREDICTED: uncharacterized protein LOC101221788 [Cucumis sativus]

 Score =  266 bits (680), Expect = 8e-69,   Method: Compositional matrix adjust.
 Identities = 210/292 (71%), Positives = 231/292 (79%), Gaps = 17/292 (5%)

Query: 19  MRRYSPPYYSPPRRGYGGRGRSPPRRGYGGGGGGYGRRK-------EQNHGSLLVRNIPL 71
           MRRYSPPY+SPPRRGYGGRGRSPP RGYGGGGGG G          EQ HGSLLVRNIP+
Sbjct: 1   MRRYSPPYHSPPRRGYGGRGRSPPGRGYGGGGGGGGGGGGGYGRRREQPHGSLLVRNIPM 60

Query: 72  DCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGR 131
           DCRPEELRAPFERFG+VRDVY+PKDYYTGEPRGFAFV+FVDPYEA+EAQ+HMNGK+FAGR
Sbjct: 61  DCRPEELRAPFERFGLVRDVYIPKDYYTGEPRGFAFVEFVDPYEASEAQYHMNGKKFAGR 120

Query: 132 EISVVLAAESRKRPEEMRQRHRFRGGSSYGGPRSSYYGRYRSRSLSRSRSPHHPQGSRSR 191
           EI+VVLAAESRKRPE+MRQR R RG S YGG R S+YGR RSRS+SRSRSP HP GSRSR
Sbjct: 121 EITVVLAAESRKRPEQMRQRSR-RGPSGYGG-RRSHYGRSRSRSVSRSRSPRHPSGSRSR 178

Query: 192 YRSRSYTPVPRQHEDYSISPRRRHIEHPGSPRGPPQERGAEYSRRSYSPGYDDSADRRNP 251
           YRSRSY+P PR   DYS+SP RRH ++P SPRG P+ER  E SR+ YSPGYD+ AD    
Sbjct: 179 YRSRSYSPAPRWRGDYSVSPGRRHTDYPESPRGAPRERDVERSRQVYSPGYDN-ADEHGQ 237

Query: 252 NGNGYGEKSGYEETQAH----WRSPPPRGVSRSPSGSRSRSRSADLSPRHTR 299
           NGNGY +KS   E Q H    WR+ P      S S S SRSRSAD SPRH R
Sbjct: 238 NGNGYHDKSPSVEHQDHLRVNWRASP---GRTSRSPSGSRSRSADASPRHGR 286

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356553842|ref|XP_003545260.1| PREDICTED: uncharacterized protein LOC100792397 [Glycine max]

 Score =  250 bits (638), Expect = 7e-64,   Method: Compositional matrix adjust.
 Identities = 166/257 (64%), Positives = 196/257 (76%), Gaps = 12/257 (4%)

Query: 19  MRRYSPPYYSPPRRGYGGRGRSPPRRGYGGGGGGYGRRKEQNHGSLLVRNIPLDCRPEEL 78
           MRR SP YYSPPRRGYGG GR     G  G  G  G R+  ++GSLLVRNIPLDCRPEEL
Sbjct: 1   MRRNSPAYYSPPRRGYGGGGRG----GGSGRRGFGGGRRRDSNGSLLVRNIPLDCRPEEL 56

Query: 79  RAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA 138
           R PFERFG VRDVY+PKDYY+GEPRGFAFVQFVDPY+A+EAQ+HMN + FAGREISVV+A
Sbjct: 57  RVPFERFGPVRDVYIPKDYYSGEPRGFAFVQFVDPYDASEAQYHMNRQIFAGREISVVVA 116

Query: 139 AESRKRPEEMRQR-HRFRGGSSYGGPRSSYYGRYRSRSLSRSRSPHHPQGSRSRYRSRSY 197
            E+RKRPEEMR R  RFRG +SYGG RSS+YGR RSRS++RSRSP +  GSR+RYRSRSY
Sbjct: 117 EETRKRPEEMRHRTSRFRGPASYGGRRSSHYGRSRSRSITRSRSPPYHSGSRNRYRSRSY 176

Query: 198 TPVPRQHEDYSISPRRRHIEHPGSPRGPPQERGAEYSRRSYSPGYDDSADRRNPNGNGYG 257
           +P PR+  DYS+SP  R  EHP SPRGPP+E+  +  RRSYSP Y +  ++     NGY 
Sbjct: 177 SPAPRRQSDYSVSP-GRQAEHPRSPRGPPREKDGDQKRRSYSPAYGNGIEQN--QSNGYA 233

Query: 258 EKSGY----EETQAHWR 270
           EKS Y    +  ++ W+
Sbjct: 234 EKSMYKSEADADRSQWK 250

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224112763|ref|XP_002316285.1| predicted protein [Populus trichocarpa] gi|222865325|gb|EEF02456.1| predicted protein [Populus trichocarpa]

 Score =  246 bits (628), Expect = 9e-63,   Method: Compositional matrix adjust.
 Identities = 160/218 (73%), Positives = 174/218 (79%), Gaps = 6/218 (2%)

Query: 57  KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEA 116
           K+QN GSLLVRNIPLDCRP+ELR PFERFGVVRDVY+PKDYYTGEPRGFAFVQFVDPYEA
Sbjct: 1   KDQNSGSLLVRNIPLDCRPDELRGPFERFGVVRDVYIPKDYYTGEPRGFAFVQFVDPYEA 60

Query: 117 AEAQHHMNGKRFAGREISVVLAAESRKRPEEMRQRHRFRGGSSYGGPRSSYYGRYRSRSL 176
            EAQH MNG+ FAGR+ISVVLAAE+RKRPEEMR R R RG SS+GG RSS YGR RSRSL
Sbjct: 61  MEAQHRMNGQIFAGRQISVVLAAETRKRPEEMRHRARVRGPSSHGG-RSSNYGRSRSRSL 119

Query: 177 SRSRSPHHPQGSRSRYRSRSYTPVPRQHEDYSISPRRRHIEHPGSPRGPPQERGAEYSRR 236
           SRS    H   SRSRYRSRSY+P PR+  DYS SP RRH  HPGSPRGPP ER  ++SRR
Sbjct: 120 SRSPR--HYPSSRSRYRSRSYSPAPRR-RDYSASPDRRHAGHPGSPRGPPPERDGDHSRR 176

Query: 237 SYSPGYDDSADRRNPNGNGYGEKSGYEETQAH-WRSPP 273
           SYSP Y    D  N NGNG+GEKS Y+  +A  WR  P
Sbjct: 177 SYSPAY-GHGDGLNENGNGFGEKSAYDFEEARAWRPSP 213

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356499101|ref|XP_003518382.1| PREDICTED: uncharacterized protein LOC100804294 [Glycine max]

 Score =  239 bits (610), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 144/214 (67%), Positives = 169/214 (78%), Gaps = 6/214 (2%)

Query: 60  NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEA 119
           ++GSLLVRNIPLDCRPEELR PFERFG VRDVY+PKDYY+GEPRGFAFVQFVDPY+A+EA
Sbjct: 45  SNGSLLVRNIPLDCRPEELRVPFERFGPVRDVYIPKDYYSGEPRGFAFVQFVDPYDASEA 104

Query: 120 QHHMNGKRFAGREISVVLAAESRKRPEEMRQRH-RFRGGSSYGGPRSSYYGRYRSRSLSR 178
           Q+HMN + FAGREISVV+A E+RKRPEEMR R  R RG + YGG RSS YGR RSRS++R
Sbjct: 105 QYHMNRQIFAGREISVVVAEETRKRPEEMRHRTSRLRGPAGYGGQRSSRYGRSRSRSVTR 164

Query: 179 SRSPHHPQGSRSRYRSRSYTPVPRQHEDYSISPRRRHIEHPGSPRGPPQERGAEYSRRSY 238
           SRSP +  GSR+RYRSRSY+P PR+  DYS+SP RR  EHP SPRGPP+ER  E  RRSY
Sbjct: 165 SRSPPYHSGSRNRYRSRSYSPAPRRQSDYSVSP-RRQAEHPRSPRGPPRERDGEQKRRSY 223

Query: 239 SPGYDDSADRRNPNGNGYGEKSGY--EETQAHWR 270
           SP Y +  ++     NGY EKS Y  +  +  W+
Sbjct: 224 SPAYGNGIEQN--QSNGYAEKSMYKSDADRGQWK 255

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255584869|ref|XP_002533150.1| serine/arginine rich splicing factor, putative [Ricinus communis] gi|223527045|gb|EEF29231.1| serine/arginine rich splicing factor, putative [Ricinus communis]

 Score =  232 bits (591), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 175/224 (78%), Positives = 187/224 (83%), Gaps = 5/224 (2%)

Query: 19  MRRYSPPYYSPPRRGYGGRGRSPPRRGYGGGGGGYGRRKEQNHGSLLVRNIPLDCRPEEL 78
           MRRYSPPYYSPPRRGYGGRGRSPPRRG+GGGGG  GRRKEQNHGSLLVRNIPLDCRPEEL
Sbjct: 1   MRRYSPPYYSPPRRGYGGRGRSPPRRGHGGGGGY-GRRKEQNHGSLLVRNIPLDCRPEEL 59

Query: 79  RAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA 138
           RAPFERFGVVRDVY+PKDYYTGEPRGFAFVQFVD Y+A EAQH MNG+ FAGREISVV+A
Sbjct: 60  RAPFERFGVVRDVYIPKDYYTGEPRGFAFVQFVDTYDAMEAQHRMNGQIFAGREISVVVA 119

Query: 139 AESRKRPEEMRQRHRFRGGSSYGGPRSSYYGRYRSRSLSRSRSPHHPQGSRSRYRSRSYT 198
           AE+RKRPEEMRQR R    S YGG RSSYYGR RSRSLS S    H  GSRSRYRSRS++
Sbjct: 120 AETRKRPEEMRQRSRIGRPSGYGG-RSSYYGRSRSRSLSHSPR--HHLGSRSRYRSRSFS 176

Query: 199 PVPRQHEDYSISPRRRHIEHPGSPRGPPQERGAEYSRRSYSPGY 242
           P PR+  DYS SP RRH +H  SP G P  R  ++  RSYSPGY
Sbjct: 177 PAPRR-RDYSASPGRRHADHARSPSGLPPGRDGDHIHRSYSPGY 219

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|222622536|gb|EEE56668.1| hypothetical protein OsJ_06104 [Oryza sativa Japonica Group]

 Score =  231 bits (588), Expect = 4e-58,   Method: Compositional matrix adjust.
 Identities = 163/260 (62%), Positives = 186/260 (71%), Gaps = 15/260 (5%)

Query: 1   AKSSLLSSLVFLVQEGSAMRRYSPPYYSPPRRGYGGRGRSPPRRGYGGGGGGYGRRKEQN 60
           A++  LS    +      MRRYSPPY SPPRRGYGGRGRSPPRRGYGG       RKEQ 
Sbjct: 22  ARAERLSRKEEVAVAYKTMRRYSPPYRSPPRRGYGGRGRSPPRRGYGG-------RKEQG 74

Query: 61  HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQ 120
            GSLLVRNIPL CR E+LR PFERFG VRDVYLPKDYYTGEPRGFAFV+FVDPY+A+EAQ
Sbjct: 75  SGSLLVRNIPLSCRAEDLRVPFERFGPVRDVYLPKDYYTGEPRGFAFVEFVDPYDASEAQ 134

Query: 121 HHMNGKRFAGREISVVLAAESRKRPEEMRQRHRFRGGSSYGGPRSSYYGRYRSRSLSRSR 180
           +HMN +   GREI+VVLAAESRKRPEEMR R R RG S + G RSS+YGR RSRS SRS 
Sbjct: 135 YHMNRQVVFGREITVVLAAESRKRPEEMRSRARVRGYSDHEGRRSSHYGRSRSRSRSRS- 193

Query: 181 SPHHPQGSRSRYRSRSYTPVPRQHEDYSISPRRRHIEHPGSPRGPPQERGAEYSRRSYSP 240
                   R R RSRSY+P PR+ +DYS SP+R+      SPR  P+E   +  RRSYSP
Sbjct: 194 -----PRYRGRPRSRSYSPAPRRRDDYSASPQRKDTHRAKSPRRQPKEHEVDKKRRSYSP 248

Query: 241 GYDDSADRRNPNGNGYGEKS 260
              D  DRR+ + NGY ++S
Sbjct: 249 ANKD-GDRRDAD-NGYEKRS 266

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|218190416|gb|EEC72843.1| hypothetical protein OsI_06591 [Oryza sativa Indica Group]

 Score =  230 bits (586), Expect = 7e-58,   Method: Compositional matrix adjust.
 Identities = 164/258 (63%), Positives = 186/258 (72%), Gaps = 18/258 (6%)

Query: 18  AMRRYSPPYYSPPRRGYGGRGRSPPRRGYGGGGGGYGRRKEQNHGSLLVRNIPLDCRPEE 77
            MRRYSPPY SPPRRGYGGRGRSPPRRGYGG       RKEQ  GSLLVRNIPL CR E+
Sbjct: 24  TMRRYSPPYRSPPRRGYGGRGRSPPRRGYGG-------RKEQGSGSLLVRNIPLSCRAED 76

Query: 78  LRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL 137
           LR PFERFG VRDVYLPKDYYTGEPRGFAFV+FVDPY+A+EAQ+HMN +   GREI+VVL
Sbjct: 77  LRVPFERFGPVRDVYLPKDYYTGEPRGFAFVEFVDPYDASEAQYHMNRQVVFGREITVVL 136

Query: 138 AAESRKRPEEMRQRHRFRGGSSYGGPRSSYYGRYRSRSLSRSRSPHHPQGSRSRYRSRSY 197
           AAESRKRPEEMR R R RG S + G RSS+YGR RSRS SRS         R R RSRSY
Sbjct: 137 AAESRKRPEEMRSRARVRGYSDHEGRRSSHYGRSRSRSRSRS------PRYRGRPRSRSY 190

Query: 198 TPVPRQHEDYSISPRRRHIEHPGSPRGPPQERGAEYSRRSYSPGYDDSADRRNPNGNGYG 257
           +P PR+ +DYS SP+R+      SPR  P+E   +  RRSYSP   D  DRR+ + NGY 
Sbjct: 191 SPAPRRRDDYSASPQRKDTHRAKSPRRQPKEHEVDKKRRSYSPANKD-GDRRDAD-NGYE 248

Query: 258 EKSGYEETQA---HWRSP 272
           ++S   ++     H RSP
Sbjct: 249 KRSPPADSDGSPPHRRSP 266

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	299
TAIR|locus:2099931	262	SCL30 "SC35-like splicing fact	0.632	0.721	0.473	7.8e-39
TAIR|locus:2086804	262	SCL30A "SC35-like splicing fac	0.304	0.347	0.637	5.6e-34
TAIR|locus:2144945	236	SCL28 "SC35-like splicing fact	0.287	0.364	0.593	2e-28
UNIPROTKB|Q7ZTJ8	258	srsf10 "MGC53149 protein" [Xen	0.304	0.352	0.461	7.6e-22
ZFIN|ZDB-GENE-040426-1415	248	zgc:65772 "zgc:65772" [Danio r	0.311	0.375	0.440	9.7e-22
UNIPROTKB|F1Q237	261	F1Q237 "Uncharacterized protei	0.297	0.340	0.426	5e-19
GENEDB_PFALCIPARUM|PFE0160c	308	PFE0160c "Ser/Arg-rich splicin	0.304	0.295	0.461	2.2e-18
UNIPROTKB|Q8I468	308	PFE0160c "Ser/Arg-rich splicin	0.304	0.295	0.461	2.2e-18
UNIPROTKB|G3MWK4	261	SRSF12 "Uncharacterized protei	0.304	0.348	0.461	7.5e-18
UNIPROTKB|Q9BRL6	282	SRSF8 "Serine/arginine-rich sp	0.294	0.312	0.409	9.1e-18

TAIR|locus:2099931 SCL30 "SC35-like splicing factor 30" [Arabidopsis thaliana (taxid:3702)]

 Score = 415 (151.1 bits), Expect = 7.8e-39, P = 7.8e-39
 Identities = 97/205 (47%), Positives = 114/205 (55%)

Query:    60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEA 119
             +HGSLLVRNIPLDCRPEELR PFERFG VRDVY+P+DYY+G+PRGFAFV+FVD Y+A EA
Sbjct:    45 SHGSLLVRNIPLDCRPEELREPFERFGPVRDVYIPRDYYSGQPRGFAFVEFVDAYDAGEA 104

Query:   120 QHHMNGKRFAGREISVVLAAESRKRPEEMRQRHRFXXXXXXXXXXXXXXXXXXXXXXXXX 179
             Q  MN + FAGREI+VV+A+ESRKRPEEMR + R                          
Sbjct:   105 QRSMNRRSFAGREITVVVASESRKRPEEMRVKTR-TRSREPSGSRDRSHGRSRSRSISRS 163

Query:   180 XXPHHPQGXXXXXXXXXXTPVPRQHEDYSISPRRRHIEHPGSPRGPPQERGAEYSRRSYS 239
               P  P                 +   YS +PRRR     G PRG   E  +  S     
Sbjct:   164 RSPRRPSDSRSRY----------RSRSYSPAPRRRG----GPPRGEEDENYSRRSYSPGY 209

Query:   240 PGYDDSADRRNPNG-NGYGEKSGYE 263
              G   +A  R+ NG N   EK GYE
Sbjct:   210 EGAAAAAPDRDRNGDNEIREKPGYE 234

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

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

GO:0016607 "nuclear speck" evidence=IDA

GO:0008380 "RNA splicing" evidence=NAS

GO:0006979 "response to oxidative stress" evidence=IDA

TAIR|locus:2086804 SCL30A "SC35-like splicing factor 30A" [Arabidopsis thaliana (taxid:3702)]

 Score = 323 (118.8 bits), Expect = 5.6e-34, Sum P(2) = 5.6e-34
 Identities = 58/91 (63%), Positives = 74/91 (81%)

Query:    63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
             SLLVRN+  DCR E+LR PFE+FG V+D+YLP+DYYTG+PRGF F+QF+DP +AAEA+H 
Sbjct:    38 SLLVRNLRHDCRQEDLRRPFEQFGPVKDIYLPRDYYTGDPRGFGFIQFMDPADAAEAKHQ 97

Query:   123 MNGKRFAGREISVVLAAESRKRPEEMRQRHR 153
             M+G    GRE++VV A E+RK+P EMR R R
Sbjct:    98 MDGYLLLGRELTVVFAEENRKKPTEMRTRDR 128

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

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

GO:0016607 "nuclear speck" evidence=IDA

GO:0008380 "RNA splicing" evidence=NAS

GO:0005829 "cytosol" evidence=IDA

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

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

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

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

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

TAIR|locus:2144945 SCL28 "SC35-like splicing factor 28" [Arabidopsis thaliana (taxid:3702)]

 Score = 278 (102.9 bits), Expect = 2.0e-28, Sum P(2) = 2.0e-28
 Identities = 51/86 (59%), Positives = 66/86 (76%)

Query:    64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
             LL+RN+PLD RP +LR  FERFG ++D+YLP++YYTGEPRGF FV++    +AAEA   M
Sbjct:    49 LLIRNLPLDARPNDLRDSFERFGPLKDIYLPRNYYTGEPRGFGFVKYRYAEDAAEAMKRM 108

Query:   124 NGKRFAGREISVVLAAESRKRPEEMR 149
             N K   GREI++V A E+RK P+EMR
Sbjct:   109 NHKVIGGREIAIVFAEENRKTPQEMR 134

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0016607 "nuclear speck" evidence=IDA

GO:0007059 "chromosome segregation" evidence=RCA

GO:0007062 "sister chromatid cohesion" evidence=RCA

GO:0007129 "synapsis" evidence=RCA

GO:0007131 "reciprocal meiotic recombination" evidence=RCA

GO:0033044 "regulation of chromosome organization" evidence=RCA

GO:0042138 "meiotic DNA double-strand break formation" evidence=RCA

GO:0045132 "meiotic chromosome segregation" evidence=RCA

UNIPROTKB|Q7ZTJ8 srsf10 "MGC53149 protein" [Xenopus laevis (taxid:8355)]

 Score = 215 (80.7 bits), Expect = 7.6e-22, Sum P(2) = 7.6e-22
 Identities = 42/91 (46%), Positives = 58/91 (63%)

Query:    61 HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQ 120
             + SL VRNI  D R E+LR  F R+G + DVY+P DYY   PRGFA+VQF D  +A +A 
Sbjct:     9 NSSLFVRNIADDIRSEDLRREFGRYGPIVDVYVPLDYYNRRPRGFAYVQFEDVRDAEDAL 68

Query:   121 HHMNGKRFAGREISVVLAAESRKRPEEMRQR 151
             H+++ K   GR+I +  A   RK P +M+ +
Sbjct:    69 HNLDKKWICGRQIEIQFAQGDRKTPHQMKAK 99

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

ZFIN|ZDB-GENE-040426-1415 zgc:65772 "zgc:65772" [Danio rerio (taxid:7955)]

 Score = 219 (82.2 bits), Expect = 9.7e-22, Sum P(2) = 9.7e-22
 Identities = 41/93 (44%), Positives = 61/93 (65%)

Query:    61 HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQ 120
             + SL VRNI  + RPE+LR  F R+G + DVY+P D+Y+  PRGFA++QF D  +A +A 
Sbjct:     9 NSSLFVRNISDESRPEDLRREFGRYGPIVDVYIPLDFYSRRPRGFAYIQFEDVRDAEDAL 68

Query:   121 HHMNGKRFAGREISVVLAAESRKRPEEMRQRHR 153
             H+++ K   GR+I +  A   RK P +M+ + R
Sbjct:    69 HNLDRKWVCGRQIEIQFAQGDRKTPGQMKNKER 101

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

UNIPROTKB|F1Q237 F1Q237 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 198 (74.8 bits), Expect = 5.0e-19, Sum P(2) = 5.0e-19
 Identities = 38/89 (42%), Positives = 57/89 (64%)

Query:    63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
             SL VRN+  + R E+L   F R+G + DVY+P D+YT  PRGFA+VQF D  +A +A H+
Sbjct:    11 SLFVRNVADNTRSEDLPREFGRYGPIVDVYVPLDFYTRHPRGFAYVQFEDVRDAEDALHN 70

Query:   123 MNGKRFAGREISVVLAAESRKRPEEMRQR 151
             ++ K   GR+I +  A   +K P +M+ +
Sbjct:    71 LDRKWICGRQIEIQFAQGDQKTPNQMKAK 99

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GENEDB_PFALCIPARUM|PFE0160c PFE0160c "Ser/Arg-rich splicing factor, putative" [Plasmodium falciparum (taxid:5833)]

 Score = 222 (83.2 bits), Expect = 2.2e-18, P = 2.2e-18
 Identities = 42/91 (46%), Positives = 55/91 (60%)

Query:    63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
             SLL+R +  D  P  +R  F+RFG ++DVYLP DYYT EPRGF FV+F D  +A +A   
Sbjct:    13 SLLIRKLKFDTSPSIVREKFKRFGAIKDVYLPIDYYTKEPRGFGFVEFYDAKDAEQALKE 72

Query:   123 MNGKRFAGREISVVLAAESRKRPEEMRQRHR 153
             MNG    G  I V +A + R  P  MR + +
Sbjct:    73 MNGSEIDGSRIEVFVAQKGRSDPRHMRYKEK 103

GO:0005681 "spliceosomal complex" evidence=ISS

GO:0008380 "RNA splicing" evidence=ISS

UNIPROTKB|Q8I468 PFE0160c "Ser/Arg-rich splicing factor, putative" [Plasmodium falciparum 3D7 (taxid:36329)]

 Score = 222 (83.2 bits), Expect = 2.2e-18, P = 2.2e-18
 Identities = 42/91 (46%), Positives = 55/91 (60%)

Query:    63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
             SLL+R +  D  P  +R  F+RFG ++DVYLP DYYT EPRGF FV+F D  +A +A   
Sbjct:    13 SLLIRKLKFDTSPSIVREKFKRFGAIKDVYLPIDYYTKEPRGFGFVEFYDAKDAEQALKE 72

Query:   123 MNGKRFAGREISVVLAAESRKRPEEMRQRHR 153
             MNG    G  I V +A + R  P  MR + +
Sbjct:    73 MNGSEIDGSRIEVFVAQKGRSDPRHMRYKEK 103

GO:0005681 "spliceosomal complex" evidence=ISS

GO:0008380 "RNA splicing" evidence=ISS

UNIPROTKB|G3MWK4 SRSF12 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 217 (81.4 bits), Expect = 7.5e-18, P = 7.5e-18
 Identities = 42/91 (46%), Positives = 59/91 (64%)

Query:    63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
             SL VRN+    RPE+LR  F R+G + DVY+P D+YT  PRGFA+VQF D  +A +A ++
Sbjct:    11 SLFVRNVADATRPEDLRREFGRYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYN 70

Query:   123 MNGKRFAGREISVVLAAESRKRPEEMRQRHR 153
             +N K   GR+I +  A   RK P +M+ + R
Sbjct:    71 LNRKWVCGRQIEIQFAQGDRKTPGQMKSKER 101

GO:0000395 "mRNA 5'-splice site recognition" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|Q9BRL6 SRSF8 "Serine/arginine-rich splicing factor 8" [Homo sapiens (taxid:9606)]

 Score = 167 (63.8 bits), Expect = 9.1e-18, Sum P(2) = 9.1e-18
 Identities = 36/88 (40%), Positives = 53/88 (60%)

Query:    63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
             +L V N+     P+ LR  FE++G V DVY+P++ +T  PRGFAFV+F D  +A +A+  
Sbjct:    15 TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74

Query:   123 MNGKRFAGREISVVLAAESRKRPEEMRQ 150
             M+G    GRE+ V +A   R+     RQ
Sbjct:    75 MDGAELDGRELRVQVARYGRRDLPRSRQ 102

GO:0000166 "nucleotide binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	299
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	2e-24
smart00360	73	smart00360, RRM, RNA recognition motif	2e-23
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	1e-20
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	5e-19
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	2e-18
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	6e-18
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	2e-17
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	4e-17
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	5e-17
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	6e-17
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	2e-16
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	3e-16
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	5e-16
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	1e-14
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	1e-14
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	2e-14
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	7e-14
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-13
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	1e-13
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	1e-12
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	1e-12
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	6e-12
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	1e-11
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	1e-11
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	2e-11
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	2e-11
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	2e-11
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	2e-11
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	5e-11
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	5e-11
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	6e-11
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	7e-11
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	3e-10
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	4e-10
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	4e-10
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	6e-10
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	7e-10
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	7e-10
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	7e-10
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	7e-10
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	8e-10
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	1e-09
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	1e-09
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	2e-09
cd12232	89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	2e-09
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	3e-09
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	3e-09
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	3e-09
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	4e-09
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	4e-09
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	4e-09
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	7e-09
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	7e-09
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	8e-09
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	9e-09
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	1e-08
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	1e-08
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	2e-08
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	2e-08
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-08
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	2e-08
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	3e-08
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	3e-08
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	3e-08
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	3e-08
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	3e-08
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	3e-08
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	4e-08
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	4e-08
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	4e-08
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	4e-08
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	4e-08
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	5e-08
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	6e-08
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	7e-08
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	7e-08
cd12534	83	cd12534, RRM_SARFH, RNA recognition motif in Droso	8e-08
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	8e-08
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	9e-08
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	1e-07
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	1e-07
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	1e-07
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	1e-07
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	2e-07
cd12423	74	cd12423, RRM3_PTBP1_like, RNA recognition motif 3	2e-07
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	2e-07
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	3e-07
cd12282	91	cd12282, RRM2_TatSF1_like, RNA recognition motif 2	3e-07
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	3e-07
cd12550	76	cd12550, RRM_II_PABPN1, RNA recognition motif in t	3e-07
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	3e-07
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	3e-07
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	4e-07
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	6e-07
cd12317	72	cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition mot	6e-07
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	7e-07
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	7e-07
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	1e-06
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	1e-06
cd12277	86	cd12277, RRM3_MEI2_EAR1_like, RNA recognition moti	1e-06
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	1e-06
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	1e-06
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-06
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	2e-06
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	2e-06
cd12280	81	cd12280, RRM_FET, RNA recognition motif in the FET	2e-06
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	2e-06
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	2e-06
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	2e-06
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	2e-06
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	3e-06
cd12296	71	cd12296, RRM1_Prp24, RNA recognition motif 1 in fu	3e-06
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	3e-06
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	3e-06
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	3e-06
cd12607	67	cd12607, RRM2_RBM4, RNA recognition motif 2 in ver	3e-06
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	3e-06
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	3e-06
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	3e-06
cd12299	71	cd12299, RRM4_Prp24, RNA recognition motif 4 in fu	3e-06
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	4e-06
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	4e-06
cd12431	80	cd12431, RRM_ALKBH8, RNA recognition motif in alky	4e-06
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	5e-06
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	5e-06
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	5e-06
cd12561	81	cd12561, RRM1_RBM5_like, RNA recognition motif 1 i	6e-06
cd12285	85	cd12285, RRM3_RBM39_like, RNA recognition motif 3	6e-06
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	8e-06
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	1e-05
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	1e-05
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	1e-05
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	1e-05
cd12748	76	cd12748, RRM4_RBM12B, RNA recognition motif 4 in R	1e-05
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-05
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	2e-05
cd12257	72	cd12257, RRM1_RBM26_like, RNA recognition motif 1	2e-05
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	2e-05
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	2e-05
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	2e-05
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	2e-05
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	3e-05
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	3e-05
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	3e-05
cd12662	77	cd12662, RRM3_MYEF2, RNA recognition motif 3 in ve	3e-05
cd12496	74	cd12496, RRM3_RBM46, RNA recognition motif 3 in ve	3e-05
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	4e-05
cd12253	79	cd12253, RRM_PIN4_like, RNA recognition motif in y	4e-05
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	5e-05
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	6e-05
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	7e-05
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	7e-05
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	7e-05
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	7e-05
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	7e-05
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	8e-05
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	8e-05
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	9e-05
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	9e-05
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	9e-05
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	1e-04
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	1e-04
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	1e-04
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	1e-04
cd12482	79	cd12482, RRM1_hnRNPR, RNA recognition motif 1 in v	1e-04
cd12527	71	cd12527, RRM2_EAR1_like, RNA recognition motif 2 i	1e-04
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	1e-04
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	1e-04
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	1e-04
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	2e-04
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	2e-04
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	2e-04
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	2e-04
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	2e-04
cd12569	72	cd12569, RRM4_RBM19, RNA recognition motif 4 in RN	2e-04
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	3e-04
cd12303	86	cd12303, RRM_spSet1p_like, RNA recognition motif i	3e-04
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	3e-04
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	4e-04
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	4e-04
cd12697	76	cd12697, RRM3_ROD1, RNA recognition motif 3 in ver	4e-04
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	4e-04
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	4e-04
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	4e-04
cd12533	84	cd12533, RRM_EWS, RNA recognition motif in vertebr	4e-04
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	4e-04
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	4e-04
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	4e-04
cd12562	86	cd12562, RRM2_RBM5_like, RNA recognition motif 2 i	5e-04
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	5e-04
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	5e-04
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	6e-04
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	6e-04
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	6e-04
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	6e-04
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	6e-04
cd12755	86	cd12755, RRM2_RBM5, RNA recognition motif 2 in ver	6e-04
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	6e-04
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	6e-04
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	7e-04
cd12535	86	cd12535, RRM_FUS_TAF15, RNA recognition motif in v	7e-04
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	7e-04
cd12568	72	cd12568, RRM3_MRD1, RNA recognition motif 3 in yea	8e-04
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	9e-04
cd12598	72	cd12598, RRM1_SRSF9, RNA recognition motif 1 in ve	9e-04
cd12364	81	cd12364, RRM_RDM1, RNA recognition motif of RAD52	0.001
cd12497	74	cd12497, RRM3_RBM47, RNA recognition motif 3 in ve	0.001
TIGR01649	481	TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus spl	0.001
cd12645	81	cd12645, RRM_SRSF3, RNA recognition motif in verte	0.001
cd12420	79	cd12420, RRM_RBPMS_like, RNA recognition motif in	0.001
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	0.001
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	0.001
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	0.001
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	0.002
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	0.002
cd12274	71	cd12274, RRM2_NEFsp, RNA recognition motif 2 in ve	0.002
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	0.002
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	0.002
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	0.002
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	0.002
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	0.003
cd12485	78	cd12485, RRM1_RBM47, RNA recognition motif 1 found	0.003
cd12646	77	cd12646, RRM_SRSF7, RNA recognition motif in verte	0.003
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	0.003
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	0.003
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	0.003
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	0.004
cd12498	83	cd12498, RRM3_ACF, RNA recognition motif 3 in vert	0.004
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	0.004
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	0.004
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	0.004

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

 Score = 93.6 bits (233), Expect = 2e-24
 Identities = 39/83 (46%), Positives = 55/83 (66%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           SL VRN+    RP++LR  F ++G + DVY+P D+YT  PRGFA+VQF D  +A +A ++
Sbjct: 2   SLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYY 61

Query: 123 MNGKRFAGREISVVLAAESRKRP 145
           ++  RF GREI +  A   RK P
Sbjct: 62  LDRTRFLGREIEIQFAQGDRKTP 84

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

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

 Score = 91.1 bits (227), Expect = 2e-23
 Identities = 32/73 (43%), Positives = 43/73 (58%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           +L V N+P D   EELR  F +FG V  V L +D  TG+ +GFAFV+F    +A +A   
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 123 MNGKRFAGREISV 135
           +NGK   GR + V
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 83.5 bits (207), Expect = 1e-20
 Identities = 29/72 (40%), Positives = 43/72 (59%), Gaps = 1/72 (1%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L V N+P D   E+LR  F +FG +  V + +D   G+ +GFAFV+F  P +A +A   +
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK-DGKSKGFAFVEFESPEDAEKALEAL 59

Query: 124 NGKRFAGREISV 135
           NGK   GR++ V
Sbjct: 60  NGKELDGRKLKV 71

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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 79.2 bits (196), Expect = 5e-19
 Identities = 28/70 (40%), Positives = 42/70 (60%), Gaps = 1/70 (1%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L V N+P D   E+L+  F +FG +  + + +D  TG  +GFAFV+F D  +A +A   +
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDE-TGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 124 NGKRFAGREI 133
           NGK   GRE+
Sbjct: 60  NGKELGGREL 69

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

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

 Score = 78.1 bits (192), Expect = 2e-18
 Identities = 41/83 (49%), Positives = 54/83 (65%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           SL VRNI  D R E+LR  F R+G + DVY+P D+YT  PRGFA+VQF D  +A +A H+
Sbjct: 2   SLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHN 61

Query: 123 MNGKRFAGREISVVLAAESRKRP 145
           ++ K   GR+I +  A   RK P
Sbjct: 62  LDRKWICGRQIEIQFAQGDRKTP 84

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

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

 Score = 76.3 bits (188), Expect = 6e-18
 Identities = 29/74 (39%), Positives = 48/74 (64%)

Query: 62  GSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQH 121
           G L VRN+P  C+ ++L   F +FG + +V++  D  +G+ +GFA+V F+DP +A +A  
Sbjct: 3   GRLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYK 62

Query: 122 HMNGKRFAGREISV 135
            ++GK F GR I +
Sbjct: 63  ELDGKVFQGRLIHI 76

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

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

 Score = 74.6 bits (184), Expect = 2e-17
 Identities = 30/75 (40%), Positives = 45/75 (60%), Gaps = 1/75 (1%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L+VRN+P  C   +L+  F  FG V +V +P+    G+ +GFAFVQF    +A +A   +
Sbjct: 2   LIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKP-DGKKKGFAFVQFTSKADAEKAIKGV 60

Query: 124 NGKRFAGREISVVLA 138
           NGK+  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|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 = 73.9 bits (182), Expect = 4e-17
 Identities = 31/68 (45%), Positives = 40/68 (58%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L VRN+P     EELR  FE FG + +V+LP D  T   +GFAFV F+ P  A +A   +
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 124 NGKRFAGR 131
           +G  F GR
Sbjct: 62  DGSIFQGR 69

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

 Score = 73.9 bits (182), Expect = 5e-17
 Identities = 35/72 (48%), Positives = 47/72 (65%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L V N+     P++LR  FE++G V DVY+P+D YT E RGFAFV+F D  +A +A   M
Sbjct: 1   LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60

Query: 124 NGKRFAGREISV 135
           +GK   GRE+ V
Sbjct: 61  DGKELDGRELRV 72

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

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

 Score = 73.9 bits (181), Expect = 6e-17
 Identities = 39/83 (46%), Positives = 54/83 (65%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           SL VRN+    RPE+LR  F R+G + DVY+P D+YT  PRGFA++QF D  +A +A ++
Sbjct: 2   SLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYN 61

Query: 123 MNGKRFAGREISVVLAAESRKRP 145
           +N K   GR+I +  A   RK P
Sbjct: 62  LNRKWVCGRQIEIQFAQGDRKTP 84

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

>gnl|CDD|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 = 72.6 bits (179), Expect = 2e-16
 Identities = 31/74 (41%), Positives = 37/74 (50%)

Query: 62  GSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQH 121
             L V  +      +EL A F +FG V +V L KD  TGE RGF FV F    +A  A  
Sbjct: 2   NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 122 HMNGKRFAGREISV 135
            +NGK   GR I V
Sbjct: 62  DLNGKELEGRVIKV 75

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

 Score = 71.5 bits (176), Expect = 3e-16
 Identities = 25/60 (41%), Positives = 35/60 (58%)

Query: 76  EELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV 135
           ++LR  FE FG +  V L +D  TG  +G+ F+QF D  +A +A   +NG   AGR I V
Sbjct: 13  DDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLNGFELAGRPIKV 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|240854 cd12408, RRM_eIF3G_like, RNA recognition motif in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins

 Score = 71.0 bits (175), Expect = 5e-16
 Identities = 26/66 (39%), Positives = 36/66 (54%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           ++ V N+  D   ++LR  F  FG +  VYL KD  TG+ RGFAFV F    +A  A   
Sbjct: 1   TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60

Query: 123 MNGKRF 128
           +NG  +
Sbjct: 61  LNGFGY 66

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

 Score = 67.3 bits (165), Expect = 1e-14
 Identities = 31/75 (41%), Positives = 37/75 (49%), Gaps = 8/75 (10%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L VRN+PL    E+LR  F  +G V  V   KDY        AFV F +  +A +A   M
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKDY--------AFVHFEERDDAVKAMEEM 55

Query: 124 NGKRFAGREISVVLA 138
           NGK   G  I V LA
Sbjct: 56  NGKELEGSPIEVSLA 70

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

 Score = 66.9 bits (164), Expect = 1e-14
 Identities = 25/74 (33%), Positives = 42/74 (56%), Gaps = 1/74 (1%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           S+ V N+     PEEL+  F+  G +  + +  D +TG+P+GFA+++F+D   + E    
Sbjct: 1   SIFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDK-SSVENALL 59

Query: 123 MNGKRFAGREISVV 136
           +N   F GR+I V 
Sbjct: 60  LNESEFRGRQIKVT 73

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

 Score = 66.9 bits (164), Expect = 2e-14
 Identities = 29/72 (40%), Positives = 41/72 (56%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L V  +  +   + L A F  FG ++D+ +P DY T + RGFAFV+F +P +AA A  +M
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 124 NGKRFAGREISV 135
           N     GR I V
Sbjct: 61  NESELFGRTIRV 72

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

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

 Score = 65.5 bits (160), Expect = 7e-14
 Identities = 27/70 (38%), Positives = 42/70 (60%)

Query: 62  GSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQH 121
           G L +RN+   C  E+L   F ++G + +V+LP D  T +P+GFAFV ++ P  A +A  
Sbjct: 3   GRLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFA 62

Query: 122 HMNGKRFAGR 131
            ++G  F GR
Sbjct: 63  ELDGTVFQGR 72

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

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

 Score = 64.5 bits (158), Expect = 1e-13
 Identities = 28/70 (40%), Positives = 37/70 (52%), Gaps = 2/70 (2%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L VRN+P     E+LR  F  +G V  V L ++     PRGFAFV+F  P +A  A   +
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRN--KDRPRGFAFVEFASPEDAEAALKKL 58

Query: 124 NGKRFAGREI 133
           NG    GR +
Sbjct: 59  NGLVLDGRTL 68

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

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

 Score = 64.6 bits (158), Expect = 1e-13
 Identities = 25/78 (32%), Positives = 39/78 (50%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           +L VRN+P D   E+L   F   G ++  ++ KD  + + RGF +V F    +A  A   
Sbjct: 1   TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60

Query: 123 MNGKRFAGREISVVLAAE 140
               +F GR+I V  A +
Sbjct: 61  KKKTKFGGRKIHVEFAKK 78

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

 Score = 62.2 bits (152), Expect = 1e-12
 Identities = 28/75 (37%), Positives = 38/75 (50%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L V N+P +   E+L+  F +FG V    +  D  TG  RGF FV+     EA  A   +
Sbjct: 2   LYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEKL 61

Query: 124 NGKRFAGREISVVLA 138
           NG  F GR ++V  A
Sbjct: 62  NGTDFGGRTLTVNEA 76

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 = 61.8 bits (151), Expect = 1e-12
 Identities = 27/71 (38%), Positives = 42/71 (59%), Gaps = 4/71 (5%)

Query: 65  LVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMN 124
           L RN+      + L+  F  +G V+DV LP D     PRG+A+V+F  P +A +A  HM+
Sbjct: 6   LTRNV----NKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHMD 61

Query: 125 GKRFAGREISV 135
           G +  G+E++V
Sbjct: 62  GGQIDGQEVTV 72

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

 Score = 60.3 bits (147), Expect = 6e-12
 Identities = 28/81 (34%), Positives = 40/81 (49%), Gaps = 5/81 (6%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEA-----A 117
           ++ +RN+P D   EEL+  F +FG V+   + KD  TG  +G AFV+F     A     A
Sbjct: 2   TVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEA 61

Query: 118 EAQHHMNGKRFAGREISVVLA 138
                 +G    GR + V LA
Sbjct: 62  ADNAEDSGLSLDGRRLIVTLA 82

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

>gnl|CDD|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 = 59.1 bits (144), Expect = 1e-11
 Identities = 23/64 (35%), Positives = 37/64 (57%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L V  +P     E++RA FE +G + +V + +D  TG+ +G AFV+F    EA +A   +
Sbjct: 2   LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEAL 61

Query: 124 NGKR 127
           +GK 
Sbjct: 62  HGKV 65

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

 Score = 59.0 bits (143), Expect = 1e-11
 Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 1/75 (1%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L V  +P     EEL   F++ GVV+ V L     +G+P+G A+V++ +   A++A   M
Sbjct: 5   LFVSGLPFSVTKEELEKLFKKHGVVKSVRLVT-NRSGKPKGLAYVEYENESSASQAVLKM 63

Query: 124 NGKRFAGREISVVLA 138
           +G     + ISV ++
Sbjct: 64  DGTEIKEKTISVAIS 78

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

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

 Score = 58.8 bits (143), Expect = 2e-11
 Identities = 29/77 (37%), Positives = 40/77 (51%), Gaps = 4/77 (5%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPR---GFAFVQFVDPYEAAEAQ 120
           + VRN+      ++LR  F +FG V  + +PK     + R   GFAFV F D   +AE  
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDA-SSAENA 61

Query: 121 HHMNGKRFAGREISVVL 137
             +NG    GR+ISV L
Sbjct: 62  LQLNGTELGGRKISVSL 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|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 = 58.8 bits (143), Expect = 2e-11
 Identities = 30/68 (44%), Positives = 38/68 (55%), Gaps = 1/68 (1%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L+VRN+P +   +ELR  F  FG V+ V LPK +  G  RGFAFV+FV   EA  A   +
Sbjct: 3   LIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFD-GSHRGFAFVEFVTKQEAQNAMEAL 61

Query: 124 NGKRFAGR 131
                 GR
Sbjct: 62  KSTHLYGR 69

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

 Score = 58.4 bits (142), Expect = 2e-11
 Identities = 25/69 (36%), Positives = 32/69 (46%), Gaps = 8/69 (11%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAA---EAQ 120
           + V  +  D   E+LR  F +FG V DVY+PK +     R FAFV F DP  A       
Sbjct: 3   VFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKPF-----RAFAFVTFADPEVAQSLCGED 57

Query: 121 HHMNGKRFA 129
           H + G    
Sbjct: 58  HIIKGVSVH 66

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

 Score = 58.5 bits (142), Expect = 2e-11
 Identities = 25/75 (33%), Positives = 40/75 (53%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L+V  +P D   EELR+ FE  G +    + +D  TG+  G+ FV +VD  +A +A + +
Sbjct: 3   LIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTL 62

Query: 124 NGKRFAGREISVVLA 138
           NG     + + 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|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 57.4 bits (139), Expect = 5e-11
 Identities = 25/58 (43%), Positives = 32/58 (55%)

Query: 76  EELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREI 133
           E LRA F  FG + D  + KD  TG+ +G+ FV FV   +A  A   MNG+   GR I
Sbjct: 14  ETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSMNGQWLGGRAI 71

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

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

 Score = 57.6 bits (140), Expect = 5e-11
 Identities = 22/70 (31%), Positives = 38/70 (54%), Gaps = 1/70 (1%)

Query: 66  VRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNG 125
           V+N+  D   E+L+  F ++G +    + KD   G+ +GF FV F +   A +A   +NG
Sbjct: 6   VKNLGEDMDDEKLKELFGKYGKITSAKVMKDD-EGKSKGFGFVNFENHEAAQKAVEELNG 64

Query: 126 KRFAGREISV 135
           K   G+++ 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|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 62.6 bits (152), Expect = 6e-11
 Identities = 36/81 (44%), Positives = 44/81 (54%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L V N+  +   +ELR  FE FG + DV L +D  TG  +GF F+QF D  EA EA   M
Sbjct: 189 LYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVM 248

Query: 124 NGKRFAGREISVVLAAESRKR 144
           NG   AGR I V  A +S   
Sbjct: 249 NGFELAGRPIKVGYAQDSTYL 269

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|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 = 57.2 bits (138), Expect = 7e-11
 Identities = 29/80 (36%), Positives = 42/80 (52%)

Query: 62  GSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQH 121
           G L +  +  D   + L   F ++G + +V + KD  T   RGF FV F +P +A +A  
Sbjct: 1   GKLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMM 60

Query: 122 HMNGKRFAGREISVVLAAES 141
            MNGK   GR+I V  A +S
Sbjct: 61  AMNGKSVDGRQIRVDQAGKS 80

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

 Score = 59.6 bits (143), Expect = 3e-10
 Identities = 37/114 (32%), Positives = 55/114 (48%), Gaps = 1/114 (0%)

Query: 55  RRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPY 114
           ++ ++ + +L V N+P D   E+LR  F++FG V+ V L +D  TG+ RGFAFV+F    
Sbjct: 109 QKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEE 168

Query: 115 EAAEAQHHMNGKRFAGREISVVLA-AESRKRPEEMRQRHRFRGGSSYGGPRSSY 167
            A +A   +NGK   GR + V  A   S+ R E               G     
Sbjct: 169 SAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLL 222

Length = 306

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

 Score = 55.2 bits (133), Expect = 4e-10
 Identities = 23/76 (30%), Positives = 36/76 (47%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           +L VRN+      E+L   F     ++   +  D  TGE RG+ FV F    +A EA   
Sbjct: 1   TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK 60

Query: 123 MNGKRFAGREISVVLA 138
           +  K+  GR + + +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|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 = 54.6 bits (132), Expect = 4e-10
 Identities = 29/73 (39%), Positives = 37/73 (50%)

Query: 66  VRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNG 125
           V NIP D   E+L   F   G V    L  D  TG+P+G+ F +F D   AA A  ++NG
Sbjct: 3   VGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLNG 62

Query: 126 KRFAGREISVVLA 138
             F GR + V  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|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant Mei2-like proteins

 Score = 54.2 bits (131), Expect = 6e-10
 Identities = 26/72 (36%), Positives = 37/72 (51%), Gaps = 5/72 (6%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L VRNI  +   EELRA FE+FG +R +     Y   + RGF  V + D   A  A+  +
Sbjct: 4   LFVRNINSNVEDEELRALFEQFGDIRTL-----YTACKHRGFIMVSYYDIRAARRAKRAL 58

Query: 124 NGKRFAGREISV 135
            G    GR++ +
Sbjct: 59  QGTELGGRKLDI 70

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

 Score = 53.8 bits (130), Expect = 7e-10
 Identities = 25/72 (34%), Positives = 37/72 (51%), Gaps = 8/72 (11%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L V N+P     EELRA FE++G V +  + K+Y         FV   +  +A +A   +
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTVTECDVVKNY--------GFVHMEEEEDAEDAIKAL 53

Query: 124 NGKRFAGREISV 135
           NG  F G+ I+V
Sbjct: 54  NGYEFMGKRINV 65

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

 Score = 54.2 bits (131), Expect = 7e-10
 Identities = 24/72 (33%), Positives = 40/72 (55%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L V N+PL+   E+ R     FG V   +L     TGE +G+ FV++     A +A++ +
Sbjct: 2   LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61

Query: 124 NGKRFAGREISV 135
           +GK+  GR++ V
Sbjct: 62  DGKQIGGRKLQV 73

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

 Score = 54.2 bits (131), Expect = 7e-10
 Identities = 24/75 (32%), Positives = 36/75 (48%), Gaps = 1/75 (1%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           + V  +P     + LR  F +FG + +  +  D  TG+ RG+ FV F D  E+AE     
Sbjct: 3   IFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKD-KESAERACKD 61

Query: 124 NGKRFAGREISVVLA 138
                 GR+ +V LA
Sbjct: 62  PNPIIDGRKANVNLA 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|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins

 Score = 54.2 bits (131), Expect = 7e-10
 Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 5/73 (6%)

Query: 66  VRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNG 125
           V N+       EL   FE++G +R V++ ++     P GFAFV+F DP +A +A   ++G
Sbjct: 4   VGNLGPRATKRELEDEFEKYGPLRSVWVARN-----PPGFAFVEFEDPRDAEDAVRALDG 58

Query: 126 KRFAGREISVVLA 138
           +R  G  + V L+
Sbjct: 59  RRICGNRVRVELS 71

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

 Score = 54.2 bits (131), Expect = 8e-10
 Identities = 24/72 (33%), Positives = 35/72 (48%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           + V N+P D     L   F  FG V +V + +D  T + +G+ FV   +  EA  A   +
Sbjct: 4   IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIASL 63

Query: 124 NGKRFAGREISV 135
           NG R  GR + V
Sbjct: 64  NGYRLGGRVLQV 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|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 = 53.8 bits (130), Expect = 1e-09
 Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 2/73 (2%)

Query: 64  LLVRNIPLDCRPEELRAPFERF-GVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           L+V+N+P      EL+  F +  G + DV L +    G+ R  AF+ +    EA +A+ +
Sbjct: 3   LIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTE-DGKSRRIAFIGYKTEEEAQKAKDY 61

Query: 123 MNGKRFAGREISV 135
            N       +ISV
Sbjct: 62  FNNTYINTSKISV 74

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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 52.9 bits (128), Expect = 1e-09
 Identities = 20/54 (37%), Positives = 26/54 (48%), Gaps = 5/54 (9%)

Query: 82  FERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV 135
           F  FG V  + L K        GFAFV+F     A +A  ++NG  F GR + V
Sbjct: 5   FSPFGNVEKIKLLKKK-----PGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRV 53

(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|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 53.2 bits (128), Expect = 2e-09
 Identities = 30/71 (42%), Positives = 39/71 (54%), Gaps = 7/71 (9%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDY-YTGEPRGFAFVQFVDPYEAAEA--- 119
           +LVRNIP +   +ELR  F  FG ++ V LPK    TG  RGF FV F+   +A  A   
Sbjct: 3   ILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFKA 62

Query: 120 -QH--HMNGKR 127
             H  H+ G+R
Sbjct: 63  LCHSTHLYGRR 73

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|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 = 53.3 bits (129), Expect = 2e-09
 Identities = 18/64 (28%), Positives = 32/64 (50%), Gaps = 3/64 (4%)

Query: 76  EELRAPFERFGVVRDVYLPKDYYTGEP---RGFAFVQFVDPYEAAEAQHHMNGKRFAGRE 132
           E+++    ++G V  V +P+    G      G  FV+F D  +A +AQ  + G++F GR 
Sbjct: 26  EDVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKAQLALAGRKFDGRT 85

Query: 133 ISVV 136
           +   
Sbjct: 86  VVAS 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|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 = 52.8 bits (127), Expect = 3e-09
 Identities = 22/71 (30%), Positives = 40/71 (56%)

Query: 57  KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEA 116
           K+ +   L V  IP +   ++LR  FE+FG + ++ + KD YTG  +G AF+ +     A
Sbjct: 1   KDDDAIKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESA 60

Query: 117 AEAQHHMNGKR 127
            +AQ  ++ ++
Sbjct: 61  LKAQSALHEQK 71

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

 Score = 52.2 bits (125), Expect = 3e-09
 Identities = 28/74 (37%), Positives = 34/74 (45%), Gaps = 8/74 (10%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           + V N+   C  +ELR  FE FG V +    KDY        AFV      EA  A   +
Sbjct: 3   IFVGNVSATCTSDELRGLFEEFGRVVECDKVKDY--------AFVHMEREEEALAAIEAL 54

Query: 124 NGKRFAGREISVVL 137
           NGK   GR I+V L
Sbjct: 55  NGKEVKGRRINVEL 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|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 52.3 bits (126), Expect = 3e-09
 Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 5/74 (6%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYT--GEPRGFAFVQFVDPYEAAEAQH 121
           L+V+N+P   + ++LR  FE FG + DV L    YT  G+ R F FV +    EA +A  
Sbjct: 3   LIVKNLPKGIKEDKLRKLFEAFGTITDVQLK---YTKDGKFRKFGFVGYKTEEEAQKALK 59

Query: 122 HMNGKRFAGREISV 135
           H N       +I+V
Sbjct: 60  HFNNSFIDTSKITV 73

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

 Score = 52.3 bits (126), Expect = 4e-09
 Identities = 26/78 (33%), Positives = 38/78 (48%), Gaps = 2/78 (2%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           +L V N+      ++L   F+  G V DV + +D   G  +GF  V+F     A +A   
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDD-DGRSKGFGHVEFATEEGAQKAL-E 58

Query: 123 MNGKRFAGREISVVLAAE 140
            +G+   GREI V LA E
Sbjct: 59  KSGEELLGREIRVDLATE 76

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

 Score = 52.0 bits (125), Expect = 4e-09
 Identities = 23/70 (32%), Positives = 35/70 (50%)

Query: 66  VRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNG 125
           V +I  +   + +R  F  FG ++ + +  D  T + +GFAFV++  P  A  A   MNG
Sbjct: 5   VGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQMNG 64

Query: 126 KRFAGREISV 135
               GR I 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|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 52.3 bits (126), Expect = 4e-09
 Identities = 24/65 (36%), Positives = 37/65 (56%), Gaps = 2/65 (3%)

Query: 76  EELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGRE--I 133
           ++LR  F  FG ++D+++ KD  T E +G A+V+F     AA A   MNGK   G    +
Sbjct: 17  DDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLGGDTKPL 76

Query: 134 SVVLA 138
            V++A
Sbjct: 77  KVLIA 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|241095 cd12651, RRM2_SXL, RNA recognition motif 2 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 51.4 bits (123), Expect = 7e-09
 Identities = 29/78 (37%), Positives = 39/78 (50%), Gaps = 2/78 (2%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           +L V N+P     +ELR  FE +G +    L +D  TG PRG AFV++    EA  A   
Sbjct: 2   NLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISS 61

Query: 123 MNGKRFAGRE--ISVVLA 138
           +NG    G    +SV  A
Sbjct: 62  LNGTIPPGSTMPLSVRYA 79

This subfamily corresponds to the RRM2 of the sex-lethal protein (SXL) which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

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

 Score = 51.2 bits (123), Expect = 7e-09
 Identities = 25/72 (34%), Positives = 34/72 (47%), Gaps = 1/72 (1%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           + V  +P D   EE +  F +FG V D  L +D+ TG  RGF FV F D   A E     
Sbjct: 2   IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTF-DSESAVERVFSA 60

Query: 124 NGKRFAGREISV 135
                 G+++ V
Sbjct: 61  GMLELGGKQVEV 72

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

 Score = 51.4 bits (124), Expect = 8e-09
 Identities = 21/72 (29%), Positives = 39/72 (54%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           + V  +  + + E++   F  FG +++++L  D  TG  +G+A +++    EA  A   +
Sbjct: 9   IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 124 NGKRFAGREISV 135
           NGK   G+ ISV
Sbjct: 69  NGKELLGQTISV 80

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

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

 Score = 51.0 bits (123), Expect = 9e-09
 Identities = 21/56 (37%), Positives = 28/56 (50%), Gaps = 4/56 (7%)

Query: 76  EELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEA----QHHMNGKR 127
           E LR  F ++G V D  + KD  TG  RGF FV F DP    +      H ++G+ 
Sbjct: 13  ESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAKPHVLDGRE 68

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

 Score = 51.0 bits (122), Expect = 1e-08
 Identities = 26/78 (33%), Positives = 41/78 (52%), Gaps = 2/78 (2%)

Query: 64  LLVRNIPLDCR-PEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           L++RN+P   + P +L+  F R+G VR+  +P+    G+  GFAFV       A  A  +
Sbjct: 3   LIIRNLPWSIKKPVKLKKIFGRYGKVREATIPRKR-GGKLCGFAFVTMKKRKNAEIALEN 61

Query: 123 MNGKRFAGREISVVLAAE 140
            NG    GR ++V  A +
Sbjct: 62  TNGLEIDGRPVAVDWAVQ 79

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

 Score = 50.9 bits (121), Expect = 1e-08
 Identities = 26/81 (32%), Positives = 44/81 (54%)

Query: 58  EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAA 117
           E +  +L+V  +P +   EEL++ F   G +    L +D  TG+  G+ FV ++DP +A 
Sbjct: 1   EDSKTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAE 60

Query: 118 EAQHHMNGKRFAGREISVVLA 138
           +A + +NG R   + I V  A
Sbjct: 61  KAINTLNGLRLQTKTIKVSYA 81

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

 Score = 50.3 bits (121), Expect = 2e-08
 Identities = 29/74 (39%), Positives = 40/74 (54%), Gaps = 4/74 (5%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L VRN+P     EEL   F ++G +R + +     T E RG AFV + D Y+A  A  H+
Sbjct: 5   LYVRNLPFKISSEELYDLFGKYGAIRQIRIGN---TKETRGTAFVVYEDIYDAKNACDHL 61

Query: 124 NGKRFAGREISVVL 137
           +G   A R + VVL
Sbjct: 62  SGFNVANRYL-VVL 74

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

 Score = 50.3 bits (121), Expect = 2e-08
 Identities = 21/70 (30%), Positives = 32/70 (45%)

Query: 66  VRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNG 125
           + ++P      ELR  F +FG V  + L +   TG+ +G+AFV+F  P  A      MN 
Sbjct: 4   IGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETMNN 63

Query: 126 KRFAGREISV 135
                R +  
Sbjct: 64  YLLFERLLKC 73

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

 Score = 54.8 bits (132), Expect = 2e-08
 Identities = 55/250 (22%), Positives = 87/250 (34%), Gaps = 36/250 (14%)

Query: 56  RKEQNHGS-LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPY 114
           RK +  G  L V+N+      E+LR  F   G +    +  D   G  RGF FV F +P 
Sbjct: 279 RKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDE-KGVSRGFGFVCFSNPE 337

Query: 115 EAAEAQHHMNGKRFAGREISVVLAA--ESRK-RPEEMRQRHRFRG-GSSYGGPRSSYYGR 170
           EA  A   M+G+   G+ + V LA   E R+   ++   + + R      G P     G 
Sbjct: 338 EANRAVTEMHGRMLGGKPLYVALAQRKEQRRAHLQDQFMQLQPRMRQLPMGSPMGGAMG- 396

Query: 171 YRSRSLSRSRSPHHPQGSRSRYRSRSYTPVPRQHEDYSISPRRRHIEHPGSPRGPPQERG 230
                    + P++ QG + ++  +     P         PR   +  P  P GP +  G
Sbjct: 397 ---------QPPYYGQGPQQQFNGQ-----PLGW------PRMSMMPTPMGPGGPLRPNG 436

Query: 231 AEYSRRSYSPGYDDSADRRN----PNGNGYGEKSGYEETQAHWRSP-PPRGVSRSPSGSR 285
                   +     S + +N    P          Y+        P P    S+     +
Sbjct: 437 L----APMNAVRAPSRNAQNAAQKPPMQPVMYPPNYQSLPLSQDLPQPQSTASQGGQNKK 492

Query: 286 SRSRSADLSP 295
                A  +P
Sbjct: 493 LAQVLASATP 502

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

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

 Score = 50.1 bits (120), Expect = 2e-08
 Identities = 26/63 (41%), Positives = 35/63 (55%)

Query: 76  EELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV 135
           E L+A FE+FG V    +  D  TG  RGF +V F  P +A +A   M+GK   GR I+V
Sbjct: 14  EWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEAMDGKELDGRPINV 73

Query: 136 VLA 138
             +
Sbjct: 74  DFS 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|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 50.7 bits (121), Expect = 3e-08
 Identities = 24/74 (32%), Positives = 30/74 (40%), Gaps = 3/74 (4%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           +L VRN+P D   E L   F +FG VR      D  TG  +G  FV F D Y        
Sbjct: 3   TLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNAC--- 59

Query: 123 MNGKRFAGREISVV 136
           +     AG    + 
Sbjct: 60  LKNAPAAGSTSLLS 73

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

 Score = 50.0 bits (120), Expect = 3e-08
 Identities = 22/73 (30%), Positives = 36/73 (49%)

Query: 66  VRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNG 125
           V N+P      +L   F ++G V  V + KD  T + +G AF+ F+D  +A +    +N 
Sbjct: 6   VSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKALNN 65

Query: 126 KRFAGREISVVLA 138
           K   GR +   +A
Sbjct: 66  KELFGRTLKCSIA 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|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 49.8 bits (119), Expect = 3e-08
 Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 62  GSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQH 121
             +LV+N+P +   +++R  F  +G ++ V +PK +     RGFAFV+F    EA  A +
Sbjct: 1   TKILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKF-DQSARGFAFVEFSTAKEALNAMN 59

Query: 122 HMNGKRFAGREI 133
            +      GR +
Sbjct: 60  ALKDTHLLGRRL 71

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

 Score = 49.7 bits (119), Expect = 3e-08
 Identities = 24/67 (35%), Positives = 35/67 (52%), Gaps = 4/67 (5%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAE---AQ 120
           L+V  +P     ++L+  F  FG +  V + KD  TG+ +GF FV+F D YE      +Q
Sbjct: 2   LIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFAD-YEDQVKVLSQ 60

Query: 121 HHMNGKR 127
            HM   R
Sbjct: 61  RHMIDGR 67

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|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 = 3e-08
 Identities = 23/53 (43%), Positives = 33/53 (62%), Gaps = 3/53 (5%)

Query: 78  LRAPFERFGVVR--DVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRF 128
           LR  F +FGV +   +Y+P D  TG+ +G+AFV+F  P EA EA   +NG + 
Sbjct: 24  LRKIFSKFGVGKIVGIYMPVDE-TGKTKGYAFVEFATPEEAKEAVKALNGYKL 75

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

 Score = 49.5 bits (119), Expect = 3e-08
 Identities = 27/75 (36%), Positives = 36/75 (48%), Gaps = 1/75 (1%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L V+N+      E LR  F  FG +    +  D   G  +GF FV F  P EA +A   M
Sbjct: 4   LYVKNLDDSIDDERLREEFSPFGTITSAKVMTDE-KGRSKGFGFVCFSSPEEATKAVTEM 62

Query: 124 NGKRFAGREISVVLA 138
           NG+   G+ + V LA
Sbjct: 63  NGRIIGGKPLYVALA 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|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins

 Score = 49.9 bits (120), Expect = 4e-08
 Identities = 24/72 (33%), Positives = 40/72 (55%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L V  +  D    +LR  FE +G ++ + L +D  TG+PRG+AF++F    +   A  + 
Sbjct: 4   LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYA 63

Query: 124 NGKRFAGREISV 135
           +GK+  GR + V
Sbjct: 64  DGKKIDGRRVLV 75

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

 Score = 49.5 bits (119), Expect = 4e-08
 Identities = 24/60 (40%), Positives = 31/60 (51%)

Query: 76  EELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV 135
            +LR  F R+G +  V +  D  TG  RGF FV F    +A EA+  +NG    GR I V
Sbjct: 14  RDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEIDGRRIRV 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|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 49.3 bits (117), Expect = 4e-08
 Identities = 29/75 (38%), Positives = 33/75 (44%), Gaps = 8/75 (10%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L VRN+      E L   F  FG +  V   KDY        AFV F +   A  A   M
Sbjct: 4   LFVRNLATTVTEEILEKSFSEFGKLERVKKLKDY--------AFVHFEERDAAVRAMDEM 55

Query: 124 NGKRFAGREISVVLA 138
           NGK   G EI +VLA
Sbjct: 56  NGKEIEGEEIEIVLA 70

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

 Score = 49.3 bits (118), Expect = 4e-08
 Identities = 25/75 (33%), Positives = 41/75 (54%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L+V  +P +   +E+R+ F   G +    L +D  TG+  G+ FV +VDP +A +A + +
Sbjct: 4   LIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTL 63

Query: 124 NGKRFAGREISVVLA 138
           NG R   + I 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 = 49.3 bits (117), Expect = 4e-08
 Identities = 26/79 (32%), Positives = 42/79 (53%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           +L+V  +P +   EE R+ F   G +    L +D  TG+  G+ FV ++DP +A +A + 
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 123 MNGKRFAGREISVVLAAES 141
           +NG R   + I V  A  S
Sbjct: 64  LNGLRLQTKTIKVSYARPS 82

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

 Score = 48.6 bits (116), Expect = 5e-08
 Identities = 20/74 (27%), Positives = 30/74 (40%), Gaps = 8/74 (10%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L VR  P D     +R  F  +G V++V +           FAFV+F     A  A+  +
Sbjct: 2   LYVRPFPPDTSESAIREIFSPYGAVKEVKMIS--------NFAFVEFESLESAIRAKDSV 53

Query: 124 NGKRFAGREISVVL 137
           +GK      + V  
Sbjct: 54  HGKVLNNNPLYVTY 67

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

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

 Score = 48.9 bits (116), Expect = 6e-08
 Identities = 23/73 (31%), Positives = 40/73 (54%)

Query: 61  HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQ 120
           H  + V ++  +   E++++ F  FG + D  + KD  TG+ +G+ FV F +  +A  A 
Sbjct: 1   HFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAI 60

Query: 121 HHMNGKRFAGREI 133
            HM G+   GR+I
Sbjct: 61  VHMGGQWLGGRQI 73

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|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 = 48.8 bits (117), Expect = 7e-08
 Identities = 18/72 (25%), Positives = 39/72 (54%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           + +  +P     ++++   E FG ++   L KD  TG  +G+AF +++DP    +A   +
Sbjct: 3   IFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAGL 62

Query: 124 NGKRFAGREISV 135
           NG +   ++++V
Sbjct: 63  NGMQLGDKKLTV 74

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

 Score = 48.6 bits (116), Expect = 7e-08
 Identities = 25/72 (34%), Positives = 37/72 (51%), Gaps = 2/72 (2%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L V NIP   R  +LR  F +FG + DV +   +     +GF FV F +  +A  A+  +
Sbjct: 3   LHVSNIPFRFRDPDLRQMFGQFGPILDVEII--FNERGSKGFGFVTFANSADADRAREKL 60

Query: 124 NGKRFAGREISV 135
           +G    GR+I V
Sbjct: 61  HGTVVEGRKIEV 72

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

 Score = 48.6 bits (116), Expect = 8e-08
 Identities = 28/81 (34%), Positives = 41/81 (50%), Gaps = 8/81 (9%)

Query: 66  VRNIPLDCRPEELRAPFERFGVVR--------DVYLPKDYYTGEPRGFAFVQFVDPYEAA 117
           V N+P +   ++L   F   G+++         ++L KD  TGEP+G A V + DP+ A+
Sbjct: 3   VSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPHAAS 62

Query: 118 EAQHHMNGKRFAGREISVVLA 138
            A    N K F G  I V LA
Sbjct: 63  AAIEWFNNKDFMGNTIKVSLA 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|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 48.4 bits (116), Expect = 8e-08
 Identities = 23/57 (40%), Positives = 31/57 (54%), Gaps = 6/57 (10%)

Query: 76  EELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEA-----QHHMNGKR 127
           E+LR  F ++G V  V +  D  TG+ RGFAFV F D Y+  +       H +NG R
Sbjct: 14  EDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDD-YDPVDKIVLQKYHTINGHR 69

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

 Score = 48.5 bits (116), Expect = 9e-08
 Identities = 24/61 (39%), Positives = 38/61 (62%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           + V  +P +   E L+A F ++G V  V LP+  +TG+ +GFAF++F  P EA +A  H+
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61

Query: 124 N 124
           N
Sbjct: 62  N 62

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

 Score = 48.1 bits (115), Expect = 1e-07
 Identities = 22/60 (36%), Positives = 34/60 (56%), Gaps = 3/60 (5%)

Query: 78  LRAPFERFGV-VRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQ-HHMNGKRFAGREISV 135
           L   F  FGV ++   + +D  TG  +GFAF+ + D +EA++A    MNG+    R I+V
Sbjct: 18  LYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISY-DSFEASDAAIEAMNGQYLCNRPITV 76

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

 Score = 47.9 bits (115), Expect = 1e-07
 Identities = 27/73 (36%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           S+ V N+P D   EELR  FE  G V  V + +D  TG  +GF +V F    ++      
Sbjct: 1   SVFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTK-DSVALALK 59

Query: 123 MNGKRFAGREISV 135
           +NG +  GR+I V
Sbjct: 60  LNGIKLKGRKIRV 72

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

 Score = 47.9 bits (115), Expect = 1e-07
 Identities = 23/77 (29%), Positives = 35/77 (45%), Gaps = 5/77 (6%)

Query: 64  LLVRNIPLDCRPEELRAPFERFG--VVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEA-Q 120
           L++R + L    E++           ++DV L +D  TG  RGFAFV+F    +A +   
Sbjct: 5   LILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMD 64

Query: 121 HHMNGKRFA--GREISV 135
              N   F   GR + V
Sbjct: 65  ALNNLDPFVIDGRVVRV 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|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4; Provisional

 Score = 49.7 bits (118), Expect = 1e-07
 Identities = 33/86 (38%), Positives = 37/86 (43%), Gaps = 1/86 (1%)

Query: 78  LRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL 137
           LR  F  FG V D  +  D  TG  RGF FV F D   A  A   M+GK   GR I V  
Sbjct: 51  LRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNP 110

Query: 138 AAESRKRPEEMRQRHRFR-GGSSYGG 162
           A +    P        +  GG  YGG
Sbjct: 111 ANDRPSAPRAYGGGGGYSGGGGGYGG 136

Length = 144

>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 = 47.5 bits (113), Expect = 2e-07
 Identities = 24/70 (34%), Positives = 36/70 (51%)

Query: 66  VRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNG 125
           V NIP +   E+L+  F   G V    L  D  TG+P+G+ F ++ D   A  A  ++NG
Sbjct: 3   VGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNLNG 62

Query: 126 KRFAGREISV 135
               GR++ V
Sbjct: 63  YELNGRQLRV 72

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|240869 cd12423, RRM3_PTBP1_like, RNA recognition motif 3 in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins

 Score = 47.3 bits (113), Expect = 2e-07
 Identities = 27/77 (35%), Positives = 37/77 (48%), Gaps = 10/77 (12%)

Query: 64  LLVRNIPLDCRPEELRAP---FERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQ 120
           LLV N+      EE+  P   F  FGV  DV   K  +    +  A +Q  DP +A  A 
Sbjct: 2   LLVSNLN-----EEMVTPDALFTLFGVYGDVVRVKILF--NKKDTALIQMADPQQAQTAL 54

Query: 121 HHMNGKRFAGREISVVL 137
            H+NG R  G+++ V L
Sbjct: 55  THLNGIRLHGKKLRVTL 71

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

 Score = 46.8 bits (112), Expect = 2e-07
 Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 9/73 (12%)

Query: 64  LLVRNIPLD-CRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           + V N+  D    E+L   F ++G +  + L K        G+ FVQF +  +A  A   
Sbjct: 3   VFVGNLNTDKVSKEDLEEIFSKYGKILGISLHK--------GYGFVQFDNEEDARAAVAG 54

Query: 123 MNGKRFAGREISV 135
            NG+  AG+++ +
Sbjct: 55  ENGREIAGQKLDI 67

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|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 47.0 bits (112), Expect = 3e-07
 Identities = 22/51 (43%), Positives = 30/51 (58%)

Query: 69  IPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEA 119
           IP     E+LR  F+ FG +  V + KD  TGE +GF +V+F  P +AA A
Sbjct: 8   IPKSYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVA 58

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|240728 cd12282, RRM2_TatSF1_like, RNA recognition motif 2 in HIV Tat-specific factor 1 (Tat-SF1) and similar proteins

 Score = 47.2 bits (113), Expect = 3e-07
 Identities = 21/60 (35%), Positives = 33/60 (55%), Gaps = 4/60 (6%)

Query: 76  EELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV 135
           ++LR   E+FG V+ V +    +   P G A V+F +P EA      +NG+ FAGR++  
Sbjct: 27  DDLREECEKFGQVKKVVV----FDRHPDGVASVKFKEPEEADRCIEALNGRWFAGRQLEA 82

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

 Score = 46.9 bits (112), Expect = 3e-07
 Identities = 25/75 (33%), Positives = 36/75 (48%), Gaps = 7/75 (9%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFV--DPYEAAE-AQ 120
           L V N+P     +EL+  F +FG V+   +P D  TG  +G+ FV F   D  E A   Q
Sbjct: 2   LFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQKQ 61

Query: 121 HHMNGKRFAGREISV 135
            H+      G ++ V
Sbjct: 62  KHI----LEGNKLQV 72

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

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

 Score = 46.7 bits (111), Expect = 3e-07
 Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 1/75 (1%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           S+ V N+      EEL A F   G V  V +  D ++G P+GFA+++F D  E+      
Sbjct: 1   SVYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDK-ESVRTALA 59

Query: 123 MNGKRFAGREISVVL 137
           ++   F GR+I V+ 
Sbjct: 60  LDESLFRGRQIKVMP 74

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

 Score = 46.7 bits (111), Expect = 3e-07
 Identities = 23/72 (31%), Positives = 32/72 (44%), Gaps = 8/72 (11%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           + V N+  D   EELRA FE +G V    + +         FAFV       A  A   +
Sbjct: 3   IFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQ--------FAFVHLRGEAAADRAIEEL 54

Query: 124 NGKRFAGREISV 135
           NG+   GR++ V
Sbjct: 55  NGRELHGRKLVV 66

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

 Score = 46.4 bits (111), Expect = 3e-07
 Identities = 18/50 (36%), Positives = 28/50 (56%)

Query: 86  GVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV 135
           G V +V++PKD  T   +G+ FV+F+   +A  A   MN  +  G+ I V
Sbjct: 23  GPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIMNMIKLYGKPIRV 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|240996 cd12552, RRM_Nop15p, RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins

 Score = 46.3 bits (110), Expect = 4e-07
 Identities = 21/72 (29%), Positives = 39/72 (54%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           + + ++P     +EL+  F +FG V++V + +   TG  + + F+QF++P  AA A   M
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 124 NGKRFAGREISV 135
           N     G+ + V
Sbjct: 62  NNYLLMGKVLQV 73

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

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

 Score = 46.2 bits (109), Expect = 6e-07
 Identities = 22/73 (30%), Positives = 40/73 (54%)

Query: 61  HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQ 120
           H  + V ++  +   ++++A F  FG + D  + KD  TG+ +G+ FV F + ++A  A 
Sbjct: 1   HFHVFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAI 60

Query: 121 HHMNGKRFAGREI 133
             M G+   GR+I
Sbjct: 61  QQMGGQWLGGRQI 73

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|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 = 45.7 bits (109), Expect = 6e-07
 Identities = 24/65 (36%), Positives = 36/65 (55%), Gaps = 6/65 (9%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           +LV+N+P     EELR  FE+FG +  + LP        R  A V+F++P +A +A   +
Sbjct: 3   ILVKNLPFGTTEEELRELFEKFGSLGRLLLPPS------RTIALVEFLEPSDARKAFKSL 56

Query: 124 NGKRF 128
             KRF
Sbjct: 57  AYKRF 61

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

 Score = 45.8 bits (109), Expect = 7e-07
 Identities = 21/70 (30%), Positives = 32/70 (45%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L V N+  D   + +   F  +G +  V LP D  +G P+GF +V+F     A  A   +
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 124 NGKRFAGREI 133
            G    GR +
Sbjct: 61  GGTDLLGRPV 70

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

 Score = 45.8 bits (109), Expect = 7e-07
 Identities = 28/74 (37%), Positives = 36/74 (48%), Gaps = 5/74 (6%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDP--YEAAEAQH 121
           L V N+P D   E+L A F+  G    V L  D  TG+ +G AFV+F        A   H
Sbjct: 3   LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLH 62

Query: 122 HMNGKRFAGREISV 135
           H   K   GR+I+V
Sbjct: 63  HTLLK---GRKINV 73

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

 Score = 45.3 bits (107), Expect = 1e-06
 Identities = 20/54 (37%), Positives = 29/54 (53%), Gaps = 3/54 (5%)

Query: 76  EELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPY---EAAEAQHHMNGK 126
           + LR  F +FG V D  + +D  TG  RGF F+ F  P    E  + +H ++GK
Sbjct: 13  DSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKEHILDGK 66

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

 Score = 44.8 bits (107), Expect = 1e-06
 Identities = 21/72 (29%), Positives = 35/72 (48%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L V N+      E++   F R G ++ + +  D +T  P GF FV++    +A  A  ++
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60

Query: 124 NGKRFAGREISV 135
           NG +   R I V
Sbjct: 61  NGTKLDDRIIRV 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|240723 cd12277, RRM3_MEI2_EAR1_like, RNA recognition motif 3 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 45.3 bits (108), Expect = 1e-06
 Identities = 22/68 (32%), Positives = 34/68 (50%), Gaps = 3/68 (4%)

Query: 64  LLVRNIPLDCRPEELRAPFER--FGVVRD-VYLPKDYYTGEPRGFAFVQFVDPYEAAEAQ 120
           +++RNIP     E L    +    G   D +YLP D+      G+AF+ FV+P  A +  
Sbjct: 1   VMIRNIPNKYTQEMLLQLLDEHGKGGAYDFLYLPIDFKNKCNVGYAFINFVNPEYAEKFY 60

Query: 121 HHMNGKRF 128
              NGK++
Sbjct: 61  KAFNGKKW 68

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

 Score = 44.9 bits (107), Expect = 1e-06
 Identities = 25/75 (33%), Positives = 37/75 (49%), Gaps = 1/75 (1%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           ++V+N+P     + LR  FE  G V DV + +    G+ R F FV F    +A +A  + 
Sbjct: 3   IIVKNLPKYVTEDRLREHFESKGEVTDVKVMRT-RDGKSRRFGFVGFKSEEDAQQAVKYF 61

Query: 124 NGKRFAGREISVVLA 138
           N       +ISV LA
Sbjct: 62  NKTFIDTSKISVELA 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|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 48.8 bits (116), Expect = 1e-06
 Identities = 26/79 (32%), Positives = 41/79 (51%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           +L+V  +P     EE+R+ F   G +    L +D  TG+  G+ FV +V P +A +A + 
Sbjct: 5   NLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNS 64

Query: 123 MNGKRFAGREISVVLAAES 141
           +NG R   + I V  A  S
Sbjct: 65  LNGLRLQNKTIKVSYARPS 83

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

 Score = 48.3 bits (115), Expect = 2e-06
 Identities = 30/100 (30%), Positives = 46/100 (46%), Gaps = 4/100 (4%)

Query: 57  KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEA 116
             +   +L V+N+      ++LR  F +FG +    + KD  +G  RGFAFV F    +A
Sbjct: 174 PLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDG-SGRSRGFAFVNFEKHEDA 232

Query: 117 AEAQHHMNGKRFAGREISVVLA---AESRKRPEEMRQRHR 153
           A+A   MNGK+    +    L    A+ R   E   +R  
Sbjct: 233 AKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKF 272

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

 Score = 45.0 bits (107), Expect = 2e-06
 Identities = 20/73 (27%), Positives = 40/73 (54%)

Query: 66  VRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNG 125
           V ++  D   +++++ FE FG ++   L  D  TG+ +G+ F+++ +P  A +A   MN 
Sbjct: 5   VASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASMNL 64

Query: 126 KRFAGREISVVLA 138
               G+++ V  A
Sbjct: 65  FDLGGQQLRVGKA 77

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

>gnl|CDD|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 = 44.5 bits (106), Expect = 2e-06
 Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 6/69 (8%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           ++ V N+P     EEL+  F  FG + +V + KD      +G+AFV+F     AA A   
Sbjct: 2   TVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD------KGYAFVRFDTHEAAATAIVA 55

Query: 123 MNGKRFAGR 131
           +NG    G+
Sbjct: 56  VNGTSINGQ 64

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

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

 Score = 44.6 bits (106), Expect = 2e-06
 Identities = 24/79 (30%), Positives = 34/79 (43%), Gaps = 7/79 (8%)

Query: 66  VRNIPLDCRPEELRAPFERFGVV---RDVYLPKDY-YT---GEPRGFAFVQFVDPYEAAE 118
           +  +P D   + L   F   G++   +  + P    YT    EP+G A V + DP  A  
Sbjct: 3   ISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKETEPKGEATVTYDDPSAAQA 62

Query: 119 AQHHMNGKRFAGREISVVL 137
           A    NG  F G +I V L
Sbjct: 63  AIEWFNGYEFRGNKIKVSL 81

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

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

 Score = 44.7 bits (106), Expect = 2e-06
 Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 7/73 (9%)

Query: 69  IPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRF 128
           +P +    +LR  F +FG V +V +  D+    PRGF F+ F    E+ ++   +  + F
Sbjct: 10  LPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITF----ESEDSVDQVVNEHF 65

Query: 129 ---AGREISVVLA 138
               G+++ V  A
Sbjct: 66  HDINGKKVEVKRA 78

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|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 = 44.2 bits (105), Expect = 2e-06
 Identities = 21/72 (29%), Positives = 35/72 (48%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L + ++P +   ++L   F  FG V    +  D  TG+ + F FV + +P  A  A   M
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 124 NGKRFAGREISV 135
           NG +  G+ + V
Sbjct: 61  NGFQVGGKRLKV 72

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

 Score = 44.4 bits (106), Expect = 2e-06
 Identities = 23/77 (29%), Positives = 36/77 (46%), Gaps = 7/77 (9%)

Query: 63  SLLVRNIPLDCRPEELR----APFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAE 118
           +L + N+    + +EL+    A F +FG V D+   K   T + RG AFV F D   A  
Sbjct: 1   TLYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASK---TLKMRGQAFVVFKDVESATN 57

Query: 119 AQHHMNGKRFAGREISV 135
           A   + G  F  + + +
Sbjct: 58  ALRALQGFPFYDKPMRI 74

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

 Score = 44.3 bits (104), Expect = 2e-06
 Identities = 25/79 (31%), Positives = 39/79 (49%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           +L+V  +P +   +ELR+ F   G V    L +D   G   G+ FV +V+  +A  A + 
Sbjct: 3   NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINT 62

Query: 123 MNGKRFAGREISVVLAAES 141
           +NG R   + I V  A  S
Sbjct: 63  LNGLRLQSKTIKVSYARPS 81

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

 Score = 44.3 bits (104), Expect = 3e-06
 Identities = 25/79 (31%), Positives = 42/79 (53%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           +L+V  +P +   EE ++ F   G +    L +D  TG+  G+ FV +VDP +A +A + 
Sbjct: 5   NLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINT 64

Query: 123 MNGKRFAGREISVVLAAES 141
           +NG +   + I V  A  S
Sbjct: 65  LNGLKLQTKTIKVSYARPS 83

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

 Score = 44.2 bits (105), Expect = 3e-06
 Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 5/75 (6%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           ++ V+N+P D    ++R  F+  G +R+V + +     E    A ++F    EA  A   
Sbjct: 2   TVKVKNLPKDTTENKIRQFFKDCGEIREVKIVES----EGGLVAVIEFETEDEALAALTK 57

Query: 123 MNGKRFAGREISVVL 137
            + KR  G EISV  
Sbjct: 58  -DHKRLGGNEISVSR 71

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|241105 cd12661, RRM3_hnRNPM, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 44.2 bits (104), Expect = 3e-06
 Identities = 25/72 (34%), Positives = 34/72 (47%), Gaps = 2/72 (2%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           + VRN+P D   + L+  F   G V  +Y       G+ +G   V+F  P  A  A   M
Sbjct: 2   IFVRNLPFDFTWKMLKDKFNECGHV--LYADIKMENGKSKGCGVVRFESPEVAERACRMM 59

Query: 124 NGKRFAGREISV 135
           NG +  GREI V
Sbjct: 60  NGYKLNGREIDV 71

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

 Score = 44.2 bits (105), Expect = 3e-06
 Identities = 22/55 (40%), Positives = 28/55 (50%), Gaps = 1/55 (1%)

Query: 66  VRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQ 120
           V  IP D   EELR  F RFG V+DV +  D   G  +G+ FV F    +A +  
Sbjct: 7   VGGIPPDTTEEELRDFFSRFGSVKDVKIITD-RAGVSKGYGFVTFETQEDAEKIL 60

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

 Score = 44.2 bits (104), Expect = 3e-06
 Identities = 26/75 (34%), Positives = 33/75 (44%), Gaps = 8/75 (10%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L VRN+      E L   F +FG +  V   KDY        AF+ F +   A +A   M
Sbjct: 4   LFVRNLANTVTEEILEKAFGQFGKLERVKKLKDY--------AFIHFDERDGAVKAMEEM 55

Query: 124 NGKRFAGREISVVLA 138
           NGK   G  I +V A
Sbjct: 56  NGKELEGENIEIVFA 70

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

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

 Score = 43.9 bits (103), Expect = 3e-06
 Identities = 25/72 (34%), Positives = 34/72 (47%), Gaps = 8/72 (11%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L V NI   C  +ELRA FE +G V +  + KDY        AFV      +A EA   +
Sbjct: 3   LHVGNISSSCTNQELRAKFEEYGPVIECDIVKDY--------AFVHMERAEDAVEAIRGL 54

Query: 124 NGKRFAGREISV 135
           +   F G+ + V
Sbjct: 55  DNTEFQGKRMHV 66

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

 Score = 44.0 bits (104), Expect = 3e-06
 Identities = 20/57 (35%), Positives = 30/57 (52%), Gaps = 4/57 (7%)

Query: 75  PEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEA----AEAQHHMNGKR 127
            E LR  F +FG +++  + +D  T   RGF FV F DP       A+  H ++GK+
Sbjct: 12  AEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQGPHELDGKK 68

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 = 43.6 bits (103), Expect = 3e-06
 Identities = 17/73 (23%), Positives = 27/73 (36%), Gaps = 4/73 (5%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           ++     P      +++  FE  G VR V +         +  AF+ F +   A  A   
Sbjct: 1   TVYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTV----QPHAFITFENLEAAQLAIET 56

Query: 123 MNGKRFAGREISV 135
           +NG    G  I V
Sbjct: 57  LNGASVDGNCIKV 69

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

 Score = 47.8 bits (113), Expect = 3e-06
 Identities = 29/85 (34%), Positives = 43/85 (50%), Gaps = 7/85 (8%)

Query: 66  VRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNG 125
           V +I  + R + +R  F+ FG ++ + +  D  TG+ +GFAFV++  P  A  A   MNG
Sbjct: 112 VGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNG 171

Query: 126 KRFAGREISVVLAAESRKRPEEMRQ 150
           +   GR I V        RP  M Q
Sbjct: 172 QMLGGRNIKV-------GRPSNMPQ 189

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|240745 cd12299, RRM4_Prp24, RNA recognition motif 4 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 43.8 bits (104), Expect = 3e-06
 Identities = 20/72 (27%), Positives = 35/72 (48%), Gaps = 7/72 (9%)

Query: 63  SLLVRNIPLDCRPEELRAPFE-RFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQH 121
           ++ + N+      E+++A FE     VR + L  D+        A V+F  P +A +A  
Sbjct: 2   TIGLFNVSDTVNEEQIKAFFEKIGPDVRKIELFPDH------EGALVEFESPSDAGKASL 55

Query: 122 HMNGKRFAGREI 133
            +NG +F G+ I
Sbjct: 56  SLNGSQFGGKTI 67

This subfamily corresponds to the RRM4 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|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 43.8 bits (104), Expect = 4e-06
 Identities = 26/74 (35%), Positives = 35/74 (47%), Gaps = 5/74 (6%)

Query: 64  LLVRNIPLDCRPEELRAPFERFG-VVR-DVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQH 121
           + VRN+P     ++L+  F   G V+R DV    D   G  +GF  V F  P +A  A  
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDND---GRSKGFGTVLFESPEDAQRAIE 57

Query: 122 HMNGKRFAGREISV 135
             NG    GRE+ V
Sbjct: 58  MFNGYDLEGRELEV 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|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 44.2 bits (105), Expect = 4e-06
 Identities = 19/54 (35%), Positives = 31/54 (57%)

Query: 82  FERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV 135
           F ++G + D+ L +D  TG+ +GFAF+ + D      A  ++NG +  GR I V
Sbjct: 30  FSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNLNGIKLLGRTIRV 83

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

 Score = 43.8 bits (104), Expect = 4e-06
 Identities = 24/77 (31%), Positives = 36/77 (46%), Gaps = 8/77 (10%)

Query: 63  SLLVRNIPLDC--RPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQ 120
            L+V N  L      EEL   FE++G V D+ +P     G+P  + FV +    +AA A 
Sbjct: 3   HLVVANGGLGNGVSREELLRVFEKYGTVEDLVMP----PGKP--YCFVSYSSIEDAAAAY 56

Query: 121 HHMNGKRFAGREISVVL 137
             +NGK     + +  L
Sbjct: 57  DALNGKELELPQQNKPL 73

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

 Score = 43.4 bits (103), Expect = 5e-06
 Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           ++ V  + L  R  +L   F + G VRDV + +D  +   +G A+V+F D  E+      
Sbjct: 1   TVFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDE-ESVPLALG 59

Query: 123 MNGKRFAGREISV 135
           + G+R  G+ I V
Sbjct: 60  LTGQRLLGQPIMV 72

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

 Score = 43.3 bits (103), Expect = 5e-06
 Identities = 23/80 (28%), Positives = 34/80 (42%), Gaps = 9/80 (11%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH- 122
           L V  +       +L   F RFG V DV + K    G  RGFA++        +EAQ   
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDL----RTSEAQLKK 57

Query: 123 ----MNGKRFAGREISVVLA 138
               +NG ++ G  + +  A
Sbjct: 58  CKSTLNGTKWKGSVLKIEEA 77

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

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

 Score = 43.8 bits (104), Expect = 5e-06
 Identities = 25/73 (34%), Positives = 32/73 (43%), Gaps = 2/73 (2%)

Query: 64  LLVRNIPLD-CRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           L V  +P        LR  F + G      L      G+PRGFAFV++    +A EAQ  
Sbjct: 5   LFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAP-NGQPRGFAFVEYATAEDAEEAQQA 63

Query: 123 MNGKRFAGREISV 135
           +NG    G  I V
Sbjct: 64  LNGHSLQGSPIRV 76

This subfamily corresponds to the RRM3 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only. . Length = 92

>gnl|CDD|241005 cd12561, RRM1_RBM5_like, RNA recognition motif 1 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 43.5 bits (103), Expect = 6e-06
 Identities = 23/64 (35%), Positives = 33/64 (51%), Gaps = 1/64 (1%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVV-RDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           +++R +PL    E++R      GV  +DV L +   TG  RGFAFV+F+   EA      
Sbjct: 5   IMLRGLPLSVTEEDIRNALVSHGVEPKDVRLMRRKTTGASRGFAFVEFMSLEEATRWMEL 64

Query: 123 MNGK 126
             GK
Sbjct: 65  NQGK 68

This subgroup corresponds to the RRM1 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both, RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 81

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

 Score = 43.3 bits (103), Expect = 6e-06
 Identities = 15/53 (28%), Positives = 26/53 (49%), Gaps = 4/53 (7%)

Query: 83  ERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV 135
            +FG V  + + K+     P G  +V+F     A +    +NG+ F GR+I+ 
Sbjct: 33  SKFGPVEHIKVDKN----SPEGVVYVKFKTVEAAQKCIQALNGRWFDGRQITA 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|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 46.5 bits (110), Expect = 8e-06
 Identities = 32/139 (23%), Positives = 53/139 (38%), Gaps = 9/139 (6%)

Query: 6   LSSLVFLVQEGSAMRRYSPPYYSPPRRGYGGRGRSPPRRGYGGGGGGYGRRKEQNHGSLL 65
            + L    Q+ +  ++++    SPP       G +   +     G GY          + 
Sbjct: 223 TAVLAHQQQQHAVAQQHAAQRASPPATDGQTAGLAAGAQIAASDGAGY---------CIF 273

Query: 66  VRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNG 125
           V N+  D     L   F  FG V++V + +D  T + +G+ FV   +  EAA A   +NG
Sbjct: 274 VYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNG 333

Query: 126 KRFAGREISVVLAAESRKR 144
                R + V        R
Sbjct: 334 YTLGNRVLQVSFKTNKAYR 352

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

 Score = 42.6 bits (101), Expect = 1e-05
 Identities = 15/52 (28%), Positives = 24/52 (46%)

Query: 82  FERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREI 133
           F   G V  V + ++  TG+  G+ FV+F     A +A   +NGK     + 
Sbjct: 20  FAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSLNGKPIPNTQQ 71

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

 Score = 42.3 bits (100), Expect = 1e-05
 Identities = 25/73 (34%), Positives = 35/73 (47%), Gaps = 1/73 (1%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           +L V N+      E L   F + G +  V +PKD   G+P+ FAFV F        A   
Sbjct: 3   TLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDP-NGKPKSFAFVTFKHEVSVPYAIQL 61

Query: 123 MNGKRFAGREISV 135
           +NG R  GRE+ +
Sbjct: 62  LNGIRLFGRELRI 74

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

 Score = 42.5 bits (101), Expect = 1e-05
 Identities = 15/60 (25%), Positives = 21/60 (35%), Gaps = 13/60 (21%)

Query: 82  FERFG------VVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV 135
           F  FG      V  D         G  +G+ FV F     A  A   +NG     +++ V
Sbjct: 23  FSAFGNILSCKVATDE-------NGGSKGYGFVHFETEEAAVRAIEKVNGMLLNDKKVFV 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|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 42.2 bits (100), Expect = 1e-05
 Identities = 19/56 (33%), Positives = 30/56 (53%), Gaps = 1/56 (1%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEA 119
           + V  IP D   +EL   FE+ G + ++ L  D+ +G  RG+AFV + +   A  A
Sbjct: 4   VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDF-SGLNRGYAFVTYTNKEAAQRA 58

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|241192 cd12748, RRM4_RBM12B, RNA recognition motif 4 in RNA-binding protein 12B (RBM12B) and similar proteins

 Score = 42.1 bits (99), Expect = 1e-05
 Identities = 24/69 (34%), Positives = 35/69 (50%), Gaps = 3/69 (4%)

Query: 66  VRNIPLDCRPEELRAPFERFGVV-RDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMN 124
            RN P D    E++  F  F +   D+YL  D   G   G A V+F    +A +A+  +N
Sbjct: 5   ARNFPFDVTKVEVQKFFAPFNIDEDDIYLLYD-DKGVGLGEALVKFKSEEQAMKAE-RLN 62

Query: 125 GKRFAGREI 133
           G+RF G E+
Sbjct: 63  GQRFLGTEV 71

This subgroup corresponds to the RRM4 of RBM12B which contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Its biological role remains unclear. . Length = 76

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

 Score = 45.3 bits (107), Expect = 2e-05
 Identities = 34/146 (23%), Positives = 53/146 (36%), Gaps = 12/146 (8%)

Query: 14  QEGSAMRRYSPPYYSPPR----RGYGGRGRSPPRRGYGGGGGGYGRRKEQNHG------- 62
           ++ S  RR    Y         R      R    R Y       GR  ++          
Sbjct: 31  RDRSRRRRDRDYYRGRRGRSRSRSPNRYYRPRGDRSYRRDDRRSGRNTKEPLTEAERDDR 90

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           ++ V  + L  R  +L   F + G VRDV   KD  +   +G A+V+F D  E+      
Sbjct: 91  TVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYD-VESVIKALA 149

Query: 123 MNGKRFAGREISVVLAAESRKRPEEM 148
           + G+   GR I V  +   + R  + 
Sbjct: 150 LTGQMLLGRPIIVQSSQAEKNRAAKA 175

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

 Score = 42.1 bits (99), Expect = 2e-05
 Identities = 20/60 (33%), Positives = 25/60 (41%)

Query: 76  EELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV 135
             L A F  F    D  +  D  +G  RG+ FV F    +A  A + MNGK    R I  
Sbjct: 14  ATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEMNGKWLGSRPIRC 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|240703 cd12257, RRM1_RBM26_like, RNA recognition motif 1 in vertebrate RNA-binding protein 26 (RBM26) and similar proteins

 Score = 41.8 bits (99), Expect = 2e-05
 Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 7/58 (12%)

Query: 63  SLLVRNIPLD-CRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEA 119
           +L VRNIP +     +L   F +FG + ++ +  +         A VQF    EA +A
Sbjct: 3   TLEVRNIPPELNNITKLNEHFSKFGTIVNIQVNYN------PESALVQFSTSEEAKKA 54

This subfamily corresponds to the RRM1 of RBM26, and the RRM of RBM27. RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions. RBM27 contains only one RRM; its biological function remains unclear. . Length = 72

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

 Score = 42.2 bits (100), Expect = 2e-05
 Identities = 22/80 (27%), Positives = 34/80 (42%), Gaps = 7/80 (8%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPR-----GFAFVQFVDPYEAA 117
           +L V+N+      E L+  FE+ G VR V + K      P      G+ FV+F     A 
Sbjct: 2   TLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQ 61

Query: 118 EAQHHMNGKRFAGR--EISV 135
           +A   + G    G   E+ +
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|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 = 41.9 bits (99), Expect = 2e-05
 Identities = 17/62 (27%), Positives = 30/62 (48%), Gaps = 2/62 (3%)

Query: 76  EELRAPFERFGV--VRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREI 133
           E+L       GV  V+ +   +    G+ +GFA+V+F     AA  +  + G+ F G++ 
Sbjct: 13  EDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKEKLEGREFNGKKC 72

Query: 134 SV 135
            V
Sbjct: 73  VV 74

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

 Score = 41.7 bits (98), Expect = 2e-05
 Identities = 19/56 (33%), Positives = 26/56 (46%), Gaps = 4/56 (7%)

Query: 76  EELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQF--VDPYE-AAEAQHH-MNGKR 127
           ++++  F +FG V D  L  D  T   RGF FV F   D  +   E   H +N K 
Sbjct: 14  DDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEIHFHEINNKM 69

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

 Score = 41.6 bits (98), Expect = 2e-05
 Identities = 19/73 (26%), Positives = 32/73 (43%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           +L V  +    +  +L+  F ++G V    +  +  +   R F FV      EAA+   H
Sbjct: 1   NLWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQH 60

Query: 123 MNGKRFAGREISV 135
           ++     GR ISV
Sbjct: 61  LHRTELHGRVISV 73

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

 Score = 41.1 bits (97), Expect = 3e-05
 Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 6/72 (8%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L V N+P D   EE +  F ++G V +V+L K+      +GF F++      A +A+  +
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE------KGFGFIRLDTRTNAEKAKAEL 57

Query: 124 NGKRFAGREISV 135
           +G    GR++ V
Sbjct: 58  DGIMRKGRQLRV 69

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

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

 Score = 41.6 bits (97), Expect = 3e-05
 Identities = 24/72 (33%), Positives = 35/72 (48%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           + V N+  D     L   F  FG V +V + +D+ T + +GF FV   +  EAA A   +
Sbjct: 6   IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 124 NGKRFAGREISV 135
           NG R   R + V
Sbjct: 66  NGYRLGDRVLQV 77

This subgroup corresponds to the RRM3 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

>gnl|CDD|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen D (HuD)

 Score = 41.6 bits (97), Expect = 3e-05
 Identities = 24/72 (33%), Positives = 35/72 (48%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           + V N+  D     L   F  FG V +V + +D+ T + +GF FV   +  EAA A   +
Sbjct: 6   IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 124 NGKRFAGREISV 135
           NG R   R + V
Sbjct: 66  NGYRLGDRVLQV 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|241106 cd12662, RRM3_MYEF2, RNA recognition motif 3 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 41.2 bits (96), Expect = 3e-05
 Identities = 25/74 (33%), Positives = 38/74 (51%), Gaps = 2/74 (2%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           + VRN+P D   ++L+  F + G V  ++       G+ +G   V+F  P  A +A   M
Sbjct: 2   IFVRNLPFDLTWQKLKEKFSQCGHV--MFAEIKMENGKSKGCGTVRFDSPESAEKACRLM 59

Query: 124 NGKRFAGREISVVL 137
           NG +  GREI V L
Sbjct: 60  NGIKINGREIDVRL 73

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

 Score = 41.2 bits (96), Expect = 3e-05
 Identities = 29/77 (37%), Positives = 37/77 (48%), Gaps = 10/77 (12%)

Query: 64  LLVRNIPLDCRPEELRAPFERF--GVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQH 121
           L VRN+ +    E ++A F +F  GVV  V   +DY        AFV F +  +A  A  
Sbjct: 4   LYVRNLMISTTEETIKAEFNKFKPGVVERVKKLRDY--------AFVHFFNREDAVAAMS 55

Query: 122 HMNGKRFAGREISVVLA 138
            MNGK   G  I V LA
Sbjct: 56  VMNGKCIDGASIEVTLA 72

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

 Score = 40.8 bits (96), Expect = 4e-05
 Identities = 24/70 (34%), Positives = 38/70 (54%), Gaps = 3/70 (4%)

Query: 66  VRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNG 125
           V N+P D R  ++   F ++G ++ + L K+   G P  FAFV+F DP +A +A    +G
Sbjct: 4   VGNLPGDIRERDIEDLFYKYGPIKAIDL-KNRRRGPP--FAFVEFEDPRDAEDAVRGRDG 60

Query: 126 KRFAGREISV 135
             F G  + V
Sbjct: 61  YDFDGYRLRV 70

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|240699 cd12253, RRM_PIN4_like, RNA recognition motif in yeast RNA-binding protein PIN4, fission yeast RNA-binding post-transcriptional regulators cip1, cip2 and similar proteins

 Score = 40.9 bits (96), Expect = 4e-05
 Identities = 22/73 (30%), Positives = 33/73 (45%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           +++++NIP   R E+L    E  G+         +  G  RG AF  F  P EA      
Sbjct: 3   AIVIKNIPFSLRKEQLLDIIEDLGIPLPYAFNYHFDNGVFRGLAFANFRSPEEAQTVVEA 62

Query: 123 MNGKRFAGREISV 135
           +NG   +GR + V
Sbjct: 63  LNGYEISGRRLRV 75

This subfamily corresponds to the RRM in PIN4, also termed psi inducibility protein 4 or modifier of damage tolerance Mdt1, a novel phosphothreonine (pThr)-containing protein that specifically interacts with the pThr-binding site of the Rad53 FHA1 domain. It is encoded by gene MDT1 (YBL051C) from yeast Saccharomyces cerevisiae. PIN4 is involved in normal G2/M cell cycle progression in the absence of DNA damage and functions as a novel target of checkpoint-dependent cell cycle arrest pathways. It contains an N-terminal RRM, a nuclear localization signal, a coiled coil, and a total of 15 SQ/TQ motifs. cip1 (Csx1-interacting protein 1) and cip2 (Csx1-interacting protein 2) are novel cytoplasmic RRM-containing proteins that counteract Csx1 function during oxidative stress. They are not essential for viability in fission yeast Schizosaccharomyces pombe. Both cip1 and cip2 contain one RRM. Like PIN4, Cip2 also possesses an R3H motif that may function in sequence-specific binding to single-stranded nucleic acids. . Length = 79

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

 Score = 40.3 bits (95), Expect = 5e-05
 Identities = 23/72 (31%), Positives = 31/72 (43%), Gaps = 1/72 (1%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L V N+  D   E+L   F R G V+ V +  D  +G   G A V F    +A  A    
Sbjct: 3   LRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDR-SGRSEGTADVVFEKREDAERAIKQF 61

Query: 124 NGKRFAGREISV 135
           NG    G+ + V
Sbjct: 62  NGVLLDGQPMQV 73

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

 Score = 40.3 bits (95), Expect = 6e-05
 Identities = 21/76 (27%), Positives = 36/76 (47%)

Query: 60  NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEA 119
           N   + V ++  +   E L   F ++   +   + +D  TG+ +G+ FV F DP +  +A
Sbjct: 5   NDFRIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKA 64

Query: 120 QHHMNGKRFAGREISV 135
              MNGK    R I +
Sbjct: 65  MKEMNGKYVGNRPIKL 80

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

 Score = 40.3 bits (95), Expect = 7e-05
 Identities = 16/39 (41%), Positives = 23/39 (58%)

Query: 100 GEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA 138
           G+PRG+ FV F    EA +A   +NGK   G+++ V  A
Sbjct: 41  GQPRGYCFVTFETKEEAEKALKSLNGKTALGKKLVVRWA 79

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

 Score = 40.3 bits (95), Expect = 7e-05
 Identities = 18/60 (30%), Positives = 29/60 (48%)

Query: 76  EELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV 135
           E+L   F RFG ++   + +D  TG+   +AF++F    +  EA   M+      R I V
Sbjct: 18  EDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKMDNVLIDDRRIHV 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|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 40.1 bits (94), Expect = 7e-05
 Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 1/61 (1%)

Query: 76  EELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV 135
             L   F   G +  V +P D  TG  +GFA+++F       +A   ++G    G  + V
Sbjct: 18  RSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKAL-ELDGSDLGGGNLVV 76

Query: 136 V 136
            
Sbjct: 77  D 77

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

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

 Score = 43.8 bits (103), Expect = 7e-05
 Identities = 53/205 (25%), Positives = 66/205 (32%), Gaps = 31/205 (15%)

Query: 64  LLVRNIPLDCRPEELRAPFERF--GVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQH 121
           L VRN+      E +   F  F  G V  V   +DY        AFV F D  +A +A  
Sbjct: 236 LYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIRDY--------AFVHFEDREDAVKAMD 287

Query: 122 HMNGKRFAGREISVVLAAESRKRPEEMRQRHRFRGGSSYGGPRSSYYGRYR--SRSLSRS 179
            +NGK   G EI V LA    K+      R     G      R S    Y   SRSL+  
Sbjct: 288 ELNGKELEGSEIEVTLAKPVDKKSYVRYTRGTGGRGKERQAARQSLGQVYDPASRSLAYE 347

Query: 180 RSPHHPQGSRSRYRSRSYTPVPRQHEDYSISPRRRHIEHPGSPRGPPQERGAE-YSRRSY 238
              +HP  + S +  R                    I   G    P +  G   Y    Y
Sbjct: 348 DYYYHPPYAPSLHFPR----------------MPGPIRGRGRGGAPSRAAGGRGYPPYGY 391

Query: 239 SPGYDDSADRRNPNGNGYGEKSGYE 263
              Y D       +  G  E   Y 
Sbjct: 392 EAYYGDY--YGYHDYRGKYEDKYYG 414

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

 Score = 40.1 bits (94), Expect = 7e-05
 Identities = 21/56 (37%), Positives = 28/56 (50%), Gaps = 1/56 (1%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEA 119
           L V N+P D   +EL+  F+ FG V +V +      G    F FV F DP EA + 
Sbjct: 6   LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDP-EAVQK 60

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

 Score = 40.2 bits (94), Expect = 8e-05
 Identities = 23/74 (31%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           S+ V N+      EEL A F   G +  V +  D ++G P+G+A+++F    ++ EA   
Sbjct: 1   SVYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEF-ATRDSVEAAVA 59

Query: 123 MNGKRFAGREISVV 136
           ++   F GR I V+
Sbjct: 60  LDESSFRGRVIKVL 73

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

 Score = 39.9 bits (93), Expect = 8e-05
 Identities = 25/59 (42%), Positives = 31/59 (52%)

Query: 77  ELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV 135
           +LR  F R+G +  V +  D  TG  RGFAFV F    ++ EA  H NG    GR I V
Sbjct: 15  DLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMELDGRRIRV 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|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 = 39.7 bits (93), Expect = 9e-05
 Identities = 19/66 (28%), Positives = 30/66 (45%), Gaps = 8/66 (12%)

Query: 74  RPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREI 133
           R E++   FE FG +    + K         FAFV+F D  +A +A   ++G R  G  +
Sbjct: 13  REEDIEKLFEPFGPLVRCDIRKT--------FAFVEFEDSEDATKALEALHGSRIDGSVL 64

Query: 134 SVVLAA 139
           +V    
Sbjct: 65  TVEFVK 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|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins

 Score = 39.6 bits (93), Expect = 9e-05
 Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 8/71 (11%)

Query: 68  NIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKR 127
            +P   R  ++   F+ +G +R++ L          GF FV+F DP +A +A + +NGK 
Sbjct: 6   RLPYRARERDVERFFKGYGRIREINLK--------NGFGFVEFEDPRDADDAVYELNGKE 57

Query: 128 FAGREISVVLA 138
             G  + V  A
Sbjct: 58  LCGERVIVEHA 68

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|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 39.7 bits (93), Expect = 9e-05
 Identities = 25/71 (35%), Positives = 36/71 (50%), Gaps = 2/71 (2%)

Query: 66  VRNIPLDCRPEELRAPF-ERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMN 124
           + NIP D + ++L+  F E+ G V  V L KD   G+ RG   V+F D     +A   MN
Sbjct: 4   ISNIPYDLKWQDLKDLFREKVGEVTYVELFKDEE-GKSRGCGVVEFKDKESVQKALETMN 62

Query: 125 GKRFAGREISV 135
                GR++ V
Sbjct: 63  RYELKGRKLVV 73

This subfamily corresponds to the RRM1 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. 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). 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 = 76

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

 Score = 39.5 bits (93), Expect = 1e-04
 Identities = 21/76 (27%), Positives = 32/76 (42%), Gaps = 9/76 (11%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRD----VYLPKDYYTGEPRGFAFVQFVDPYEAAEA 119
           + +R +P     E++R  F    +  D    VY      TGE    A+V+F  P +A  A
Sbjct: 2   VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGE----AYVEFASPEDARRA 57

Query: 120 QHHMNGKRFAGREISV 135
               +  +  GR I V
Sbjct: 58  L-RKHNNKMGGRYIEV 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|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate nucleolin

 Score = 39.8 bits (93), Expect = 1e-04
 Identities = 23/73 (31%), Positives = 35/73 (47%), Gaps = 4/73 (5%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           +L V+N+P +   +EL+  FE      D+ LP     G  +G A+++F    EA +A   
Sbjct: 5   TLFVKNLPYNITVDELKEVFED---AVDIRLPS-GKDGSSKGIAYIEFKTEAEAEKALEE 60

Query: 123 MNGKRFAGREISV 135
             G    GR I 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|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins family

 Score = 39.6 bits (93), Expect = 1e-04
 Identities = 20/63 (31%), Positives = 28/63 (44%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L V  +P     +EL A F  +G +    +  D  TG  RG  F++F    EA  A   +
Sbjct: 3   LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62

Query: 124 NGK 126
           NG 
Sbjct: 63  NGT 65

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

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

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 24/73 (32%), Positives = 36/73 (49%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           +L V  + L    E LR  F R+G +R + L +D  TG  +G+AFV++    +A  A   
Sbjct: 5   TLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRD 64

Query: 123 MNGKRFAGREISV 135
            +     G EI 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|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 39.6 bits (92), Expect = 1e-04
 Identities = 21/56 (37%), Positives = 30/56 (53%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEA 119
           + V  IP D   +EL   FE+ G + D+ L  D  +G+ RG+AF+ F     A EA
Sbjct: 4   VFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEA 59

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

 Score = 39.4 bits (92), Expect = 1e-04
 Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 5/74 (6%)

Query: 62  GSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQH 121
           G+L++ N+      E LR+ F+ +G V+++       T   R   FV+F D  +AA+A  
Sbjct: 2   GTLVIFNLDPTVSSETLRSIFQVYGDVKELR-----ETPCKREQRFVEFFDVRDAAKALR 56

Query: 122 HMNGKRFAGREISV 135
            MNGK  +G+ + +
Sbjct: 57  AMNGKEISGKPVVI 70

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

 Score = 39.3 bits (92), Expect = 1e-04
 Identities = 25/64 (39%), Positives = 38/64 (59%), Gaps = 1/64 (1%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           +L V N+ +    EELR  FER+GVV DV + K    G+   +AFV+F++   A  A+  
Sbjct: 4   TLFVGNLEITITEEELRRAFERYGVVEDVDI-KRPPRGQGNAYAFVKFLNLDMAHRAKVA 62

Query: 123 MNGK 126
           M+G+
Sbjct: 63  MSGQ 66

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

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

 Score = 39.6 bits (92), Expect = 1e-04
 Identities = 23/59 (38%), Positives = 32/59 (54%)

Query: 77  ELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV 135
           +LR  F ++G + DV +  D  +   RGFAFV F +  +A EA+   NG    GR I V
Sbjct: 25  DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 83

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

 Score = 39.2 bits (91), Expect = 1e-04
 Identities = 27/76 (35%), Positives = 36/76 (47%), Gaps = 1/76 (1%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           + V  IP D   +EL   FE+ G + D+ L  D  TG  RG+AFV F     A EA    
Sbjct: 4   IFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAVKLY 63

Query: 124 NGKRF-AGREISVVLA 138
           N      G+ I V ++
Sbjct: 64  NNHEIRPGKHIGVCIS 79

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

 Score = 39.7 bits (92), Expect = 2e-04
 Identities = 22/72 (30%), Positives = 35/72 (48%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           + + N+  D     L   F  FG V +V + +D+ T + +GF FV   +  EAA A   +
Sbjct: 4   IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63

Query: 124 NGKRFAGREISV 135
           NG R   + + V
Sbjct: 64  NGYRLGDKILQV 75

This subgroup corresponds to the RRM3 of HuR, also termed ELAV-like protein 1 (ELAV-1), the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 84

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

 Score = 39.3 bits (91), Expect = 2e-04
 Identities = 23/81 (28%), Positives = 37/81 (45%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           + V N+  +     L   F  FG V +V + +D+ T + +GF FV   +  EAA A   +
Sbjct: 4   IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 124 NGKRFAGREISVVLAAESRKR 144
           NG R   R + V      + +
Sbjct: 64  NGYRLGDRVLQVSFKTSKQHK 84

This subgroup corresponds to the RRM3 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 85

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

 Score = 38.8 bits (90), Expect = 2e-04
 Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 4/67 (5%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEA----AEA 119
           + +  +  D   ++L+  F +FG V D  L  D  TG  RGF FV F +         + 
Sbjct: 1   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60

Query: 120 QHHMNGK 126
           +H +NGK
Sbjct: 61  EHKLNGK 67

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

 Score = 38.7 bits (91), Expect = 2e-04
 Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 6/64 (9%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L ++N+P +   E L   F +F   ++V L         RG AFV+F    +A  A   +
Sbjct: 5   LFLQNLPEETTKEMLEMLFNQFPGFKEVRLVP------RRGIAFVEFETEEQATVALQAL 58

Query: 124 NGKR 127
            G +
Sbjct: 59  QGFK 62

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

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

 Score = 38.9 bits (91), Expect = 2e-04
 Identities = 22/75 (29%), Positives = 35/75 (46%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L++  +P     EE R+ F   G V++  + +D  TG   GF FV +    +A  A   +
Sbjct: 3   LIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTL 62

Query: 124 NGKRFAGREISVVLA 138
           NG +   + I V  A
Sbjct: 63  NGLQLQNKRIKVAYA 77

This subfamily corresponds to the RRM1 of SXL which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 81

>gnl|CDD|241013 cd12569, RRM4_RBM19, RNA recognition motif 4 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 38.5 bits (90), Expect = 2e-04
 Identities = 22/57 (38%), Positives = 30/57 (52%), Gaps = 8/57 (14%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGF-AFVQFVDPYEAAEA 119
           +LV+N+P      ELR  F +FG +  V LP       P G  A V+F++P EA  A
Sbjct: 3   ILVKNLPAGTLTAELRELFSKFGSLGRVLLP-------PAGITAIVEFLEPSEAKLA 52

This subgroup corresponds to the RRM4 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 = 72

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

 Score = 38.3 bits (90), Expect = 3e-04
 Identities = 25/77 (32%), Positives = 36/77 (46%), Gaps = 7/77 (9%)

Query: 61  HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFA-FVQFVDPYEAAEA 119
            G+LLV N+      +ELR+ F +FG V+D+           R    FV+F D   A  A
Sbjct: 1   QGTLLVFNLDSPISDQELRSLFSQFGEVKDIRETP------LRPSQKFVEFYDIRAAEAA 54

Query: 120 QHHMNGKRFAGREISVV 136
              +NG+ F G  + V 
Sbjct: 55  LDALNGRPFLGGRLKVK 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|240749 cd12303, RRM_spSet1p_like, RNA recognition motif in fission yeast Schizosaccharomyces pombe SET domain-containing protein 1 (spSet1p) and similar proteins

 Score = 38.9 bits (91), Expect = 3e-04
 Identities = 21/82 (25%), Positives = 34/82 (41%), Gaps = 8/82 (9%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH- 122
           +L+  +     P+++R  F  FG + +  L  D  TG+  G   V F        A H  
Sbjct: 1   ILITGLSPLTTPKQIRMHFRPFGEIEESELKLDPRTGQSLGICRVTFRGDPLRPSAAHEA 60

Query: 123 -------MNGKRFAGREISVVL 137
                  +NG+R  G+ + V L
Sbjct: 61  AKAAVDGLNGRRIGGKRVRVEL 82

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

 Score = 38.6 bits (90), Expect = 3e-04
 Identities = 18/38 (47%), Positives = 22/38 (57%)

Query: 76  EELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDP 113
           E LR  F ++G V D  + KD  T   RGF FV+F DP
Sbjct: 14  ETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDP 51

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|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 = 4e-04
 Identities = 24/78 (30%), Positives = 35/78 (44%), Gaps = 1/78 (1%)

Query: 63  SLLVRNIPLDCRPEELRAPF-ERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQH 121
           S+ V ++  D     L+  F  R+  VR   +  D  TG  +G+ FV+F D  E   A  
Sbjct: 3   SIFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALT 62

Query: 122 HMNGKRFAGREISVVLAA 139
            MNG   + R + V  A 
Sbjct: 63  EMNGVYCSSRPMRVSPAT 80

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

 Score = 38.1 bits (89), Expect = 4e-04
 Identities = 14/31 (45%), Positives = 19/31 (61%)

Query: 105 FAFVQFVDPYEAAEAQHHMNGKRFAGREISV 135
           +AFV++ D   AA A   MNG+   G+EI V
Sbjct: 39  YAFVEYYDHRSAAAALQTMNGRLILGQEIKV 69

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

>gnl|CDD|241141 cd12697, RRM3_ROD1, RNA recognition motif 3 in vertebrate regulator of differentiation 1 (Rod1)

 Score = 38.0 bits (88), Expect = 4e-04
 Identities = 27/76 (35%), Positives = 36/76 (47%), Gaps = 6/76 (7%)

Query: 64  LLVRNI-PLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           LLV N+ P    P  L   F  FGV  DV+  K  +  +    A VQ  D  +A  A  H
Sbjct: 3   LLVSNLNPDAITPHGL---FILFGVYGDVHRVKIMFNKKEN--ALVQMADATQAQLAMSH 57

Query: 123 MNGKRFAGREISVVLA 138
           +NG+R  G+ I   L+
Sbjct: 58  LNGQRLYGKVIRATLS 73

This subgroup corresponds to the RRM3 of ROD1 coding protein Rod1, 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. Rod1 contains four repeats of RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and does have RNA binding activities. . Length = 76

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

 Score = 38.1 bits (89), Expect = 4e-04
 Identities = 23/73 (31%), Positives = 31/73 (42%), Gaps = 8/73 (10%)

Query: 64  LLVRNIPLDCRPEELRAPF-ERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           L + N+  D    +LR  F E    V  V + K        G+AFV   D   A +A   
Sbjct: 1   LYIGNLSSDVNESDLRQLFEEHKIPVSSVLVKK-------GGYAFVDCPDQSWADKAIEK 53

Query: 123 MNGKRFAGREISV 135
           +NGK   G+ I 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|240718 cd12272, RRM2_PHIP1, RNA recognition motif 2 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 37.8 bits (88), Expect = 4e-04
 Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 2/73 (2%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           ++ + N+  D   +++R  F+    +  V L  D  TGE +GF  V F D  E+ +A   
Sbjct: 1   TVYIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADE-ESLDAALK 58

Query: 123 MNGKRFAGREISV 135
           ++G    GR I +
Sbjct: 59  LDGTVLCGRPIRI 71

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

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

 Score = 37.8 bits (88), Expect = 4e-04
 Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 3/72 (4%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           + V N+P D R  E+   F ++G + D+ L        P G+AF++F D  +A +A    
Sbjct: 2   VYVGNLPGDIREREVEDLFYKYGPIVDIDLK---LPPRPPGYAFIEFEDARDAEDAIRGR 58

Query: 124 NGKRFAGREISV 135
           +G  F G+ + V
Sbjct: 59  DGYDFDGQRLRV 70

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

 Score = 38.3 bits (89), Expect = 4e-04
 Identities = 25/72 (34%), Positives = 36/72 (50%), Gaps = 12/72 (16%)

Query: 76  EELRAPFERFGVVR----------DVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNG 125
           EEL   F+  GVV+          ++Y  K+  TG+P+G A V + DP  A  A    +G
Sbjct: 15  EELADFFKHCGVVKINKRTGQPMVNIYTDKE--TGKPKGDATVSYEDPPSAKAAVEWFDG 72

Query: 126 KRFAGREISVVL 137
           K F G ++ V L
Sbjct: 73  KDFQGSKLKVSL 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|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 41.2 bits (96), Expect = 4e-04
 Identities = 26/92 (28%), Positives = 40/92 (43%)

Query: 47  GGGGGGYGRRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFA 106
            G GG        +  +L+V  +P D    EL A F   G +    + +DY TG   G+A
Sbjct: 93  LGSGGSDDNDTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYA 152

Query: 107 FVQFVDPYEAAEAQHHMNGKRFAGREISVVLA 138
           FV F    ++  A  ++NG     + + V  A
Sbjct: 153 FVDFGSEADSQRAIKNLNGITVRNKRLKVSYA 184

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

 Score = 41.4 bits (97), Expect = 4e-04
 Identities = 22/82 (26%), Positives = 39/82 (47%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           + + N+PL    ++++   E FG ++   L KD  TG  +G+AF ++ DP     A   +
Sbjct: 298 IYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAAL 357

Query: 124 NGKRFAGREISVVLAAESRKRP 145
           NGK     ++ V  A     + 
Sbjct: 358 NGKDTGDNKLHVQRACVGANQA 379

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

 Score = 38.0 bits (88), Expect = 4e-04
 Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 5/70 (7%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L+V N+      + L+  FE+   +R   +P++   G P+G+AFV+F    +A EA +  
Sbjct: 4   LVVNNLSYSASEDSLQEVFEKATSIR---IPQN--NGRPKGYAFVEFESAEDAKEALNSC 58

Query: 124 NGKRFAGREI 133
           N     GR I
Sbjct: 59  NNTEIEGRSI 68

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|241006 cd12562, RRM2_RBM5_like, RNA recognition motif 2 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 37.9 bits (88), Expect = 5e-04
 Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 1/39 (2%)

Query: 80  APFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAE 118
           AP+     V ++ L KD  T + RGFAFVQ     EA++
Sbjct: 24  APYASL-SVSNIRLIKDKQTQQNRGFAFVQLSSALEASQ 61

This subgroup corresponds to the RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both, RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 86

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

 Score = 38.0 bits (88), Expect = 5e-04
 Identities = 24/78 (30%), Positives = 38/78 (48%), Gaps = 2/78 (2%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           +L V  +P     +EL   F ++G +    + +D  TG  RG  F++F    EA EA   
Sbjct: 2   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKG 61

Query: 123 MNGKRFAG--REISVVLA 138
           +NG++  G    I+V  A
Sbjct: 62  LNGQKPEGASEPITVKFA 79

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|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 38.1 bits (89), Expect = 5e-04
 Identities = 14/36 (38%), Positives = 20/36 (55%)

Query: 91  VYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGK 126
           V + ++  TG P G+ FV+F D   A    H +NGK
Sbjct: 30  VKIIRNKLTGGPAGYCFVEFADEATAERCLHKLNGK 65

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

 Score = 37.8 bits (88), Expect = 6e-04
 Identities = 19/57 (33%), Positives = 25/57 (43%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEA 119
            L V  + L      LR  F R+G + +  +  D  T   RGF F+ F    EA EA
Sbjct: 4   KLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEA 60

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

 Score = 37.2 bits (87), Expect = 6e-04
 Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 1/57 (1%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEA 119
           ++ V N+      +ELR  F + G + DV L K+ Y G+ +G+A+V+F +     EA
Sbjct: 1   TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKN-YKGKSKGYAYVEFENEESVQEA 56

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

 Score = 37.5 bits (87), Expect = 6e-04
 Identities = 20/67 (29%), Positives = 32/67 (47%), Gaps = 4/67 (5%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEA---- 119
           + V  +  D   ++L+  F +FG V D  +  D  TG  RGF FV F D     +     
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60

Query: 120 QHHMNGK 126
           +H ++G+
Sbjct: 61  EHKLDGR 67

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

 Score = 37.2 bits (87), Expect = 6e-04
 Identities = 18/69 (26%), Positives = 29/69 (42%), Gaps = 6/69 (8%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L V  +       EL   F+RFG +R +    DY  G  R +A++++     A  A+  +
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAIRRI----DYDPG--RNYAYIEYESIEAAQAAKEAL 54

Query: 124 NGKRFAGRE 132
            G    G  
Sbjct: 55  RGFPLGGPG 63

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

 Score = 37.3 bits (87), Expect = 6e-04
 Identities = 20/58 (34%), Positives = 31/58 (53%), Gaps = 8/58 (13%)

Query: 76  EELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQF-----VDPYEAAEAQHH-MNGKR 127
           E++R  F +FG + ++ LP D  T + RGF F+ F     V   +  E Q H + GK+
Sbjct: 14  EKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVK--KILETQFHVIGGKK 69

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|241199 cd12755, RRM2_RBM5, RNA recognition motif 2 in vertebrate RNA-binding protein 5 (RBM5)

 Score = 37.6 bits (87), Expect = 6e-04
 Identities = 21/59 (35%), Positives = 31/59 (52%), Gaps = 4/59 (6%)

Query: 63  SLLVRNI-PLDCRPEELRA--PFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAE 118
           ++++RNI P       L A  P+     V ++ L KD  T + RGFAFVQ     EA++
Sbjct: 4   TIILRNIAPHTVVDSILTALAPYASL-AVNNIRLIKDKQTQQNRGFAFVQLSSALEASQ 61

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|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 37.7 bits (87), Expect = 6e-04
 Identities = 18/49 (36%), Positives = 26/49 (53%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVD 112
           + V  I  D     LR  FE++G +  + +  D  +G+ RGFAFV F D
Sbjct: 3   IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 51

This subgroup corresponds to the RRM2 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, 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. Moreover, hnRNP A1, together with the scaffold protein septin 6, serves as host proteins to form a complex with NS5b and viral RNA, and further play 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 = 77

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

 Score = 37.3 bits (86), Expect = 6e-04
 Identities = 19/67 (28%), Positives = 32/67 (47%), Gaps = 4/67 (5%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEA----AEA 119
           + V  +  D   ++L+  F +FG V D  +  D  TG  RGF F+ F D         + 
Sbjct: 2   MFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQK 61

Query: 120 QHHMNGK 126
           +H ++G+
Sbjct: 62  EHRLDGR 68

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

 Score = 37.4 bits (86), Expect = 7e-04
 Identities = 17/39 (43%), Positives = 23/39 (58%)

Query: 75  PEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDP 113
           P+ LR  F +FG +R+  + +D  T   RGF FV F DP
Sbjct: 13  PDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADP 51

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|240979 cd12535, RRM_FUS_TAF15, RNA recognition motif in vertebrate fused in Ewing's sarcoma protein (FUS), TATA-binding protein-associated factor 15 (TAF15) and similar proteins

 Score = 37.6 bits (87), Expect = 7e-04
 Identities = 23/84 (27%), Positives = 40/84 (47%), Gaps = 8/84 (9%)

Query: 60  NHGSLLVRNIPLDCRPEELRAPFERFGVVRD--------VYLPKDYYTGEPRGFAFVQFV 111
           ++ ++ V+ +  D   E +   F++ G+++         + L  D  TG+ +G A V F 
Sbjct: 1   DNNTIFVQGLGEDVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 60

Query: 112 DPYEAAEAQHHMNGKRFAGREISV 135
           DP  A  A    +GK F+G  I V
Sbjct: 61  DPPSAKAAIDWFDGKEFSGNPIKV 84

This subgroup corresponds to the RRM of FUS and TAF15. FUS (TLS or Pigpen or hnRNP P2), also termed 75 kDa DNA-pairing protein (POMp75), or oncoprotein TLS (Translocated in liposarcoma), is 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 multi-functional protein and has been implicated in pre-mRNA splicing, chromosome stability, cell spreading, and transcription. FUS was originally identified in human myxoid and round cell liposarcomas as an oncogenic fusion with the stress-induced DNA-binding transcription factor CHOP (CCAAT enhancer-binding homologous protein) and later as hnRNP P2, a component of hnRNP H complex assembled on pre-mRNA. It can form ternary complexes with hnRNP A1 and hnRNP C1/C2. Additional research indicates that FUS binds preferentially to GGUG-containing RNAs. In the presence of Mg2+, it can bind both single- and double-stranded DNA (ssDNA/dsDNA) and promote ATP-independent annealing of complementary ssDNA and D-loop formation in superhelical dsDNA. FUS has been shown to be recruited by single stranded noncoding RNAs to the regulatory regions of target genes such as cyclin D1, where it represses transcription by disrupting complex formation. TAF15 (TAFII68), also termed TATA-binding protein-associated factor 2N (TAF2N), or RNA-binding protein 56 (RBP56), originally identified as a TAF in the general transcription initiation TFIID complex, is a novel RNA/ssDNA-binding protein with homology to the proto-oncoproteins FUS and EWS (also termed EWSR1), belonging to the FET family as well. TAF15 likely functions in RNA polymerase II (RNAP II) transcription by interacting with TFIID and subunits of RNAP II itself. TAF15 is also associated with U1 snRNA, chromatin and RNA, in a complex distinct from the Sm-containing U1 snRNP that functions in splicing. Like other members in the FET family, both FUS and TAF15 contain 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. . Length = 86

>gnl|CDD|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 37.2 bits (86), Expect = 7e-04
 Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 6/72 (8%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L V N+P D   EE+R  FE++G   ++++ KD      +GF F++      A  A+  +
Sbjct: 4   LFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKD------KGFGFIRLETRTLAEIAKAEL 57

Query: 124 NGKRFAGREISV 135
           +     G+++ V
Sbjct: 58  DNMPLRGKQLRV 69

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|241012 cd12568, RRM3_MRD1, RNA recognition motif 3 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 37.0 bits (86), Expect = 8e-04
 Identities = 23/66 (34%), Positives = 32/66 (48%), Gaps = 8/66 (12%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRG-FAFVQFVDPYEAAEAQHH 122
           +LV+N P     EELR  FE  G +  V +P       P G  A V+F +P +A  A   
Sbjct: 3   ILVKNFPYGTTAEELRDLFEPHGKLTRVLMP-------PAGTIAIVEFANPQQARLAFKA 55

Query: 123 MNGKRF 128
           +  +RF
Sbjct: 56  LAYRRF 61

This subgroup corresponds to the RRM3 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 = 72

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

 Score = 37.0 bits (86), Expect = 9e-04
 Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 3/73 (4%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           +L + N+       +LR  FERFG + D+ + K    G    +AF+Q+ D     +A   
Sbjct: 4   TLFIGNLEKTTTYSDLREAFERFGEIIDIDIKK---QGGNPAYAFIQYADIASVVKAMRK 60

Query: 123 MNGKRFAGREISV 135
           M+G+      + +
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|241042 cd12598, RRM1_SRSF9, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 9 (SRSF9)

 Score = 37.1 bits (86), Expect = 9e-04
 Identities = 25/63 (39%), Positives = 36/63 (57%), Gaps = 3/63 (4%)

Query: 66  VRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNG 125
           V N+P D R ++L   F ++G +RD+ L K+     P  FAFV+F DP +A +A    NG
Sbjct: 4   VGNLPSDVREKDLEDLFYKYGRIRDIEL-KNRRGLVP--FAFVRFEDPRDAEDAVFGRNG 60

Query: 126 KRF 128
             F
Sbjct: 61  YDF 63

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

>gnl|CDD|240810 cd12364, RRM_RDM1, RNA recognition motif of RAD52 motif-containing protein 1 (RDM1) and similar proteins

 Score = 37.0 bits (86), Expect = 0.001
 Identities = 17/55 (30%), Positives = 26/55 (47%)

Query: 76  EELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAG 130
           E L + F +FG++  V +  +     P  +AFV+F     A+ AQ   NGK    
Sbjct: 19  ESLCSAFSQFGLLYSVKVFPNAAVATPGFYAFVKFYSARAASRAQKACNGKWLFQ 73

This subfamily corresponds to the RRM of RDM1, also termed RAD52 homolog B, a novel factor involved in the cellular response to the anti-cancer drug cisplatin in vertebrates. RDM1 contains a small RD motif that shares with the recombination and repair protein RAD52, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RD motif is responsible for the acidic pH-dependent DNA-binding properties of RDM1. It interacts with ss- and dsDNA, and may act as a DNA-damage recognition factor by recognizing the distortions of the double helix caused by cisplatin-DNA adducts in vitro. In addition, due to the presence of RRM, RDM1 can bind to RNA as well as DNA. . Length = 81

>gnl|CDD|240941 cd12497, RRM3_RBM47, RNA recognition motif 3 in vertebrate RNA-binding protein 47 (RBM47)

 Score = 36.9 bits (85), Expect = 0.001
 Identities = 24/77 (31%), Positives = 36/77 (46%), Gaps = 10/77 (12%)

Query: 64  LLVRNIPLDCRPEELRAPFERF--GVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQH 121
           L VRN+ ++   + ++  F +F  G V  V   +DY        AFV F    +A  A +
Sbjct: 4   LYVRNLMIETSEDTIKKTFGQFNPGCVERVKKIRDY--------AFVHFTSREDAVHAMN 55

Query: 122 HMNGKRFAGREISVVLA 138
           ++NG    G  I V LA
Sbjct: 56  NLNGTELEGSCIEVTLA 72

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|233508 TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus splicing factor family

 Score = 39.8 bits (93), Expect = 0.001
 Identities = 32/119 (26%), Positives = 46/119 (38%), Gaps = 15/119 (12%)

Query: 20  RRYSPPYYSP--PRRGYGGRGRSPPRRGYGGGGGGYGRRKEQNHGSLLVRNI-PLDCRPE 76
            R  PP+  P   R  Y     +P    YG  GGG G         L+V  +       +
Sbjct: 239 DRMGPPHGPPSRYRPAYEAAPLAPAISSYGPAGGGPG-------SVLMVSGLHQEKVNCD 291

Query: 77  ELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV 135
            L   F  F V  +V   K       +  A ++  DPY+A  A  H+NG +  G+ + V
Sbjct: 292 RL---FNLFCVYGNVERVKFMKN--KKETALIEMADPYQAQLALTHLNGVKLFGKPLRV 345

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). Length = 481

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

 Score = 36.9 bits (85), Expect = 0.001
 Identities = 26/85 (30%), Positives = 43/85 (50%), Gaps = 16/85 (18%)

Query: 70  PLDCR-----------PEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAE 118
           PLDC+             EL   F  +G +R V++ ++     P GFAFV+F DP +AA+
Sbjct: 2   PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAAD 56

Query: 119 AQHHMNGKRFAGREISVVLAAESRK 143
           A   ++G+   G  + V L+   ++
Sbjct: 57  AVRELDGRTLCGCRVRVELSNGEKR 81

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|240866 cd12420, RRM_RBPMS_like, RNA recognition motif in RNA-binding protein with multiple splicing (RBP-MS)-like proteins

 Score = 36.9 bits (86), Expect = 0.001
 Identities = 25/79 (31%), Positives = 33/79 (41%), Gaps = 2/79 (2%)

Query: 63  SLLVRNIPLDCRPEELRAPFERF-GVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQH 121
           +L V  +P D +  EL   F  F G      + K+   GE +   FV F     AA A  
Sbjct: 2   TLFVSGLPSDVKERELAHLFRPFPGYEASRLVFKEKKGGEKQPVGFVDFSSAQCAAAAMD 61

Query: 122 HMNGKRFAGREISVVLAAE 140
            + G RF   + S VL  E
Sbjct: 62  ALQGYRFDP-DTSSVLRLE 79

This subfamily corresponds to the RRM of RNA-binding proteins with multiple splicing (RBP-MS)-like proteins, including protein products of RBPMS genes (RBP-MS and its paralogue RBP-MS2), the Drosophila couch potato (cpo), and Caenorhabditis elegans Mec-8 genes. RBP-MS may be involved in regulation of mRNA translation and localization during Xenopus laevis development. It has also been shown to physically interact with Smad2, Smad3 and Smad4, and stimulates Smad-mediated transactivation. Cpo may play an important role in regulating normal function of the nervous system, whereas mutations in Mec-8 affect mechanosensory and chemosensory neuronal function. All members contain a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Some uncharacterized family members contain two RRMs; this subfamily includes their RRM1. Their RRM2 shows high sequence homology to the RRM of yeast proteins scw1, Whi3, and Whi4. Length = 79

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

 Score = 36.6 bits (85), Expect = 0.001
 Identities = 21/70 (30%), Positives = 32/70 (45%), Gaps = 1/70 (1%)

Query: 66  VRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNG 125
           V N+      ++L+  F+  G V    + +D   G+ RG   VQF  P EA +A    NG
Sbjct: 3   VANLDYKVGWKKLKEVFKLAGKVVRADIKEDK-EGKSRGMGVVQFEHPIEAVQAISMFNG 61

Query: 126 KRFAGREISV 135
           +    R + V
Sbjct: 62  QMLFDRPMRV 71

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|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 = 0.001
 Identities = 20/76 (26%), Positives = 32/76 (42%), Gaps = 7/76 (9%)

Query: 66  VRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTG------EPRGFAFVQFVDPYEAAEA 119
           + N+      E+L    + F  V  V +P     G       P G A+ +F  P +A + 
Sbjct: 4   ISNLSYSSSEEDLEEFLKDFEPV-SVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQAEKV 62

Query: 120 QHHMNGKRFAGREISV 135
              +NGK F  R++ V
Sbjct: 63  VKDLNGKVFKNRKLFV 78

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

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

 Score = 36.5 bits (84), Expect = 0.001
 Identities = 17/47 (36%), Positives = 25/47 (53%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQF 110
           + V  + ++   E+++  FE+FG V D  L  D  T   RGF FV F
Sbjct: 2   IFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTF 48

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|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP DL) and similar proteins

 Score = 36.1 bits (83), Expect = 0.002
 Identities = 16/41 (39%), Positives = 23/41 (56%)

Query: 72  DCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVD 112
           D   E+++  F  FG + ++ LP D  T E RGF FV + D
Sbjct: 10  DTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTD 50

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|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 36.6 bits (84), Expect = 0.002
 Identities = 23/66 (34%), Positives = 31/66 (46%), Gaps = 4/66 (6%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQF--VDPYEAAEAQ- 120
           L V  I  D     LR  FE +G +  + +  D  +G+ RGF FV F   DP +    Q 
Sbjct: 3   LFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVLQK 62

Query: 121 -HHMNG 125
            H +NG
Sbjct: 63  YHTING 68

This subgroup corresponds to the RRM2 of hnRNP A2/B1, an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

>gnl|CDD|240720 cd12274, RRM2_NEFsp, RNA recognition motif 2 in vertebrate putative RNA exonuclease NEF-sp

 Score = 36.0 bits (83), Expect = 0.002
 Identities = 15/50 (30%), Positives = 26/50 (52%)

Query: 76  EELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNG 125
           E L+  F +   +  ++LPKD  +G+P  + F++F     A  A  H+ G
Sbjct: 13  EFLQERFGQLSDLEAIFLPKDLLSGKPAKYCFLKFRQSQSATAALDHITG 62

This subfamily corresponds to the RRM2 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|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 36.0 bits (83), Expect = 0.002
 Identities = 23/68 (33%), Positives = 31/68 (45%), Gaps = 4/68 (5%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQ--- 120
           L V  +  D    +L   F +FG V    +  D  TG+ RGF FV F +   A +A    
Sbjct: 2   LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVVK 61

Query: 121 -HHMNGKR 127
            H +NG R
Sbjct: 62  FHPINGHR 69

This subgroup corresponds to the RRM2 of hnRNP A0, a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

>gnl|CDD|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score = 36.0 bits (83), Expect = 0.002
 Identities = 17/55 (30%), Positives = 24/55 (43%)

Query: 84  RFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA 138
           RF   +   +  D  TG  RG+ FV+F D  +   A   M G    GR + +  A
Sbjct: 25  RFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALIEMQGVYCGGRPMRISTA 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|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 35.8 bits (83), Expect = 0.002
 Identities = 17/55 (30%), Positives = 26/55 (47%), Gaps = 4/55 (7%)

Query: 76  EELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQ----HHMNGK 126
           + L+  F ++G + D  + KD  T   RGF FV F    E   A     H ++G+
Sbjct: 14  DSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNARPHKVDGR 68

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

 Score = 35.6 bits (82), Expect = 0.002
 Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 8/72 (11%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L V N+P +   +E+R+ FE++G V +  + K+Y         FV   D   A EA  ++
Sbjct: 3   LFVGNLPPEATEQEIRSLFEQYGKVLECDIIKNY--------GFVHMDDKTAADEAIRNL 54

Query: 124 NGKRFAGREISV 135
           +  +  G  I+V
Sbjct: 55  HHYKLHGVAINV 66

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|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 35.7 bits (82), Expect = 0.003
 Identities = 18/49 (36%), Positives = 27/49 (55%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVD 112
           + V  I  D     LR  FE++G +  + + +D  +G+ RGFAFV F D
Sbjct: 3   IFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDD 51

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|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate RNA-binding protein 47 (RBM47)

 Score = 35.7 bits (82), Expect = 0.003
 Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 1/61 (1%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           + V  IP D   +EL   FE  G + ++ L  D+  G+ RG+AFV +   +EA  A   +
Sbjct: 4   VFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDF-DGKNRGYAFVMYTQKHEAKRAVREL 62

Query: 124 N 124
           N
Sbjct: 63  N 63

This subgroup corresponds to the RRM1 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 = 78

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

 Score = 35.8 bits (82), Expect = 0.003
 Identities = 23/68 (33%), Positives = 37/68 (54%), Gaps = 5/68 (7%)

Query: 77  ELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV 136
           EL   F  +G +R V++ ++     P GFAFV+F DP +A +A   ++GK   G  + V 
Sbjct: 15  ELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVE 69

Query: 137 LAAESRKR 144
           L+    +R
Sbjct: 70  LSTGMPRR 77

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

 Score = 35.4 bits (81), Expect = 0.003
 Identities = 19/55 (34%), Positives = 30/55 (54%), Gaps = 4/55 (7%)

Query: 76  EELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEA----AEAQHHMNGK 126
           E LR  F +FG V++  + +D  T   RGF FV F+D        A+++H ++ K
Sbjct: 15  EGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSK 69

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|241116 cd12672, RRM_DAZL, RNA recognition motif in vertebrate deleted in azoospermia-like (DAZL) proteins

 Score = 35.6 bits (82), Expect = 0.003
 Identities = 21/69 (30%), Positives = 38/69 (55%), Gaps = 4/69 (5%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQF---VDPYEAAEA 119
           ++ V  I +     E+R+ F ++G V++V +  D  TG  +G+ FV F   VD  +  E+
Sbjct: 7   TVFVGGIDIRMDETEIRSFFAKYGSVKEVKIITD-RTGVSKGYGFVSFYDDVDVQKIVES 65

Query: 120 QHHMNGKRF 128
           Q + +GK+ 
Sbjct: 66  QINFHGKKL 74

This subgroup corresponds to the RRM of DAZL, also termed SPGY-like-autosomal, encoded by the autosomal homolog of DAZ gene, DAZL. It is ancestral to the deleted in azoospermia (DAZ) protein. DAZL is germ-cell-specific RNA-binding protein that contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a DAZ motif, a protein-protein interaction domain. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 82

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

 Score = 35.4 bits (82), Expect = 0.003
 Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 2/73 (2%)

Query: 66  VRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNG 125
           V N+P +    +L A F+   V + V L +D  T + +GF +V+F D     EA    +G
Sbjct: 6   VGNLPFNTVQGDLDAIFKDLSV-KSVRLVRDKETDKFKGFCYVEFEDVESLKEAL-EYDG 63

Query: 126 KRFAGREISVVLA 138
             F  R + V +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|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast nucleolar protein 13 (Nop13p) and similar proteins

 Score = 35.1 bits (81), Expect = 0.004
 Identities = 26/72 (36%), Positives = 37/72 (51%), Gaps = 3/72 (4%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L V N+  +   +ELRA F R G +R V +     +G+ +GFAFV F +   A  A   +
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNA---L 57

Query: 124 NGKRFAGREISV 135
            GK   GR + V
Sbjct: 58  KGKHLNGRALRV 69

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

 Score = 35.4 bits (81), Expect = 0.004
 Identities = 26/77 (33%), Positives = 34/77 (44%), Gaps = 10/77 (12%)

Query: 64  LLVRNIPLDCRPEELRAPFERF--GVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQH 121
           L VRN+ L    E +   F     G V  V   +DY        AFV F +  +A +A +
Sbjct: 11  LYVRNLMLSTTEETIEKEFNSIKPGAVERVKKIRDY--------AFVHFSNREDAVDAMN 62

Query: 122 HMNGKRFAGREISVVLA 138
            +NGK   G  I V LA
Sbjct: 63  ALNGKVIDGSPIEVTLA 79

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|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)

 Score = 35.3 bits (81), Expect = 0.004
 Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           +L V N+      E +   F + G V  V +PKD   G+P+ FAFV F        A + 
Sbjct: 3   TLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDK-DGKPKQFAFVNFKHEVSVPYAMNL 61

Query: 123 MNGKRFAGREISV 135
           +NG +  GR +++
Sbjct: 62  LNGIKLYGRPLNI 74

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|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering time control protein FCA and similar proteins

 Score = 35.3 bits (81), Expect = 0.004
 Identities = 21/64 (32%), Positives = 33/64 (51%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L V ++P     +E+R  FE  G V +V + KD  TG  +G  FV++    EA  A   +
Sbjct: 2   LFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRAL 61

Query: 124 NGKR 127
           + +R
Sbjct: 62  HNQR 65

This subgroup corresponds to the RRM1 of FCA, a gene controlling flowering time in Arabidopsis, encoding a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. 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|241037 cd12593, RRM_RBM11, RNA recognition motif in vertebrate RNA-binding protein 11 (RBM11)

 Score = 34.9 bits (80), Expect = 0.004
 Identities = 25/73 (34%), Positives = 33/73 (45%), Gaps = 1/73 (1%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           +L V N+    R E L   F + G +  V + KD   G+P+ F FV F        A   
Sbjct: 3   TLFVGNLECRVREEILYELFLQAGPLTKVTICKDK-EGKPKSFGFVCFKHSESVPYAIAL 61

Query: 123 MNGKRFAGREISV 135
           +NG R  GR I V
Sbjct: 62  LNGIRLYGRPIKV 74

This subfamily corresponds to the RRM or RBM11, a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. RBM11 is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. RBM11 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM of RBM11 is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	299
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.9
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.88
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.84
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.77
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.76
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.72
KOG0122	270	consensus Translation initiation factor 3, subunit	99.72
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.71
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.71
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.69
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.69
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.66
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.64
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.63
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.63
PLN03120	260	nucleic acid binding protein; Provisional	99.61
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.6
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.59
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.58
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.58
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.58
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.58
smart00362	72	RRM_2 RNA recognition motif.	99.58
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.57
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.57
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.56
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.55
PLN03213	759	repressor of silencing 3; Provisional	99.55
PLN03121	243	nucleic acid binding protein; Provisional	99.54
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.53
smart00360	71	RRM RNA recognition motif.	99.53
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.52
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.52
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.52
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.51
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.51
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.49
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.49
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.48
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.48
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.46
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.46
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.45
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.45
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.44
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.43
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.41
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.41
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.4
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.4
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.39
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.39
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.39
smart00361	70	RRM_1 RNA recognition motif.	99.38
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.38
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.37
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.34
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.34
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.26
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.22
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.21
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.2
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.19
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	99.18
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.16
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.15
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	99.13
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.11
KOG0533	243	consensus RRM motif-containing protein [RNA proces	99.1
KOG1995	351	consensus Conserved Zn-finger protein [General fun	99.1
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	99.09
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.07
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.05
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	99.03
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.02
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.99
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.97
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.97
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	98.94
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.94
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.93
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.93
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.93
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	98.92
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.87
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.84
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.81
KOG0151	877	consensus Predicted splicing regulator, contains R	98.76
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	98.65
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.64
KOG0226	290	consensus RNA-binding proteins [General function p	98.59
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.58
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	98.56
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	98.52
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	98.5
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.45
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	98.45
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.38
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.35
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	98.34
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.32
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	98.28
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.25
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	98.07
KOG4210	285	consensus Nuclear localization sequence binding pr	98.03
KOG2314	698	consensus Translation initiation factor 3, subunit	98.01
COG5175	480	MOT2 Transcriptional repressor [Transcription]	98.01
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.98
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.97
KOG1548	382	consensus Transcription elongation factor TAT-SF1	97.96
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	97.8
KOG3152	278	consensus TBP-binding protein, activator of basal	97.8
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	97.76
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.71
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	97.68
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	97.64
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.63
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.63
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.58
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	97.56
KOG1996	378	consensus mRNA splicing factor [RNA processing and	97.54
KOG2135	526	consensus Proteins containing the RNA recognition	97.25
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	97.22
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	97.16
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	97.12
KOG4207	256	consensus Predicted splicing factor, SR protein su	97.06
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	96.98
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	96.95
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	96.88
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	96.83
KOG4660	549	consensus Protein Mei2, essential for commitment t	96.77
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	96.7
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	96.69
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	96.66
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	96.66
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	96.66
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	96.63
KOG2068	327	consensus MOT2 transcription factor [Transcription	96.57
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	96.25
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	96.13
KOG2591	684	consensus c-Mpl binding protein, contains La domai	96.02
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	95.63
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	95.11
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	94.89
KOG4210	285	consensus Nuclear localization sequence binding pr	94.67
KOG2318	650	consensus Uncharacterized conserved protein [Funct	94.3
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	93.83
KOG4019	193	consensus Calcineurin-mediated signaling pathway i	91.9
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	90.58
KOG4410	396	consensus 5-formyltetrahydrofolate cyclo-ligase [C	89.54
PF07530	68	PRE_C2HC: Associated with zinc fingers; InterPro:	89.43
smart00596	69	PRE_C2HC PRE_C2HC domain.	89.27
KOG4483	528	consensus Uncharacterized conserved protein [Funct	89.24
PF03468	116	XS: XS domain; InterPro: IPR005380 The XS (rice ge	85.76
KOG4365	572	consensus Uncharacterized conserved protein [Funct	82.12
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	80.74
COG5638	622	Uncharacterized conserved protein [Function unknow	80.33

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

Probab=99.90  E-value=4.2e-22  Score=167.38  Aligned_cols=89  Identities=40%  Similarity=0.688  Sum_probs=83.7

Q ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEE
Q 043443           55 RRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREIS  134 (299)
Q Consensus        55 ~~~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~  134 (299)
                      +++.+..++|.|-||.+.|+.++|..+|++||.|.+|.|++|+.|.+++|||||.|.+..||++||++|||.+|+|+.|.
T Consensus         7 PPdv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelr   86 (256)
T KOG4207|consen    7 PPDVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELR   86 (256)
T ss_pred             CCCcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceee
Confidence            45667789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEcccCCC
Q 043443          135 VVLAAESRK  143 (299)
Q Consensus       135 V~~a~~~~~  143 (299)
                      |++|+-...
T Consensus        87 Vq~arygr~   95 (256)
T KOG4207|consen   87 VQMARYGRP   95 (256)
T ss_pred             ehhhhcCCC
Confidence            999985443

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

Probab=99.88  E-value=1.4e-21  Score=160.41  Aligned_cols=80  Identities=30%  Similarity=0.578  Sum_probs=74.3

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      +..++|||+||+..+++.||+.+|.+||.|..|||..++     .|||||||+++.||++|+..|||+.|+|..|.|+++
T Consensus         8 ~~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP-----PGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S   82 (195)
T KOG0107|consen    8 NGNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP-----PGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELS   82 (195)
T ss_pred             CCCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC-----CCceEEeccCcccHHHHHhhcCCccccCceEEEEee
Confidence            347899999999999999999999999999999998754     899999999999999999999999999999999999


Q ss_pred             ccCCC
Q 043443          139 AESRK  143 (299)
Q Consensus       139 ~~~~~  143 (299)
                      +....
T Consensus        83 ~G~~r   87 (195)
T KOG0107|consen   83 TGRPR   87 (195)
T ss_pred             cCCcc
Confidence            86543

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

Probab=99.84  E-value=4.7e-20  Score=151.81  Aligned_cols=85  Identities=33%  Similarity=0.466  Sum_probs=80.4

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      ...++|||+|||++++|++|+++|.+||.|+.|.|+.+..+++++|||||+|.+.++|+.||+.||+++|+|+.|+|+++
T Consensus        32 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a  111 (144)
T PLN03134         32 LMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPA  111 (144)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeC
Confidence            45679999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCC
Q 043443          139 AESRK  143 (299)
Q Consensus       139 ~~~~~  143 (299)
                      ..+..
T Consensus       112 ~~~~~  116 (144)
T PLN03134        112 NDRPS  116 (144)
T ss_pred             CcCCC
Confidence            86544

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.77  E-value=5.1e-18  Score=158.47  Aligned_cols=84  Identities=27%  Similarity=0.451  Sum_probs=79.9

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      .....++|||+|||+++|+++|+++|.+||+|+.|.|+.+..+++++|||||+|.++++|+.||+.||+++|.+++|+|.
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~  182 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVS  182 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeee
Confidence            44568899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             Eccc
Q 043443          137 LAAE  140 (299)
Q Consensus       137 ~a~~  140 (299)
                      ++++
T Consensus       183 ~a~p  186 (346)
T TIGR01659       183 YARP  186 (346)
T ss_pred             cccc
Confidence            9875

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).

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

Probab=99.76  E-value=6.1e-17  Score=143.09  Aligned_cols=88  Identities=24%  Similarity=0.471  Sum_probs=82.1

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      .++-+||||+-|+++++|..|+..|.+||.|+.|.||.++.||+++|||||+|+++.+++.|.+..+|++|+|+.|.|.+
T Consensus        98 gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDv  177 (335)
T KOG0113|consen   98 GDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDV  177 (335)
T ss_pred             CCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEe
Confidence            35678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCCc
Q 043443          138 AAESRKRP  145 (299)
Q Consensus       138 a~~~~~~~  145 (299)
                      -.......
T Consensus       178 ERgRTvkg  185 (335)
T KOG0113|consen  178 ERGRTVKG  185 (335)
T ss_pred             cccccccc
Confidence            87654443

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.72  E-value=3.8e-17  Score=153.05  Aligned_cols=83  Identities=27%  Similarity=0.380  Sum_probs=78.8

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      ...+|||+|||+.+++++|.++|++||.|+.|.|+.+..++.++|||||+|.+.++|..||+.|||..|+|+.|.|.|+.
T Consensus       268 ~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~  347 (352)
T TIGR01661       268 AGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKT  347 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcc
Confidence            34579999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cCC
Q 043443          140 ESR  142 (299)
Q Consensus       140 ~~~  142 (299)
                      .+.
T Consensus       348 ~~~  350 (352)
T TIGR01661       348 NKA  350 (352)
T ss_pred             CCC
Confidence            653

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

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

Probab=99.72  E-value=5.4e-17  Score=139.90  Aligned_cols=86  Identities=33%  Similarity=0.525  Sum_probs=81.9

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEE
Q 043443           56 RKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV  135 (299)
Q Consensus        56 ~~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V  135 (299)
                      +...+.++|-|.||+.+++|++|+++|.+||.|..|.|..|+.||.++|||||.|.+.++|.+||..|||.-++.-.|.|
T Consensus       184 R~R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrv  263 (270)
T KOG0122|consen  184 RERDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRV  263 (270)
T ss_pred             ccCCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEE
Confidence            34457899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEcccC
Q 043443          136 VLAAES  141 (299)
Q Consensus       136 ~~a~~~  141 (299)
                      +|+++.
T Consensus       264 EwskP~  269 (270)
T KOG0122|consen  264 EWSKPS  269 (270)
T ss_pred             EecCCC
Confidence            999874

>PF00076 RRM_1: RNA recognition motif

Probab=99.71  E-value=6.4e-17  Score=115.64  Aligned_cols=70  Identities=37%  Similarity=0.701  Sum_probs=66.7

Q ss_pred             EEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEE
Q 043443           64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREIS  134 (299)
Q Consensus        64 l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~  134 (299)
                      |||+|||.++++++|+++|.+||.|..|.|..+ .++...+||||+|.+.++|+.||+.|||..|+|+.|+
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 6788899999999999999999999999999999885

(a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.71  E-value=5.6e-17  Score=151.93  Aligned_cols=83  Identities=31%  Similarity=0.547  Sum_probs=78.8

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      ..++|||+|||..+++++|+++|..||+|..|.|+.++.+++++|||||+|.+.++|+.||+.|||+.|.|+.|.|++++
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            36799999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             cCC
Q 043443          140 ESR  142 (299)
Q Consensus       140 ~~~  142 (299)
                      +..
T Consensus        82 ~~~   84 (352)
T TIGR01661        82 PSS   84 (352)
T ss_pred             ccc
Confidence            543

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

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

Probab=99.69  E-value=4.6e-17  Score=127.42  Aligned_cols=81  Identities=23%  Similarity=0.441  Sum_probs=77.9

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      ..+||||+||++.++|++|.++|.++|+|..|.|-.|+.+..+.|||||+|.+.++|+.||..|+|+.|+.++|.|.|..
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            57899999999999999999999999999999999999999999999999999999999999999999999999999975


Q ss_pred             c
Q 043443          140 E  140 (299)
Q Consensus       140 ~  140 (299)
                      .
T Consensus       115 G  115 (153)
T KOG0121|consen  115 G  115 (153)
T ss_pred             c
Confidence            3

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.69  E-value=2.4e-16  Score=147.27  Aligned_cols=84  Identities=33%  Similarity=0.498  Sum_probs=77.6

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCC--eeEEEEE
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAG--REISVVL  137 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~G--r~i~V~~  137 (299)
                      ..++|||+|||..+||++|+++|.+||+|+.|.|+.++.++++++||||+|++.++|++||+.||+++|.+  +.|+|.+
T Consensus       192 ~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~  271 (346)
T TIGR01659       192 KDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRL  271 (346)
T ss_pred             ccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEE
Confidence            35789999999999999999999999999999999999999999999999999999999999999999876  6899999


Q ss_pred             cccCCC
Q 043443          138 AAESRK  143 (299)
Q Consensus       138 a~~~~~  143 (299)
                      ++....
T Consensus       272 a~~~~~  277 (346)
T TIGR01659       272 AEEHGK  277 (346)
T ss_pred             CCcccc
Confidence            886443

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).

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

Probab=99.66  E-value=2.5e-16  Score=124.43  Aligned_cols=88  Identities=23%  Similarity=0.404  Sum_probs=82.7

Q ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeE
Q 043443           54 GRRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREI  133 (299)
Q Consensus        54 ~~~~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i  133 (299)
                      +++...+...|||.++...+||++|.+.|..||+|++|+|..|..||..+|||+|+|++.++|++||..|||..|.|+.|
T Consensus        65 gPqrSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v  144 (170)
T KOG0130|consen   65 GPQRSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNV  144 (170)
T ss_pred             CCccceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCce
Confidence            44556678899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcccC
Q 043443          134 SVVLAAES  141 (299)
Q Consensus       134 ~V~~a~~~  141 (299)
                      .|.|+.-+
T Consensus       145 ~VDw~Fv~  152 (170)
T KOG0130|consen  145 SVDWCFVK  152 (170)
T ss_pred             eEEEEEec
Confidence            99999753

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

Probab=99.64  E-value=7.7e-16  Score=127.76  Aligned_cols=80  Identities=31%  Similarity=0.540  Sum_probs=73.0

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      ..++|||+|||.+|.+.||+++|-+||.|.+|+|...+   ...+||||+|++..||+.||..-||..++|..|.|+|+.
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~---g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfpr   81 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRP---GPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPR   81 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCC---CCCCeeEEEecCccchhhhhhcccccccCcceEEEEecc
Confidence            46799999999999999999999999999999997543   457899999999999999999999999999999999997


Q ss_pred             cCC
Q 043443          140 ESR  142 (299)
Q Consensus       140 ~~~  142 (299)
                      ...
T Consensus        82 ggr   84 (241)
T KOG0105|consen   82 GGR   84 (241)
T ss_pred             CCC
Confidence            543

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

Probab=99.63  E-value=5.1e-16  Score=133.41  Aligned_cols=82  Identities=27%  Similarity=0.445  Sum_probs=75.9

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      +..-++|||++|+|.+..++|.++|++||+|+++.|+.|+.+++++||+||+|.+.+.|+.||+. -+-+|+|++..|++
T Consensus         9 DT~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnl   87 (247)
T KOG0149|consen    9 DTTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNL   87 (247)
T ss_pred             CceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccch
Confidence            44568999999999999999999999999999999999999999999999999999999999984 55689999999999


Q ss_pred             ccc
Q 043443          138 AAE  140 (299)
Q Consensus       138 a~~  140 (299)
                      |--
T Consensus        88 A~l   90 (247)
T KOG0149|consen   88 ASL   90 (247)
T ss_pred             hhh
Confidence            864

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.63  E-value=2.2e-15  Score=108.29  Aligned_cols=70  Identities=40%  Similarity=0.667  Sum_probs=64.7

Q ss_pred             EEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEE
Q 043443           64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREIS  134 (299)
Q Consensus        64 l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~  134 (299)
                      |||+|||+.+++++|.++|..||.|..|.+..++. +..+++|||+|.+.++|+.||+.+++..|+|+.|.
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 ....

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.61  E-value=3.2e-15  Score=132.23  Aligned_cols=76  Identities=21%  Similarity=0.356  Sum_probs=70.6

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEccc
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAE  140 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~  140 (299)
                      ..+|||+||++.+++++|++||+.||+|+.|.|+.+.   ...|||||+|.+.++|+.||. |||..|.|+.|.|.++..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~---~~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSEN---ERSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecC---CCCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccC
Confidence            4699999999999999999999999999999998875   357899999999999999996 999999999999999864

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

Probab=99.60  E-value=4.2e-15  Score=137.64  Aligned_cols=85  Identities=29%  Similarity=0.491  Sum_probs=78.5

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCcee-CCeeEE
Q 043443           56 RKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRF-AGREIS  134 (299)
Q Consensus        56 ~~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l-~Gr~i~  134 (299)
                      ....-.+.|||+.||.++.|++|..||++.|+|-++.|++|+.+|.++|||||+|.+.++|+.||+.||+++| .|+.|.
T Consensus        78 ~~p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~ig  157 (506)
T KOG0117|consen   78 PPPPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLG  157 (506)
T ss_pred             CCCCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeE
Confidence            3335568999999999999999999999999999999999999999999999999999999999999999998 589998


Q ss_pred             EEEccc
Q 043443          135 VVLAAE  140 (299)
Q Consensus       135 V~~a~~  140 (299)
                      |+++..
T Consensus       158 vc~Sva  163 (506)
T KOG0117|consen  158 VCVSVA  163 (506)
T ss_pred             EEEeee
Confidence            888764

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

Probab=99.59  E-value=6.7e-15  Score=144.54  Aligned_cols=83  Identities=27%  Similarity=0.458  Sum_probs=78.6

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      ....+|||+|||+.+++++|+++|+.||.|..|.|+.+..++.++|||||+|.+.++|+.||+.|||+.|+|+.|.|.++
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            34679999999999999999999999999999999999889999999999999999999999999999999999999998


Q ss_pred             ccC
Q 043443          139 AES  141 (299)
Q Consensus       139 ~~~  141 (299)
                      ...
T Consensus       373 ~~~  375 (509)
T TIGR01642       373 CVG  375 (509)
T ss_pred             ccC
Confidence            753

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

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

Probab=99.58  E-value=5.3e-15  Score=145.85  Aligned_cols=80  Identities=31%  Similarity=0.533  Sum_probs=76.5

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      ..++|||+||++.+++++|+++|.+||.|..|.|+.|+.+++++|||||+|.+.++|+.||+.|||..|+|+.|.|.+..
T Consensus       106 ~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~  185 (612)
T TIGR01645       106 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  185 (612)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecccc
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999998654

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

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

Probab=99.58  E-value=4e-15  Score=133.12  Aligned_cols=81  Identities=36%  Similarity=0.555  Sum_probs=75.3

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      ....+|+|.|||+...+.||..+|++||.|.+|.|+.+  ...+|||+||+|++.+||++|-++|||.+|.|++|.|..+
T Consensus        94 ~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfN--ERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~A  171 (376)
T KOG0125|consen   94 DTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFN--ERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNA  171 (376)
T ss_pred             CCCceeEeecCCccccCccHHHHHHhhCceeeEEEEec--cCCCCccceEEecChhhHHHHHHHhhcceeeceEEEEecc
Confidence            35689999999999999999999999999999999876  4578999999999999999999999999999999999999


Q ss_pred             ccC
Q 043443          139 AES  141 (299)
Q Consensus       139 ~~~  141 (299)
                      +..
T Consensus       172 Tar  174 (376)
T KOG0125|consen  172 TAR  174 (376)
T ss_pred             chh
Confidence            853

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

Probab=99.58  E-value=7.9e-15  Score=142.24  Aligned_cols=80  Identities=44%  Similarity=0.614  Sum_probs=77.2

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEccc
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAE  140 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~  140 (299)
                      ..+|||+|||..+++++|+++|.+||.|..|.|+.+..++.++|||||+|.+.++|+.||+.|||.+|.|+.|.|.|+..
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~~  265 (457)
T TIGR01622       186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQD  265 (457)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccC
Confidence            68999999999999999999999999999999999988899999999999999999999999999999999999999874

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=99.58  E-value=9.1e-15  Score=144.20  Aligned_cols=82  Identities=18%  Similarity=0.318  Sum_probs=78.2

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      ..++|||+||+.++++++|+++|+.||.|+.|.|+.++.++..+|||||+|.+.++|..||+.||+.+|+|+.|.|.++.
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi  282 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  282 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecC
Confidence            45799999999999999999999999999999999999899999999999999999999999999999999999999988


Q ss_pred             cC
Q 043443          140 ES  141 (299)
Q Consensus       140 ~~  141 (299)
                      ..
T Consensus       283 ~p  284 (612)
T TIGR01645       283 TP  284 (612)
T ss_pred             CC
Confidence            53

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=99.58  E-value=1.6e-14  Score=102.32  Aligned_cols=72  Identities=39%  Similarity=0.746  Sum_probs=67.1

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        63 ~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      +|||.|||..+++++|+++|.+||.|..|.+..+.  +.+.++|||+|.+.++|+.|++.|++..|.|+.|.|.
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            58999999999999999999999999999988765  6778999999999999999999999999999998873

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

Probab=99.57  E-value=2.8e-16  Score=129.98  Aligned_cols=81  Identities=25%  Similarity=0.492  Sum_probs=77.4

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      +..-|||+|||+.+||.||..+|++||+|++|.|+.|+.||+++||||+.|++......||..|||..|.|+.|.|.+..
T Consensus        34 dsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~  113 (219)
T KOG0126|consen   34 DSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVS  113 (219)
T ss_pred             cceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeecc
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999998865


Q ss_pred             c
Q 043443          140 E  140 (299)
Q Consensus       140 ~  140 (299)
                      .
T Consensus       114 ~  114 (219)
T KOG0126|consen  114 N  114 (219)
T ss_pred             c
Confidence            3

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

Probab=99.57  E-value=1e-14  Score=143.46  Aligned_cols=79  Identities=33%  Similarity=0.528  Sum_probs=72.2

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeC-CeeEEEEE
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFA-GREISVVL  137 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~-Gr~i~V~~  137 (299)
                      ...++|||+|||.+++|++|.++|++||.|.+|.|++| .++.++|||||+|.+.++|++||+.||+.+|. |+.|.|.+
T Consensus        56 ~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~  134 (578)
T TIGR01648        56 GRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCI  134 (578)
T ss_pred             CCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCccccccc
Confidence            34689999999999999999999999999999999999 78999999999999999999999999999885 77766654


Q ss_pred             c
Q 043443          138 A  138 (299)
Q Consensus       138 a  138 (299)
                      +
T Consensus       135 S  135 (578)
T TIGR01648       135 S  135 (578)
T ss_pred             c
Confidence            4

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

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

Probab=99.56  E-value=1.9e-14  Score=139.53  Aligned_cols=82  Identities=29%  Similarity=0.456  Sum_probs=76.9

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      +....+|||+|||..+++++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|++||. |+|+.|.|..|.|.+
T Consensus        86 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~  164 (457)
T TIGR01622        86 ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQS  164 (457)
T ss_pred             ccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEee
Confidence            3457799999999999999999999999999999999999999999999999999999999997 899999999999998


Q ss_pred             ccc
Q 043443          138 AAE  140 (299)
Q Consensus       138 a~~  140 (299)
                      +..
T Consensus       165 ~~~  167 (457)
T TIGR01622       165 SQA  167 (457)
T ss_pred             cch
Confidence            754

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

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

Probab=99.55  E-value=1.8e-14  Score=143.41  Aligned_cols=78  Identities=31%  Similarity=0.484  Sum_probs=75.3

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEccc
Q 043443           63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAE  140 (299)
Q Consensus        63 ~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~  140 (299)
                      +|||+|||.++||++|.++|.+||.|..|.|+.|..|++++|||||+|.+.++|++||+.||+..|.|+.|.|.|+..
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~~   79 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQR   79 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccc
Confidence            799999999999999999999999999999999999999999999999999999999999999999999999999753

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

>PLN03213 repressor of silencing 3; Provisional

Probab=99.55  E-value=1.9e-14  Score=134.81  Aligned_cols=77  Identities=22%  Similarity=0.315  Sum_probs=71.2

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCH--HHHHHHHHhhCCceeCCeeEEEEE
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDP--YEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~--~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      ...+||||||++.|+++||..+|..||.|..|.|+.  .+|  +|||||+|.+.  .++.+||..|||.+|.|+.|+|+.
T Consensus         9 ~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpR--ETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNK   84 (759)
T PLN03213          9 GGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVR--TKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEK   84 (759)
T ss_pred             cceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEec--ccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEee
Confidence            357999999999999999999999999999999994  456  89999999987  789999999999999999999999


Q ss_pred             ccc
Q 043443          138 AAE  140 (299)
Q Consensus       138 a~~  140 (299)
                      |++
T Consensus        85 AKP   87 (759)
T PLN03213         85 AKE   87 (759)
T ss_pred             ccH
Confidence            975

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.54  E-value=3.6e-14  Score=123.83  Aligned_cols=77  Identities=17%  Similarity=0.245  Sum_probs=70.2

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      ...+|||+||++.+|+++|++||+.||+|.+|.|+.+.   ...+||||+|.++++|+.||. |||..|.++.|.|..+.
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~   79 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWG   79 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCc
Confidence            34799999999999999999999999999999999874   445899999999999999995 99999999999998876


Q ss_pred             c
Q 043443          140 E  140 (299)
Q Consensus       140 ~  140 (299)
                      .
T Consensus        80 ~   80 (243)
T PLN03121         80 Q   80 (243)
T ss_pred             c
Confidence            4

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

Probab=99.53  E-value=1.6e-14  Score=119.65  Aligned_cols=81  Identities=28%  Similarity=0.366  Sum_probs=77.8

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      +...||||+||+..++++.|.++|-+.|.|..|.|+.|+.+...+|||||||.++++|+-||+.||...|.|++|+|..+
T Consensus         7 nqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~ka   86 (203)
T KOG0131|consen    7 NQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKA   86 (203)
T ss_pred             CCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEec
Confidence            45689999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             c
Q 043443          139 A  139 (299)
Q Consensus       139 ~  139 (299)
                      .
T Consensus        87 s   87 (203)
T KOG0131|consen   87 S   87 (203)
T ss_pred             c
Confidence            7

>smart00360 RRM RNA recognition motif

Probab=99.53  E-value=4.8e-14  Score=99.40  Aligned_cols=71  Identities=42%  Similarity=0.697  Sum_probs=66.8

Q ss_pred             EeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           66 VRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        66 V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      |+|||..+++++|+++|.+||.|..|.+..++.++.++++|||+|.+.++|+.|++.|++..|.|+.|.|.
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            67999999999999999999999999999887778899999999999999999999999999999998873

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

Probab=99.52  E-value=8.1e-15  Score=124.71  Aligned_cols=86  Identities=33%  Similarity=0.544  Sum_probs=81.4

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      ....+|||++|..+++|.-|...|-.||.|+.|.|+.|..+++.+|||||+|+..+||.+||..||+.+|.|+.|.|.+|
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~A   87 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA   87 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeec
Confidence            45679999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 043443          139 AESRKR  144 (299)
Q Consensus       139 ~~~~~~  144 (299)
                      ++.+..
T Consensus        88 kP~kik   93 (298)
T KOG0111|consen   88 KPEKIK   93 (298)
T ss_pred             CCcccc
Confidence            976543

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

Probab=99.52  E-value=5.6e-14  Score=139.86  Aligned_cols=83  Identities=31%  Similarity=0.487  Sum_probs=77.8

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      ..++|||+||+..+++++|+++|++||.|+.|.|+.+ .++.++|||||+|.+.++|++||..|||..|+|+.|.|.++.
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            4678999999999999999999999999999999988 688999999999999999999999999999999999999998


Q ss_pred             cCCC
Q 043443          140 ESRK  143 (299)
Q Consensus       140 ~~~~  143 (299)
                      .+..
T Consensus       363 ~k~~  366 (562)
T TIGR01628       363 RKEQ  366 (562)
T ss_pred             CcHH
Confidence            6543

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

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

Probab=99.52  E-value=6.6e-14  Score=123.93  Aligned_cols=80  Identities=41%  Similarity=0.676  Sum_probs=77.1

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEccc
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAE  140 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~  140 (299)
                      .++|||+|||+.+++++|.++|.+||.|..|.|+.++.++..+|||||+|.+.++|+.||..|++..|.|+.|.|.++..
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~  194 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQP  194 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeecccc
Confidence            59999999999999999999999999999999999988999999999999999999999999999999999999999753

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

Probab=99.51  E-value=8.3e-14  Score=105.37  Aligned_cols=81  Identities=27%  Similarity=0.507  Sum_probs=73.7

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      .+.+..|||.|||+.+|.+++.++|.+||.|..|.|-..+   ..+|.|||.|++..+|++|+.+|+|..+++..|.|-+
T Consensus        15 pevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k---~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vly   91 (124)
T KOG0114|consen   15 PEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTK---ETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLY   91 (124)
T ss_pred             hhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCcc---CcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEe
Confidence            3456789999999999999999999999999999998765   4589999999999999999999999999999999988


Q ss_pred             cccC
Q 043443          138 AAES  141 (299)
Q Consensus       138 a~~~  141 (299)
                      .++.
T Consensus        92 yq~~   95 (124)
T KOG0114|consen   92 YQPE   95 (124)
T ss_pred             cCHH
Confidence            7753

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability

Probab=99.51  E-value=1.6e-13  Score=97.62  Aligned_cols=74  Identities=41%  Similarity=0.694  Sum_probs=68.4

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        63 ~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      +|+|.|||..+++++|+++|..||.|..+.+..+..+ ...++|||+|.+.++|..|++.|++..|+|..|.|.+
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            4899999999999999999999999999999877544 6689999999999999999999999999999999864

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).

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

Probab=99.49  E-value=9.8e-14  Score=121.45  Aligned_cols=79  Identities=29%  Similarity=0.458  Sum_probs=74.3

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      ...++|+|||+||+..++|++|++.|..||.|.+|.|.++      +||+||.|++.|.|..||..||+++|.|..|++.
T Consensus       160 ssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~------qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCs  233 (321)
T KOG0148|consen  160 SSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD------QGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCS  233 (321)
T ss_pred             CCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc------cceEEEEecchhhHHHHHHHhcCceeCceEEEEe
Confidence            3457899999999999999999999999999999999988      6999999999999999999999999999999999


Q ss_pred             EcccC
Q 043443          137 LAAES  141 (299)
Q Consensus       137 ~a~~~  141 (299)
                      |-+..
T Consensus       234 WGKe~  238 (321)
T KOG0148|consen  234 WGKEG  238 (321)
T ss_pred             ccccC
Confidence            98753

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

Probab=99.49  E-value=4.1e-14  Score=123.78  Aligned_cols=82  Identities=30%  Similarity=0.514  Sum_probs=78.7

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEccc
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAE  140 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~  140 (299)
                      ...|||+-|...|+-++|++.|.+||+|.++.|++|..|++++||+||.|.+.++|+.||..|||+.|+++.|...||+-
T Consensus        62 hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATR  141 (321)
T KOG0148|consen   62 HFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATR  141 (321)
T ss_pred             ceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeecccccc
Confidence            56899999999999999999999999999999999999999999999999999999999999999999999999999986


Q ss_pred             CC
Q 043443          141 SR  142 (299)
Q Consensus       141 ~~  142 (299)
                      +.
T Consensus       142 Kp  143 (321)
T KOG0148|consen  142 KP  143 (321)
T ss_pred             Cc
Confidence            54

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

Probab=99.48  E-value=1.6e-13  Score=135.21  Aligned_cols=74  Identities=35%  Similarity=0.496  Sum_probs=69.2

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcC--CCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFERF--GVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~~~--G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      ..+|||+||++.+++++|+++|++|  |+|+.|.+++        +||||+|++.++|++||+.||+.+|+|+.|+|.|+
T Consensus       233 ~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~r--------gfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~A  304 (578)
T TIGR01648       233 VKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIR--------DYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLA  304 (578)
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeec--------CeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            4689999999999999999999999  9999998763        59999999999999999999999999999999999


Q ss_pred             ccCC
Q 043443          139 AESR  142 (299)
Q Consensus       139 ~~~~  142 (299)
                      ++..
T Consensus       305 kp~~  308 (578)
T TIGR01648       305 KPVD  308 (578)
T ss_pred             cCCC
Confidence            8753

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.

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

Probab=99.48  E-value=2.4e-13  Score=132.88  Aligned_cols=79  Identities=24%  Similarity=0.386  Sum_probs=72.6

Q ss_pred             CCCCCEEEEeCCCC-CCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           58 EQNHGSLLVRNIPL-DCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        58 ~~~~~~l~V~nLp~-~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      ....++|||+||++ .+|+++|.++|++||.|..|.|+.++     +|||||+|.+.++|+.||..|||..|.|+.|.|.
T Consensus       272 ~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~  346 (481)
T TIGR01649       272 GGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK-----KETALIEMADPYQAQLALTHLNGVKLFGKPLRVC  346 (481)
T ss_pred             CCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEE
Confidence            34678999999997 69999999999999999999998763     6999999999999999999999999999999999


Q ss_pred             EcccC
Q 043443          137 LAAES  141 (299)
Q Consensus       137 ~a~~~  141 (299)
                      +++..
T Consensus       347 ~s~~~  351 (481)
T TIGR01649       347 PSKQQ  351 (481)
T ss_pred             Ecccc
Confidence            98754

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).

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

Probab=99.46  E-value=2.7e-13  Score=118.07  Aligned_cols=85  Identities=31%  Similarity=0.562  Sum_probs=80.7

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      .++..+.|.|.-||.++|++||+.+|...|+|+.|+++.|+.+|++.||+||.|.+++||++||..|||..|..+.|+|.
T Consensus        37 t~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVS  116 (360)
T KOG0145|consen   37 TDESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVS  116 (360)
T ss_pred             cCcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEE
Confidence            34566789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EcccC
Q 043443          137 LAAES  141 (299)
Q Consensus       137 ~a~~~  141 (299)
                      ||.+.
T Consensus       117 yARPS  121 (360)
T KOG0145|consen  117 YARPS  121 (360)
T ss_pred             eccCC
Confidence            99864

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

Probab=99.46  E-value=1.4e-13  Score=130.83  Aligned_cols=83  Identities=35%  Similarity=0.568  Sum_probs=79.6

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcccC
Q 043443           62 GSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAES  141 (299)
Q Consensus        62 ~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~~  141 (299)
                      +.|||+|||+++++++|.++|...|.|..+.++.|+.||+++|||||+|.+.++|+.||..|||.+|.|++|+|.|+...
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            79999999999999999999999999999999999999999999999999999999999999999999999999999865


Q ss_pred             CCC
Q 043443          142 RKR  144 (299)
Q Consensus       142 ~~~  144 (299)
                      ...
T Consensus        99 ~~~  101 (435)
T KOG0108|consen   99 KNA  101 (435)
T ss_pred             chh
Confidence            443

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

Probab=99.45  E-value=9.9e-14  Score=122.51  Aligned_cols=72  Identities=28%  Similarity=0.497  Sum_probs=68.9

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcccC
Q 043443           62 GSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAES  141 (299)
Q Consensus        62 ~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~~  141 (299)
                      .+|||+|||..+++++|+.+|++||+|.+|+|++        .||||..++...|+.||..||+..|+|..|+|+-++.+
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvK--------NYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK   74 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVK--------NYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK   74 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeec--------ccceEEeecccccHHHHhhcccceecceEEEEEecccc
Confidence            5799999999999999999999999999999996        49999999999999999999999999999999999876

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

Probab=99.45  E-value=4.7e-13  Score=116.59  Aligned_cols=81  Identities=30%  Similarity=0.433  Sum_probs=77.7

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEccc
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAE  140 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~  140 (299)
                      ..+|||-||..+++|..|+++|..||.|..|+|++|..|.+.+||+||.+.+.++|..||..|||..|.++.|.|.|...
T Consensus       278 g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFKtn  357 (360)
T KOG0145|consen  278 GWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTN  357 (360)
T ss_pred             eeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEecC
Confidence            47999999999999999999999999999999999999999999999999999999999999999999999999999765


Q ss_pred             C
Q 043443          141 S  141 (299)
Q Consensus       141 ~  141 (299)
                      +
T Consensus       358 k  358 (360)
T KOG0145|consen  358 K  358 (360)
T ss_pred             C
Confidence            3

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

Probab=99.44  E-value=1.6e-13  Score=124.01  Aligned_cols=84  Identities=23%  Similarity=0.347  Sum_probs=80.0

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      ..+.+.|||..|.+.++.+||+-+|+.||.|..|.|+.|..||.+..||||||++.++|++|+-+|++..|+.+.|+|.|
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDF  315 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDF  315 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeeh
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccC
Q 043443          138 AAES  141 (299)
Q Consensus       138 a~~~  141 (299)
                      ++..
T Consensus       316 SQSV  319 (479)
T KOG0415|consen  316 SQSV  319 (479)
T ss_pred             hhhh
Confidence            8753

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

Probab=99.43  E-value=5.3e-13  Score=130.53  Aligned_cols=74  Identities=22%  Similarity=0.236  Sum_probs=68.4

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhh--CCceeCCeeEEEEEc
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM--NGKRFAGREISVVLA  138 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~l--ng~~l~Gr~i~V~~a  138 (299)
                      ..+|||+|||+.+++++|.++|++||.|..|.|+.+      ++||||+|++.++|+.||+.|  ++..|.|+.|.|+|+
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            468999999999999999999999999999999865      589999999999999999864  788999999999998


Q ss_pred             cc
Q 043443          139 AE  140 (299)
Q Consensus       139 ~~  140 (299)
                      ..
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).

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

Probab=99.41  E-value=1e-12  Score=121.66  Aligned_cols=79  Identities=33%  Similarity=0.479  Sum_probs=73.4

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHh-cCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFE-RFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~-~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      ...|||+|||+++.|++|+++|. +.|+|++|.|..| ..++.+|||+|||+++|.+++|++.||.++|.|+.|.|....
T Consensus        44 ~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D-~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~  122 (608)
T KOG4212|consen   44 DRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFD-ESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDH  122 (608)
T ss_pred             cceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecc-cCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccC
Confidence            34599999999999999999995 7899999999988 489999999999999999999999999999999999998876


Q ss_pred             c
Q 043443          140 E  140 (299)
Q Consensus       140 ~  140 (299)
                      .
T Consensus       123 d  123 (608)
T KOG4212|consen  123 D  123 (608)
T ss_pred             c
Confidence            5

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

Probab=99.41  E-value=4.5e-13  Score=124.32  Aligned_cols=75  Identities=37%  Similarity=0.553  Sum_probs=70.1

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEccc
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAE  140 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~  140 (299)
                      -..|||.||+.+|||+.|+++|++||.|+.|..++|        ||||.|.+.++|.+|++.|||++|+|..|.|.+|++
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            358999999999999999999999999999988865        999999999999999999999999999999999997


Q ss_pred             CCC
Q 043443          141 SRK  143 (299)
Q Consensus       141 ~~~  143 (299)
                      ..+
T Consensus       331 ~~k  333 (506)
T KOG0117|consen  331 VDK  333 (506)
T ss_pred             hhh
Confidence            543

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

Probab=99.40  E-value=2.7e-13  Score=118.56  Aligned_cols=86  Identities=24%  Similarity=0.351  Sum_probs=81.5

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      ...+.|.|||..||.+..+.||..+|-.||.|+..+|..|+.|+.+++|+||.|+++..|+.||..|||+.|+-+.|+|+
T Consensus       281 eGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQ  360 (371)
T KOG0146|consen  281 EGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQ  360 (371)
T ss_pred             cCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhh
Confidence            34578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EcccCC
Q 043443          137 LAAESR  142 (299)
Q Consensus       137 ~a~~~~  142 (299)
                      +..++.
T Consensus       361 LKRPkd  366 (371)
T KOG0146|consen  361 LKRPKD  366 (371)
T ss_pred             hcCccc
Confidence            987654

>PF13893 RRM_5: RNA recognition motif

Probab=99.40  E-value=1.9e-12  Score=89.03  Aligned_cols=56  Identities=39%  Similarity=0.691  Sum_probs=51.0

Q ss_pred             HHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           78 LRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        78 L~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      |.++|++||+|..|.+..+.     .++|||+|.+.++|+.|++.|||..|+|++|+|+|+
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            68999999999999997652     589999999999999999999999999999999986

(a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....

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

Probab=99.39  E-value=9.9e-13  Score=124.66  Aligned_cols=82  Identities=33%  Similarity=0.676  Sum_probs=75.5

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEccc
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAE  140 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~  140 (299)
                      ...|+|.|||+.|...+|+.+|+.||.|.+|.|+... .++.+|||||+|.+..+|..||+.||+.+|+|++|.|.||-+
T Consensus       117 k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~-dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~  195 (678)
T KOG0127|consen  117 KWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKK-DGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVD  195 (678)
T ss_pred             cceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCC-CCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeecc
Confidence            6789999999999999999999999999999999765 555669999999999999999999999999999999999986


Q ss_pred             CCC
Q 043443          141 SRK  143 (299)
Q Consensus       141 ~~~  143 (299)
                      +..
T Consensus       196 Kd~  198 (678)
T KOG0127|consen  196 KDT  198 (678)
T ss_pred             ccc
Confidence            543

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

Probab=99.39  E-value=1.2e-12  Score=124.21  Aligned_cols=84  Identities=33%  Similarity=0.532  Sum_probs=76.7

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhh-----CC-ceeCCe
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM-----NG-KRFAGR  131 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~l-----ng-~~l~Gr  131 (299)
                      .....+|||.|||+++|+++|.++|.+||+|.++.|+.++.|+.++|.|||.|.+..+|+.||...     .| ..|+|+
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            344689999999999999999999999999999999999999999999999999999999999865     34 678999


Q ss_pred             eEEEEEcccC
Q 043443          132 EISVVLAAES  141 (299)
Q Consensus       132 ~i~V~~a~~~  141 (299)
                      .|.|.+|...
T Consensus       369 ~Lkv~~Av~R  378 (678)
T KOG0127|consen  369 LLKVTLAVTR  378 (678)
T ss_pred             EEeeeeccch
Confidence            9999998754

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

Probab=99.39  E-value=8.1e-13  Score=122.18  Aligned_cols=88  Identities=31%  Similarity=0.526  Sum_probs=78.5

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCce-eCC--eeE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKR-FAG--REI  133 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~-l~G--r~i  133 (299)
                      .+.+.-+|||+-||..++|.||+++|++||.|.+|.|++|+.|+..+|||||.|.+.++|.+||.+|+++. |-|  ..|
T Consensus        30 ~d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pv  109 (510)
T KOG0144|consen   30 PDGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPV  109 (510)
T ss_pred             CCchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcce
Confidence            44567799999999999999999999999999999999999999999999999999999999999998764 544  688


Q ss_pred             EEEEcccCCCC
Q 043443          134 SVVLAAESRKR  144 (299)
Q Consensus       134 ~V~~a~~~~~~  144 (299)
                      .|.+|..+.++
T Consensus       110 qvk~Ad~E~er  120 (510)
T KOG0144|consen  110 QVKYADGERER  120 (510)
T ss_pred             eecccchhhhc
Confidence            88888766554

>smart00361 RRM_1 RNA recognition motif

Probab=99.38  E-value=1.8e-12  Score=93.46  Aligned_cols=61  Identities=28%  Similarity=0.485  Sum_probs=55.3

Q ss_pred             HHHHHHHHh----cCCCEeEEE-eccCCCC--CCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEE
Q 043443           75 PEELRAPFE----RFGVVRDVY-LPKDYYT--GEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV  135 (299)
Q Consensus        75 e~dL~~~F~----~~G~I~~v~-i~~d~~~--g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V  135 (299)
                      +++|+++|.    +||.|..|. |+.++.+  +.++|||||+|.+.++|++||+.|||..|.|+.|.+
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            578899998    999999995 6666656  889999999999999999999999999999999986

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

Probab=99.38  E-value=4.9e-13  Score=123.62  Aligned_cols=86  Identities=30%  Similarity=0.546  Sum_probs=77.4

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCce-eCC--eeEEEE
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKR-FAG--REISVV  136 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~-l~G--r~i~V~  136 (299)
                      +..+|||+-|+..+||+||.++|.+||.|++|.|+++. .+.++|||||+|.+.+.|..||+.|||.. |.|  .+|.|.
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            47899999999999999999999999999999999985 78999999999999999999999999975 555  589999


Q ss_pred             EcccCCCCch
Q 043443          137 LAAESRKRPE  146 (299)
Q Consensus       137 ~a~~~~~~~~  146 (299)
                      ||..++.+..
T Consensus       202 FADtqkdk~~  211 (510)
T KOG0144|consen  202 FADTQKDKDG  211 (510)
T ss_pred             ecccCCCchH
Confidence            9988766543

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

Probab=99.37  E-value=8e-13  Score=125.57  Aligned_cols=79  Identities=38%  Similarity=0.616  Sum_probs=75.6

Q ss_pred             EEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcccCC
Q 043443           64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAESR  142 (299)
Q Consensus        64 l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~~~  142 (299)
                      |||+||+.++++++|..+|+.||.|..|++++|..||.++||+||+|.+.++|.+|++.|||.+|.|+.|+|.+.+...
T Consensus       281 l~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r~  359 (549)
T KOG0147|consen  281 LYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTERV  359 (549)
T ss_pred             hhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeeec
Confidence            9999999999999999999999999999999998899999999999999999999999999999999999998877543

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

Probab=99.34  E-value=7.2e-13  Score=120.22  Aligned_cols=80  Identities=31%  Similarity=0.533  Sum_probs=76.4

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      ..|+|||+.|.+.+.|+.|...|..||.|+.|+|.||+.|++.+|||||||+-++.|+.|++.|||.+|+|+.|+|..-.
T Consensus       112 iMcRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPs  191 (544)
T KOG0124|consen  112 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  191 (544)
T ss_pred             HhHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCC
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999997543

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

Probab=99.34  E-value=9.4e-13  Score=116.37  Aligned_cols=83  Identities=31%  Similarity=0.523  Sum_probs=74.9

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      ....++|+|+||.+.++.+||.+.|++||.|.+|+|++        +|+||.|+-.++|..||..||+.+|.|+.|+|++
T Consensus        75 sk~stkl~vgNis~tctn~ElRa~fe~ygpviecdivk--------dy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~  146 (346)
T KOG0109|consen   75 SKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVK--------DYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQL  146 (346)
T ss_pred             CCCccccccCCCCccccCHHHhhhhcccCCceeeeeec--------ceeEEEEeeccchHHHHhcccccccccceeeeee
Confidence            44678999999999999999999999999999999996        4999999999999999999999999999999999


Q ss_pred             cccCCCCchhh
Q 043443          138 AAESRKRPEEM  148 (299)
Q Consensus       138 a~~~~~~~~~~  148 (299)
                      ++..-.....|
T Consensus       147 stsrlrtapgm  157 (346)
T KOG0109|consen  147 STSRLRTAPGM  157 (346)
T ss_pred             eccccccCCCC
Confidence            98655444433

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

Probab=99.26  E-value=1.6e-11  Score=120.71  Aligned_cols=76  Identities=21%  Similarity=0.269  Sum_probs=63.0

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcC------------CCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhC
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERF------------GVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMN  124 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~------------G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~ln  124 (299)
                      ......+|||+|||+.+|+++|++||.+|            +.|..|.+..      .++||||+|.+.++|+.||. ||
T Consensus       171 ~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~~~------~kg~afVeF~~~e~A~~Al~-l~  243 (509)
T TIGR01642       171 ATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNINK------EKNFAFLEFRTVEEATFAMA-LD  243 (509)
T ss_pred             CCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEECC------CCCEEEEEeCCHHHHhhhhc-CC
Confidence            34456799999999999999999999974            3444555543      37999999999999999995 99


Q ss_pred             CceeCCeeEEEEEcc
Q 043443          125 GKRFAGREISVVLAA  139 (299)
Q Consensus       125 g~~l~Gr~i~V~~a~  139 (299)
                      |+.|.|..|.|....
T Consensus       244 g~~~~g~~l~v~r~~  258 (509)
T TIGR01642       244 SIIYSNVFLKIRRPH  258 (509)
T ss_pred             CeEeeCceeEecCcc
Confidence            999999999987543

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

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

Probab=99.22  E-value=2.7e-10  Score=94.93  Aligned_cols=84  Identities=19%  Similarity=0.364  Sum_probs=70.3

Q ss_pred             CCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCce
Q 043443           48 GGGGGYGRRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKR  127 (299)
Q Consensus        48 gg~g~~~~~~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~  127 (299)
                      ++++..+++.......|.|.+||...+|+||++++.+.|.|+..++.+|       ++++|+|...+|++-||.+|+.+.
T Consensus       102 g~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-------g~GvV~~~r~eDMkYAvr~ld~~~  174 (241)
T KOG0105|consen  102 GGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-------GVGVVEYLRKEDMKYAVRKLDDQK  174 (241)
T ss_pred             CCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-------cceeeeeeehhhHHHHHHhhcccc
Confidence            3344455666677889999999999999999999999999999999887       799999999999999999999887


Q ss_pred             eC--CeeEEEEEc
Q 043443          128 FA--GREISVVLA  138 (299)
Q Consensus       128 l~--Gr~i~V~~a  138 (299)
                      +.  |....|.+-
T Consensus       175 ~~seGe~~yirv~  187 (241)
T KOG0105|consen  175 FRSEGETAYIRVR  187 (241)
T ss_pred             ccCcCcEeeEEec
Confidence            64  555444443

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

Probab=99.21  E-value=2.2e-11  Score=101.18  Aligned_cols=84  Identities=27%  Similarity=0.431  Sum_probs=77.0

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEE-EeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDV-YLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v-~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      ....|||+||.+.++|..|.++|+.||.|... .++.+..|+.+++||||.|.+.+.+.+||..|||+.++.++|+|.++
T Consensus        95 vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya  174 (203)
T KOG0131|consen   95 VGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSYA  174 (203)
T ss_pred             ccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEEE
Confidence            45789999999999999999999999998653 77888889999999999999999999999999999999999999999


Q ss_pred             ccCCC
Q 043443          139 AESRK  143 (299)
Q Consensus       139 ~~~~~  143 (299)
                      ..+..
T Consensus       175 ~k~~~  179 (203)
T KOG0131|consen  175 FKKDT  179 (203)
T ss_pred             EecCC
Confidence            86543

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

Probab=99.20  E-value=5.3e-11  Score=102.27  Aligned_cols=81  Identities=28%  Similarity=0.461  Sum_probs=73.5

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHH----HHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEE
Q 043443           59 QNHGSLLVRNIPLDCRPEELRA----PFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREIS  134 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~----~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~  134 (299)
                      ++..||||.||+..+..++|+.    +|++||+|.+|.+..   +.+.+|.|||.|.+.+.|-.|+..|+|..|.|+.|.
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            3445999999999999999888    999999999998775   568899999999999999999999999999999999


Q ss_pred             EEEcccCC
Q 043443          135 VVLAAESR  142 (299)
Q Consensus       135 V~~a~~~~  142 (299)
                      |+||+.+.
T Consensus        84 iqyA~s~s   91 (221)
T KOG4206|consen   84 IQYAKSDS   91 (221)
T ss_pred             eecccCcc
Confidence            99998654

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

Probab=99.19  E-value=5.8e-11  Score=110.16  Aligned_cols=76  Identities=32%  Similarity=0.541  Sum_probs=68.4

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      ....|+|||.|||.++||+.|++-|..||.|.+++|+.   .++.+|  .|.|.++++|+.||..|||..|+|+.|.|.|
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            34578999999999999999999999999999999953   456665  8999999999999999999999999999987


Q ss_pred             c
Q 043443          138 A  138 (299)
Q Consensus       138 a  138 (299)
                      +
T Consensus       608 ~  608 (608)
T KOG4212|consen  608 F  608 (608)
T ss_pred             C
Confidence            4

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

Probab=99.18  E-value=8.3e-11  Score=99.63  Aligned_cols=83  Identities=25%  Similarity=0.371  Sum_probs=76.0

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERF-GVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~-G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      .....++|..||..+.+.+|..+|.+| |.|..+.+..++.||.++|||||+|++.+.|+-|.+.||+..|.++.|.|.+
T Consensus        47 ~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~v  126 (214)
T KOG4208|consen   47 EIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHV  126 (214)
T ss_pred             CCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEE
Confidence            345679999999999999999999998 7788888889999999999999999999999999999999999999999988


Q ss_pred             cccC
Q 043443          138 AAES  141 (299)
Q Consensus       138 a~~~  141 (299)
                      -.+.
T Consensus       127 mppe  130 (214)
T KOG4208|consen  127 MPPE  130 (214)
T ss_pred             eCch
Confidence            7665

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

Probab=99.16  E-value=7.1e-11  Score=116.13  Aligned_cols=78  Identities=26%  Similarity=0.463  Sum_probs=72.2

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEccc
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAE  140 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~  140 (299)
                      .+||||++|+..|+|+||..+|+.||+|..|.|+..      .+||||++....+|++||.+|++..|.++.|+|.|+..
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~------R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g  494 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP------RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVG  494 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeeccC------CceeEEEEeehhHHHHHHHHHhcccccceeeEEeeecc
Confidence            579999999999999999999999999999998854      79999999999999999999999999999999999986


Q ss_pred             CCCC
Q 043443          141 SRKR  144 (299)
Q Consensus       141 ~~~~  144 (299)
                      +..+
T Consensus       495 ~G~k  498 (894)
T KOG0132|consen  495 KGPK  498 (894)
T ss_pred             CCcc
Confidence            5433

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

Probab=99.15  E-value=2.7e-11  Score=104.76  Aligned_cols=72  Identities=28%  Similarity=0.585  Sum_probs=67.4

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcccC
Q 043443           62 GSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAES  141 (299)
Q Consensus        62 ~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~~  141 (299)
                      ..|||++||+.+.+.+|+.||..||+|.+|.|.        .+|+||+|++..+|..||..||+++|++..|.|+|+...
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk--------~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~   73 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMK--------NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGK   73 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceee--------cccceeccCchhhhhcccchhcCceecceeeeeeccccc
Confidence            479999999999999999999999999999887        479999999999999999999999999999999998854

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

Probab=99.13  E-value=1.7e-10  Score=104.37  Aligned_cols=80  Identities=18%  Similarity=0.323  Sum_probs=70.6

Q ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhh-CCceeCCeeE
Q 043443           55 RRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM-NGKRFAGREI  133 (299)
Q Consensus        55 ~~~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~l-ng~~l~Gr~i  133 (299)
                      +..+..-.+|||++|...++|.+|.++|.+||+|..|.++..      +++|||+|.+.+.|+.|.+.+ |..+|+|..|
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            345566789999999999999999999999999999988865      579999999999999988655 6667899999


Q ss_pred             EEEEccc
Q 043443          134 SVVLAAE  140 (299)
Q Consensus       134 ~V~~a~~  140 (299)
                      +|.|..+
T Consensus       296 ~i~Wg~~  302 (377)
T KOG0153|consen  296 KIKWGRP  302 (377)
T ss_pred             EEEeCCC
Confidence            9999887

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

Probab=99.11  E-value=1.9e-10  Score=108.41  Aligned_cols=81  Identities=25%  Similarity=0.431  Sum_probs=73.2

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      +...|||-||+..++..+|.++|+.||+|..|.|..+.. | .+|| ||+|+++++|++||+.|||..+.+++|.|....
T Consensus        75 d~~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~-g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~  151 (369)
T KOG0123|consen   75 DPSLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDEN-G-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFE  151 (369)
T ss_pred             CCceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCC-C-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeecc
Confidence            334499999999999999999999999999999998853 3 8999 999999999999999999999999999998887


Q ss_pred             cCCC
Q 043443          140 ESRK  143 (299)
Q Consensus       140 ~~~~  143 (299)
                      .+..
T Consensus       152 ~~~e  155 (369)
T KOG0123|consen  152 RKEE  155 (369)
T ss_pred             chhh
Confidence            6544

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

Probab=99.10  E-value=3.7e-10  Score=99.70  Aligned_cols=83  Identities=25%  Similarity=0.391  Sum_probs=75.8

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      +.-.++|+|.||++.|+++||+++|..||+++.+.|..++ .|.+.|.|-|.|...+||+.||+.||++.|+|..|+|++
T Consensus        80 ~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~  158 (243)
T KOG0533|consen   80 ETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEI  158 (243)
T ss_pred             CCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEE
Confidence            3445889999999999999999999999999999888875 788999999999999999999999999999999999988


Q ss_pred             cccC
Q 043443          138 AAES  141 (299)
Q Consensus       138 a~~~  141 (299)
                      ....
T Consensus       159 i~~~  162 (243)
T KOG0533|consen  159 ISSP  162 (243)
T ss_pred             ecCc
Confidence            7653

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

Probab=99.10  E-value=3.9e-10  Score=102.75  Aligned_cols=86  Identities=28%  Similarity=0.426  Sum_probs=78.9

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEe--------EEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCcee
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVR--------DVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRF  128 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~--------~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l  128 (299)
                      ......+|||-+|+..+++++|.++|.++|.|.        .|+|.+++.|+.+++-|.|.|++...|+.||..++++.|
T Consensus        62 ~~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf  141 (351)
T KOG1995|consen   62 DKSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDF  141 (351)
T ss_pred             cccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccc
Confidence            355678999999999999999999999999885        478889999999999999999999999999999999999


Q ss_pred             CCeeEEEEEcccCC
Q 043443          129 AGREISVVLAAESR  142 (299)
Q Consensus       129 ~Gr~i~V~~a~~~~  142 (299)
                      .+.+|+|.+|....
T Consensus       142 ~gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  142 CGNTIKVSLAERRT  155 (351)
T ss_pred             cCCCchhhhhhhcc
Confidence            99999999987544

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

Probab=99.09  E-value=1.9e-10  Score=109.67  Aligned_cols=82  Identities=23%  Similarity=0.346  Sum_probs=76.3

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      ....|||.+|...|...||+.||.+||+|+-..|+.+..+...+||+||++.+.++|.+||+.|+.++|.|+.|.|+-++
T Consensus       404 ~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaK  483 (940)
T KOG4661|consen  404 LGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAK  483 (940)
T ss_pred             cccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeecc
Confidence            45689999999999999999999999999999999887777789999999999999999999999999999999999987


Q ss_pred             cC
Q 043443          140 ES  141 (299)
Q Consensus       140 ~~  141 (299)
                      ..
T Consensus       484 NE  485 (940)
T KOG4661|consen  484 NE  485 (940)
T ss_pred             cC
Confidence            54

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

Probab=99.07  E-value=3.4e-10  Score=110.60  Aligned_cols=79  Identities=25%  Similarity=0.448  Sum_probs=70.2

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCC---CCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYT---GEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~---g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      .++|||.||++.++.++|..+|.++|.|..|.|.+.+..   -.+.|||||+|.+.++|+.|++.|+|+.|+|+.|.|.+
T Consensus       515 ~t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~  594 (725)
T KOG0110|consen  515 ETKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKI  594 (725)
T ss_pred             chhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEe
Confidence            345999999999999999999999999999988765422   12459999999999999999999999999999999999


Q ss_pred             cc
Q 043443          138 AA  139 (299)
Q Consensus       138 a~  139 (299)
                      +.
T Consensus       595 S~  596 (725)
T KOG0110|consen  595 SE  596 (725)
T ss_pred             cc
Confidence            98

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

Probab=99.05  E-value=3.4e-10  Score=103.07  Aligned_cols=80  Identities=19%  Similarity=0.324  Sum_probs=75.4

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      .-++|||..++.+++|+||+.+|+.||+|.+|.+..++.++..+||+||||.+......||..||-+.|+|..|.|--+.
T Consensus       209 ~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~v  288 (544)
T KOG0124|consen  209 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  288 (544)
T ss_pred             hhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEeccccc
Confidence            35799999999999999999999999999999999999999999999999999999999999999999999999986654

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

Probab=99.03  E-value=1.8e-09  Score=102.57  Aligned_cols=81  Identities=23%  Similarity=0.406  Sum_probs=68.1

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      ...+|||.|||.++++.+|+++|.+||.|+...|..-...++..+||||+|.+.++++.||++ +-..|++++|.|+..+
T Consensus       287 ~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~  365 (419)
T KOG0116|consen  287 DGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKR  365 (419)
T ss_pred             cccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEecc
Confidence            345699999999999999999999999999876654322344459999999999999999986 5778999999999877


Q ss_pred             cC
Q 043443          140 ES  141 (299)
Q Consensus       140 ~~  141 (299)
                      ..
T Consensus       366 ~~  367 (419)
T KOG0116|consen  366 PG  367 (419)
T ss_pred             cc
Confidence            53

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

Probab=99.02  E-value=2.5e-10  Score=111.55  Aligned_cols=85  Identities=34%  Similarity=0.605  Sum_probs=78.1

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      ...+.|+|.|||+.++..+|+++|..||+|..|.|++....+...|||||+|-++.+|..|+.+|..+.|.|+.|.++|+
T Consensus       611 k~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA  690 (725)
T KOG0110|consen  611 KKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWA  690 (725)
T ss_pred             cccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehh
Confidence            34689999999999999999999999999999999987666778999999999999999999999999999999999999


Q ss_pred             ccCCC
Q 043443          139 AESRK  143 (299)
Q Consensus       139 ~~~~~  143 (299)
                      +....
T Consensus       691 ~~d~~  695 (725)
T KOG0110|consen  691 KSDNT  695 (725)
T ss_pred             ccchH
Confidence            86543

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

Probab=98.99  E-value=3.9e-10  Score=103.29  Aligned_cols=82  Identities=28%  Similarity=0.503  Sum_probs=73.2

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      +.++|||++|++.++|+.|+++|.+||+|.+|.++.|+.++..++|+||+|++.+.+..+|. ..-..|+|+.|.+..|.
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            67899999999999999999999999999999999999999999999999999888888876 35567889888888776


Q ss_pred             cCC
Q 043443          140 ESR  142 (299)
Q Consensus       140 ~~~  142 (299)
                      +..
T Consensus        84 ~r~   86 (311)
T KOG4205|consen   84 SRE   86 (311)
T ss_pred             Ccc
Confidence            543

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

Probab=98.97  E-value=7.9e-10  Score=97.66  Aligned_cols=85  Identities=31%  Similarity=0.513  Sum_probs=79.3

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEE
Q 043443           56 RKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV  135 (299)
Q Consensus        56 ~~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V  135 (299)
                      ..+.+...|||+||.+.+|.++|+.+|+.||.|..|.|+.++..+++++||||+|.+.+.++.||. ||+..|.+..|.|
T Consensus        96 ~~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~v  174 (231)
T KOG4209|consen   96 QKEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEV  174 (231)
T ss_pred             hhccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCccccccccee
Confidence            345678899999999999999999999999999999999999999999999999999999999999 9999999999999


Q ss_pred             EEcccC
Q 043443          136 VLAAES  141 (299)
Q Consensus       136 ~~a~~~  141 (299)
                      .+....
T Consensus       175 t~~r~~  180 (231)
T KOG4209|consen  175 TLKRTN  180 (231)
T ss_pred             eeeeee
Confidence            998754

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

Probab=98.97  E-value=1.8e-09  Score=93.53  Aligned_cols=71  Identities=37%  Similarity=0.564  Sum_probs=64.3

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV  135 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V  135 (299)
                      .....+.|+|.||+..+.|++|.++|.++|++.++.+.        .+++||+|.+.++|..||..|++..|.++.|+|
T Consensus        95 p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~~--------~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~  165 (216)
T KOG0106|consen   95 PSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDAR--------RNFAFVEFSEQEDAKRALEKLDGKKLNGRRISV  165 (216)
T ss_pred             cccccceeeeccchhhhhHHHHhhhhcccCCCchhhhh--------ccccceeehhhhhhhhcchhccchhhcCceeee
Confidence            34567899999999999999999999999999665552        479999999999999999999999999999999

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

Probab=98.94  E-value=1.1e-09  Score=100.59  Aligned_cols=75  Identities=20%  Similarity=0.301  Sum_probs=59.3

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCC---CCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYY---TGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        63 ~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~---~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      .|.|.||.+.+|.++|+.||..+|+|.++.|+.+..   .....-.|||.|.+...+..|.+ |.+++|-++.|.|..+
T Consensus         9 vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv~p~   86 (479)
T KOG4676|consen    9 VIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIVRPY   86 (479)
T ss_pred             eeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEEEec
Confidence            799999999999999999999999999998865321   12345689999999988888876 6666666666555443

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

Probab=98.94  E-value=9.7e-10  Score=96.45  Aligned_cols=83  Identities=23%  Similarity=0.444  Sum_probs=72.9

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCce-eCC--eeEEEE
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKR-FAG--REISVV  136 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~-l~G--r~i~V~  136 (299)
                      +..+|||+-|...-.|+|+..+|..||+|++|.+.... .|.++|+|||.|.+..+|+.||..|+|.. +-|  ..|.|.
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~-dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK   96 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGP-DGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVK   96 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCC-CCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEE
Confidence            45689999999999999999999999999999988764 78899999999999999999999999964 444  578899


Q ss_pred             EcccCCC
Q 043443          137 LAAESRK  143 (299)
Q Consensus       137 ~a~~~~~  143 (299)
                      ++...++
T Consensus        97 ~ADTdkE  103 (371)
T KOG0146|consen   97 FADTDKE  103 (371)
T ss_pred             eccchHH
Confidence            9876544

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

Probab=98.93  E-value=4.1e-10  Score=96.16  Aligned_cols=82  Identities=26%  Similarity=0.291  Sum_probs=72.3

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      .+...||||+||...|+|+.|.++|-+.|.|..|.|..++ .++.+ ||||+|.++..+.-|++.|||..|.+..|.|.+
T Consensus         6 ae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~-d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~   83 (267)
T KOG4454|consen    6 AEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQ-DQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTL   83 (267)
T ss_pred             cchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCc-cCCCc-eeeeecccccchhhhhhhcccchhccchhhccc
Confidence            3456799999999999999999999999999999998775 44555 999999999999999999999999999999887


Q ss_pred             cccC
Q 043443          138 AAES  141 (299)
Q Consensus       138 a~~~  141 (299)
                      -...
T Consensus        84 r~G~   87 (267)
T KOG4454|consen   84 RCGN   87 (267)
T ss_pred             ccCC
Confidence            6543

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

Probab=98.93  E-value=1.2e-09  Score=100.20  Aligned_cols=84  Identities=29%  Similarity=0.447  Sum_probs=76.8

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      ...+|||++||.++++++|+++|.+||.|..+.++.|..+...++|+||+|.+.+.+++++. +.-++|+++.|.|..|.
T Consensus        96 ~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA~  174 (311)
T KOG4205|consen   96 RTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRAI  174 (311)
T ss_pred             ceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceeeecCceeeEeecc
Confidence            35599999999999999999999999999999999999999999999999999999988886 58889999999999998


Q ss_pred             cCCCC
Q 043443          140 ESRKR  144 (299)
Q Consensus       140 ~~~~~  144 (299)
                      ++...
T Consensus       175 pk~~~  179 (311)
T KOG4205|consen  175 PKEVM  179 (311)
T ss_pred             chhhc
Confidence            76543

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

Probab=98.93  E-value=3.8e-09  Score=95.72  Aligned_cols=83  Identities=20%  Similarity=0.334  Sum_probs=74.8

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEe--------EEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeC
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVR--------DVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFA  129 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~--------~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~  129 (299)
                      ...++.|||.|||.++|.+++.++|.+||.|.        .|.|..+. .|+.+|-|+|.|...+.++.||+.||+..|.
T Consensus       131 ~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~-~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~r  209 (382)
T KOG1548|consen  131 PKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDN-QGKLKGDALCCYIKRESVELAIKILDEDELR  209 (382)
T ss_pred             cccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecC-CCCccCceEEEeecccHHHHHHHHhCccccc
Confidence            44567899999999999999999999999885        37777775 5999999999999999999999999999999


Q ss_pred             CeeEEEEEcccC
Q 043443          130 GREISVVLAAES  141 (299)
Q Consensus       130 Gr~i~V~~a~~~  141 (299)
                      |+.|.|+.|+..
T Consensus       210 g~~~rVerAkfq  221 (382)
T KOG1548|consen  210 GKKLRVERAKFQ  221 (382)
T ss_pred             CcEEEEehhhhh
Confidence            999999999854

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

Probab=98.92  E-value=2.5e-09  Score=100.81  Aligned_cols=74  Identities=28%  Similarity=0.398  Sum_probs=69.6

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcccC
Q 043443           62 GSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAES  141 (299)
Q Consensus        62 ~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~~  141 (299)
                      ..||||   +++|+..|.++|..+|.|..|.|+.|. |  +.|||||.|.++++|+.||..||...|.|++|.|.|+...
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd   75 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRD   75 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccC
Confidence            468999   899999999999999999999999997 6  9999999999999999999999999999999999998743

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

Probab=98.87  E-value=1.5e-08  Score=77.31  Aligned_cols=79  Identities=28%  Similarity=0.434  Sum_probs=70.6

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhc--CCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeC----CeeEEE
Q 043443           62 GSLLVRNIPLDCRPEELRAPFER--FGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFA----GREISV  135 (299)
Q Consensus        62 ~~l~V~nLp~~~te~dL~~~F~~--~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~----Gr~i~V  135 (299)
                      +||.|.|||...|.++|.+++..  .|....+.|+.|..+..+.|||||.|.+++.|....+.++|..|.    .+.+.|
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i   81 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEI   81 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEE
Confidence            79999999999999999999865  477788899999889999999999999999999999999999886    567788


Q ss_pred             EEccc
Q 043443          136 VLAAE  140 (299)
Q Consensus       136 ~~a~~  140 (299)
                      .+|+-
T Consensus        82 ~yAri   86 (97)
T PF04059_consen   82 SYARI   86 (97)
T ss_pred             ehhHh
Confidence            88864

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

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

Probab=98.84  E-value=1.7e-08  Score=86.72  Aligned_cols=83  Identities=28%  Similarity=0.375  Sum_probs=69.2

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEecc-CCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeC---CeeEEEE
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPK-DYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFA---GREISVV  136 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~-d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~---Gr~i~V~  136 (299)
                      -.||||.+||.++...+|..+|..|-..+.+.|.. ++.....+-+|||+|.+..+|++|++.|||..|+   +..|+|+
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            57999999999999999999999986666665543 2222334579999999999999999999999986   8899999


Q ss_pred             EcccCCC
Q 043443          137 LAAESRK  143 (299)
Q Consensus       137 ~a~~~~~  143 (299)
                      +|+...+
T Consensus       114 lAKSNtK  120 (284)
T KOG1457|consen  114 LAKSNTK  120 (284)
T ss_pred             ehhcCcc
Confidence            9987544

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

Probab=98.81  E-value=3.3e-09  Score=101.46  Aligned_cols=72  Identities=31%  Similarity=0.567  Sum_probs=65.5

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREIS  134 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~  134 (299)
                      .....+|+|.|||..|++++|..+|+.||+|..|.....     ..+.+||+|.|..+|+.|++.|++.+|.|+.|+
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            455789999999999999999999999999999766543     479999999999999999999999999998887

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

Probab=98.76  E-value=2.5e-08  Score=97.68  Aligned_cols=84  Identities=20%  Similarity=0.252  Sum_probs=74.7

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCC---CCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYY---TGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREI  133 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~---~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i  133 (299)
                      .+..++.|||+||+..++++.|...|..||.|..|.|++...   ......|+||.|-+..||+.|++.|+|..+.+..|
T Consensus       170 gDP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~  249 (877)
T KOG0151|consen  170 GDPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEM  249 (877)
T ss_pred             CCCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeee
Confidence            355678999999999999999999999999999998887643   23456799999999999999999999999999999


Q ss_pred             EEEEccc
Q 043443          134 SVVLAAE  140 (299)
Q Consensus       134 ~V~~a~~  140 (299)
                      ++.|++.
T Consensus       250 K~gWgk~  256 (877)
T KOG0151|consen  250 KLGWGKA  256 (877)
T ss_pred             eeccccc
Confidence            9999964

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

Probab=98.65  E-value=3.2e-07  Score=84.20  Aligned_cols=89  Identities=20%  Similarity=0.210  Sum_probs=69.9

Q ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCC---------C-------------------------
Q 043443           55 RRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYT---------G-------------------------  100 (299)
Q Consensus        55 ~~~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~---------g-------------------------  100 (299)
                      +.+....-.|+|.+|...++|.||.+.++.||.|.+|.++..+..         +                         
T Consensus        25 phk~~~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P~~r~alvefedi~~akn~Vnfaa~n~i~i~gq~Al~NyS  104 (494)
T KOG1456|consen   25 PHKPNPSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMPHKRQALVEFEDIEGAKNCVNFAADNQIYIAGQQALFNYS  104 (494)
T ss_pred             CCCCCCCceEEEeccccccchhHHHHHHhcCCceEEEEeccccceeeeeeccccchhhheehhccCcccccCchhhcccc
Confidence            334556779999999999999999999999999987654322100         0                         


Q ss_pred             ----------------------------------------------------CCccEEEEEEcCHHHHHHHHHhhCCcee
Q 043443          101 ----------------------------------------------------EPRGFAFVQFVDPYEAAEAQHHMNGKRF  128 (299)
Q Consensus       101 ----------------------------------------------------~~~g~afVeF~~~~~A~~Al~~lng~~l  128 (299)
                                                                          ++--.|+|||++.+.|++|.+.|||..|
T Consensus       105 tsq~i~R~g~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkkngVQAmVEFdsv~~AqrAk~alNGADI  184 (494)
T KOG1456|consen  105 TSQCIERPGDESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKKNGVQAMVEFDSVEVAQRAKAALNGADI  184 (494)
T ss_pred             hhhhhccCCCCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEeccceeeEEeechhHHHHHHHhhcccccc
Confidence                                                                1223789999999999999999999988


Q ss_pred             C-C-eeEEEEEcccCCC
Q 043443          129 A-G-REISVVLAAESRK  143 (299)
Q Consensus       129 ~-G-r~i~V~~a~~~~~  143 (299)
                      . | .+|+|++|++.+.
T Consensus       185 YsGCCTLKIeyAkP~rl  201 (494)
T KOG1456|consen  185 YSGCCTLKIEYAKPTRL  201 (494)
T ss_pred             cccceeEEEEecCccee
Confidence            5 3 6899999998653

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

Probab=98.64  E-value=9.9e-08  Score=90.27  Aligned_cols=77  Identities=21%  Similarity=0.365  Sum_probs=66.5

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      ....|-+.+|||.+|++||.+||+.+ .|+.+.+..  .+|++.|.|||||.+.+|+++||+ +|-..|..+-|.|--+.
T Consensus         9 ~~~~vr~rGLPwsat~~ei~~Ff~~~-~I~~~~~~r--~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~~   84 (510)
T KOG4211|consen    9 TAFEVRLRGLPWSATEKEILDFFSNC-GIENLEIPR--RNGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTAG   84 (510)
T ss_pred             cceEEEecCCCccccHHHHHHHHhcC-ceeEEEEec--cCCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEccC
Confidence            45678889999999999999999998 477766654  479999999999999999999998 58888999999987765


Q ss_pred             c
Q 043443          140 E  140 (299)
Q Consensus       140 ~  140 (299)
                      .
T Consensus        85 ~   85 (510)
T KOG4211|consen   85 G   85 (510)
T ss_pred             C
Confidence            3

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

Probab=98.59  E-value=5e-08  Score=85.27  Aligned_cols=82  Identities=23%  Similarity=0.444  Sum_probs=75.3

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      +++..+||.+-|..+++.+.|-..|.+|-......+++++-|++++||+||.|.+..|+..|+..|||+.++.+.|++.-
T Consensus       187 ~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRk  266 (290)
T KOG0226|consen  187 DEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRK  266 (290)
T ss_pred             ccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhh
Confidence            34678999999999999999999999998888889999999999999999999999999999999999999999988755


Q ss_pred             cc
Q 043443          138 AA  139 (299)
Q Consensus       138 a~  139 (299)
                      +.
T Consensus       267 S~  268 (290)
T KOG0226|consen  267 SE  268 (290)
T ss_pred             hh
Confidence            44

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

Probab=98.58  E-value=3.9e-08  Score=94.75  Aligned_cols=86  Identities=24%  Similarity=0.473  Sum_probs=80.1

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      -...+.|||++||..+++.+|.+++..||.+....++.+..+|.++||||.+|.+......||..|||+.+.+.+|.|+.
T Consensus       286 ~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~  365 (500)
T KOG0120|consen  286 PDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQR  365 (500)
T ss_pred             ccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeeh
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCCC
Q 043443          138 AAESRK  143 (299)
Q Consensus       138 a~~~~~  143 (299)
                      |.....
T Consensus       366 A~~g~~  371 (500)
T KOG0120|consen  366 AIVGAS  371 (500)
T ss_pred             hhccch
Confidence            876543

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

Probab=98.56  E-value=5.2e-07  Score=88.44  Aligned_cols=77  Identities=22%  Similarity=0.334  Sum_probs=66.2

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      .+.|-|.|+|++++.+||.+||..|-.+-.-.+++-...|+..|.|.|.|++.++|..|+..|+++.|..++|.|.+
T Consensus       867 p~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  867 PRVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             CeEEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            34888999999999999999999997664433333346799999999999999999999999999999999998865

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

Probab=98.52  E-value=3.2e-07  Score=85.07  Aligned_cols=77  Identities=26%  Similarity=0.404  Sum_probs=69.7

Q ss_pred             CCEEEEeCCC-CCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           61 HGSLLVRNIP-LDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        61 ~~~l~V~nLp-~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      ++.|.|.||. ..+|.+.|..+|..||.|..|.|..++     +-.|+|+|.+...|+.|+++|+|..|.|++|+|.+++
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            6889999995 458999999999999999999998765     4689999999999999999999999999999999998


Q ss_pred             cCC
Q 043443          140 ESR  142 (299)
Q Consensus       140 ~~~  142 (299)
                      -..
T Consensus       372 H~~  374 (492)
T KOG1190|consen  372 HTN  374 (492)
T ss_pred             Ccc
Confidence            543

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

Probab=98.50  E-value=1e-08  Score=94.29  Aligned_cols=77  Identities=13%  Similarity=0.048  Sum_probs=60.6

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      +...+|+|++|+..+...+|.++|..+|+|.+..|.-    +...-+|.|+|........|+. ++|.++.-+...+.+.
T Consensus       149 eirRt~~v~sl~~~~~l~e~~e~f~r~Gev~ya~~as----k~~s~~c~~sf~~qts~~halr-~~gre~k~qhsr~ai~  223 (479)
T KOG4676|consen  149 EIRRTREVQSLISAAILPESGESFERKGEVSYAHTAS----KSRSSSCSHSFRKQTSSKHALR-SHGRERKRQHSRRAII  223 (479)
T ss_pred             HHHhhhhhhcchhhhcchhhhhhhhhcchhhhhhhhc----cCCCcchhhhHhhhhhHHHHHH-hcchhhhhhhhhhhhc
Confidence            3457899999999999999999999999998887753    3445688899999999999998 6888877544444444


Q ss_pred             cc
Q 043443          139 AE  140 (299)
Q Consensus       139 ~~  140 (299)
                      ++
T Consensus       224 kP  225 (479)
T KOG4676|consen  224 KP  225 (479)
T ss_pred             Cc
Confidence            43

>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=98.45  E-value=4.4e-07  Score=70.61  Aligned_cols=72  Identities=19%  Similarity=0.358  Sum_probs=46.4

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCc-----eeCCeeEEEE
Q 043443           62 GSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGK-----RFAGREISVV  136 (299)
Q Consensus        62 ~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~-----~l~Gr~i~V~  136 (299)
                      +.|+|.+|+..++.++|+++|.+||.|.+|++...      ...|||-|.+.++|+.||..+.-.     .|.+..+++.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G------~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG------DTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC------CCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            57899999999999999999999999999999764      468999999999999999877433     5677777776


Q ss_pred             Ecc
Q 043443          137 LAA  139 (299)
Q Consensus       137 ~a~  139 (299)
                      +-.
T Consensus        76 vLe   78 (105)
T PF08777_consen   76 VLE   78 (105)
T ss_dssp             ---
T ss_pred             ECC
Confidence            643

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

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

Probab=98.45  E-value=2.8e-06  Score=78.14  Aligned_cols=80  Identities=21%  Similarity=0.278  Sum_probs=71.2

Q ss_pred             CCCCCEEEEeCCCCC-CCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           58 EQNHGSLLVRNIPLD-CRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~-~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      ..+.+.+.|.+|... ++.+-|..+|..||.|+.|.+++.+     .|.|+||+.+..+.+.||..||+..|.|.+|.|.
T Consensus       284 ~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-----~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~  358 (494)
T KOG1456|consen  284 GAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVC  358 (494)
T ss_pred             CCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-----cceeEEEcCcHHHHHHHHHHhccCccccceEEEe
Confidence            345789999999654 6788899999999999999998865     6899999999999999999999999999999999


Q ss_pred             EcccCC
Q 043443          137 LAAESR  142 (299)
Q Consensus       137 ~a~~~~  142 (299)
                      +++...
T Consensus       359 ~SkQ~~  364 (494)
T KOG1456|consen  359 VSKQNF  364 (494)
T ss_pred             eccccc
Confidence            998644

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

Probab=98.38  E-value=3.5e-07  Score=78.66  Aligned_cols=66  Identities=20%  Similarity=0.380  Sum_probs=55.3

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeC
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFA  129 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~  129 (299)
                      ...||||.||..+|||++|+.+|..|-....+.|...    ...+.|||+|++.+.|.+|+..|+|..|-
T Consensus       209 acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~----~g~~vaf~~~~~~~~at~am~~lqg~~~s  274 (284)
T KOG1457|consen  209 ACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRAR----GGMPVAFADFEEIEQATDAMNHLQGNLLS  274 (284)
T ss_pred             hhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecC----CCcceEeecHHHHHHHHHHHHHhhcceec
Confidence            4569999999999999999999999976665555432    23578999999999999999999998763

>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=98.35  E-value=1.8e-06  Score=63.36  Aligned_cols=70  Identities=31%  Similarity=0.449  Sum_probs=48.4

Q ss_pred             CEEEEeCCCCCCCHHH----HHHHHhcCC-CEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           62 GSLLVRNIPLDCRPEE----LRAPFERFG-VVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        62 ~~l~V~nLp~~~te~d----L~~~F~~~G-~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      +.|+|.|||.+.+...    |+.++..+| .|..|  .        .+.|+|.|.+.+.|..|++.|+|.++.|.+|.|.
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v--~--------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~   72 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV--S--------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE--e--------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            4799999999988765    556666775 66554  2        3689999999999999999999999999999999


Q ss_pred             EcccC
Q 043443          137 LAAES  141 (299)
Q Consensus       137 ~a~~~  141 (299)
                      +....
T Consensus        73 ~~~~~   77 (90)
T PF11608_consen   73 FSPKN   77 (90)
T ss_dssp             SS--S
T ss_pred             EcCCc
Confidence            98643

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

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

Probab=98.34  E-value=1.2e-07  Score=90.85  Aligned_cols=87  Identities=25%  Similarity=0.447  Sum_probs=78.7

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      ++.+..+||+-.|...++..+|.+||..+|.|..|.|+.|..++..+|.|||+|.+.+.+..||. |.|+.+.|.+|.|+
T Consensus       175 eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aia-LsGqrllg~pv~vq  253 (549)
T KOG0147|consen  175 EERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIA-LSGQRLLGVPVIVQ  253 (549)
T ss_pred             hHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhh-hcCCcccCceeEec
Confidence            34456799999999999999999999999999999999999999999999999999999999994 99999999999999


Q ss_pred             EcccCCCC
Q 043443          137 LAAESRKR  144 (299)
Q Consensus       137 ~a~~~~~~  144 (299)
                      .....+..
T Consensus       254 ~sEaeknr  261 (549)
T KOG0147|consen  254 LSEAEKNR  261 (549)
T ss_pred             ccHHHHHH
Confidence            88755443

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

Probab=98.32  E-value=1.6e-06  Score=82.18  Aligned_cols=78  Identities=32%  Similarity=0.529  Sum_probs=65.1

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeE-EEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRD-VYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~-v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      ...+|-+.+||+.||++||.+||+..-.|.. |.|+.++ .+.+.|.|||+|++.+.|++||.. |...|.-+-|.|-.+
T Consensus       102 ~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~-rgR~tGEAfVqF~sqe~ae~Al~r-hre~iGhRYIEvF~S  179 (510)
T KOG4211|consen  102 NDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQ-RGRPTGEAFVQFESQESAEIALGR-HRENIGHRYIEVFRS  179 (510)
T ss_pred             CCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccC-CCCcccceEEEecCHHHHHHHHHH-HHHhhccceEEeehh
Confidence            4568999999999999999999998765555 5555554 567899999999999999999985 778888888888766


Q ss_pred             c
Q 043443          139 A  139 (299)
Q Consensus       139 ~  139 (299)
                      .
T Consensus       180 s  180 (510)
T KOG4211|consen  180 S  180 (510)
T ss_pred             H
Confidence            4

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

Probab=98.28  E-value=2e-06  Score=79.23  Aligned_cols=79  Identities=23%  Similarity=0.344  Sum_probs=68.5

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCC-EeE--EEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGV-VRD--VYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~-I~~--v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      ...+|-+.+||+.++.+||.+||..|.. |..  |+|+.+ ..|.+.|.|||+|.+.++|..|....+.+.++.+.|.|-
T Consensus       279 ~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N-~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvf  357 (508)
T KOG1365|consen  279 SKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLN-GQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVF  357 (508)
T ss_pred             CCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEc-CCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEe
Confidence            3678999999999999999999998863 333  777766 478999999999999999999999999999989999987


Q ss_pred             Ecc
Q 043443          137 LAA  139 (299)
Q Consensus       137 ~a~  139 (299)
                      .+.
T Consensus       358 p~S  360 (508)
T KOG1365|consen  358 PCS  360 (508)
T ss_pred             ecc
Confidence            765

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

Probab=98.25  E-value=3.9e-06  Score=72.49  Aligned_cols=77  Identities=26%  Similarity=0.454  Sum_probs=67.6

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeC-CeeEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFA-GREISVV  136 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~-Gr~i~V~  136 (299)
                      ..+..+||+.|||..++.+.|..+|.+|....+|.++...     .+.|||+|.+...|..|...|++..|- ...|.|.
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            4467899999999999999999999999999998887643     689999999999999999999998875 7888888


Q ss_pred             Ecc
Q 043443          137 LAA  139 (299)
Q Consensus       137 ~a~  139 (299)
                      +++
T Consensus       218 ~a~  220 (221)
T KOG4206|consen  218 FAK  220 (221)
T ss_pred             ccC
Confidence            765

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

Probab=98.07  E-value=2.5e-06  Score=77.79  Aligned_cols=78  Identities=14%  Similarity=0.200  Sum_probs=68.1

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCC--CEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFERFG--VVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~~~G--~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      ..++||+||-|++|++||.+.+...|  .|.++++..+..+|+++|||+|...+....++.++.|-.++|.|+.-.|--.
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~~~  159 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVLSY  159 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeeecc
Confidence            46899999999999999999988766  5667788888889999999999999999999999999999999986555443

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.03  E-value=5.2e-06  Score=75.81  Aligned_cols=81  Identities=21%  Similarity=0.407  Sum_probs=73.6

Q ss_pred             CCEEE-EeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           61 HGSLL-VRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        61 ~~~l~-V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      ..+|| |+||+..+++++|+.+|..+|.|..|.+..+..++..++||||+|.+...+..|+.. +...+.+..|.|....
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            34555 999999999999999999999999999999999999999999999999999999887 8888999999999887


Q ss_pred             cCC
Q 043443          140 ESR  142 (299)
Q Consensus       140 ~~~  142 (299)
                      +..
T Consensus       263 ~~~  265 (285)
T KOG4210|consen  263 PRP  265 (285)
T ss_pred             CCc
Confidence            643

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

Probab=98.01  E-value=2.1e-05  Score=75.83  Aligned_cols=80  Identities=25%  Similarity=0.418  Sum_probs=65.6

Q ss_pred             CCCCEEEEeCCCCCCC------HHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeC-Ce
Q 043443           59 QNHGSLLVRNIPLDCR------PEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFA-GR  131 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~t------e~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~-Gr  131 (299)
                      .....|+|.|+|.--.      ..-|..+|+++|+|..+.++.+..+| .+||.|++|.+..+|+.|++.|||+.|+ .+
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~gg-tkG~lf~E~~~~~~A~~aVK~l~G~~ldknH  134 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGG-TKGYLFVEYASMRDAKKAVKSLNGKRLDKNH  134 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCC-eeeEEEEEecChhhHHHHHHhcccceecccc
Confidence            3467899999986432      23467889999999999999886555 8999999999999999999999999885 67


Q ss_pred             eEEEEEcc
Q 043443          132 EISVVLAA  139 (299)
Q Consensus       132 ~i~V~~a~  139 (299)
                      ++.|..-+
T Consensus       135 tf~v~~f~  142 (698)
T KOG2314|consen  135 TFFVRLFK  142 (698)
T ss_pred             eEEeehhh
Confidence            77776654

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=98.01  E-value=1.4e-05  Score=72.66  Aligned_cols=81  Identities=17%  Similarity=0.361  Sum_probs=62.6

Q ss_pred             CCCEEEEeCCCCCCCHHH----H--HHHHhcCCCEeEEEeccCCCC-CCCccE--EEEEEcCHHHHHHHHHhhCCceeCC
Q 043443           60 NHGSLLVRNIPLDCRPEE----L--RAPFERFGVVRDVYLPKDYYT-GEPRGF--AFVQFVDPYEAAEAQHHMNGKRFAG  130 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~d----L--~~~F~~~G~I~~v~i~~d~~~-g~~~g~--afVeF~~~~~A~~Al~~lng~~l~G  130 (299)
                      ...-|||-+|+..+..++    |  .++|.+||.|..|.|-+.... ....+.  .||+|.+.+||..||...+|..++|
T Consensus       113 QKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DG  192 (480)
T COG5175         113 QKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDG  192 (480)
T ss_pred             ecceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccC
Confidence            456789999988776555    2  489999999999877654211 111122  3999999999999999999999999


Q ss_pred             eeEEEEEccc
Q 043443          131 REISVVLAAE  140 (299)
Q Consensus       131 r~i~V~~a~~  140 (299)
                      +.|+..|...
T Consensus       193 r~lkatYGTT  202 (480)
T COG5175         193 RVLKATYGTT  202 (480)
T ss_pred             ceEeeecCch
Confidence            9999988764

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

Probab=97.98  E-value=1.9e-05  Score=53.59  Aligned_cols=52  Identities=25%  Similarity=0.515  Sum_probs=42.7

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHH
Q 043443           62 GSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQ  120 (299)
Q Consensus        62 ~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al  120 (299)
                      +.|-|.+.+.... ++|..+|..||+|+.+.+...      ..++||+|.+..+|++||
T Consensus         2 ~wI~V~Gf~~~~~-~~vl~~F~~fGeI~~~~~~~~------~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLA-EEVLEHFASFGEIVDIYVPES------TNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHH-HHHHHHHHhcCCEEEEEcCCC------CcEEEEEECCHHHHHhhC
Confidence            5788999987765 445568899999999988732      469999999999999995

>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=97.97  E-value=3.6e-05  Score=59.15  Aligned_cols=80  Identities=16%  Similarity=0.252  Sum_probs=54.1

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCC-------CCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCe
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDY-------YTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGR  131 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~-------~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr  131 (299)
                      ...+-|.|.+.|.. ....|.++|++||+|.+..-....       .......+..|+|++..+|++||. .||..|.|.
T Consensus         4 ~~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~   81 (100)
T PF05172_consen    4 DSETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGS   81 (100)
T ss_dssp             GGCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTC
T ss_pred             cCCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCc
Confidence            34567889999887 557788899999999877411100       001235799999999999999998 599999986


Q ss_pred             eE-EEEEccc
Q 043443          132 EI-SVVLAAE  140 (299)
Q Consensus       132 ~i-~V~~a~~  140 (299)
                      .| -|.++++
T Consensus        82 ~mvGV~~~~~   91 (100)
T PF05172_consen   82 LMVGVKPCDP   91 (100)
T ss_dssp             EEEEEEE-HH
T ss_pred             EEEEEEEcHH
Confidence            54 4777643

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.

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

Probab=97.96  E-value=4.4e-05  Score=69.74  Aligned_cols=79  Identities=25%  Similarity=0.466  Sum_probs=63.8

Q ss_pred             CCCCEEEEeCCCC----CCC-------HHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCce
Q 043443           59 QNHGSLLVRNIPL----DCR-------PEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKR  127 (299)
Q Consensus        59 ~~~~~l~V~nLp~----~~t-------e~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~  127 (299)
                      ...++|.|.||=.    ..+       +++|.+-..+||.|..|.|.-    .++.|.+.|.|.+.++|..||+.|+|..
T Consensus       263 r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d----~hPdGvvtV~f~n~eeA~~ciq~m~GR~  338 (382)
T KOG1548|consen  263 RADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYD----RHPDGVVTVSFRNNEEADQCIQTMDGRW  338 (382)
T ss_pred             cCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEec----cCCCceeEEEeCChHHHHHHHHHhcCee
Confidence            4568999999822    233       245666678999999997763    3678999999999999999999999999


Q ss_pred             eCCeeEEEEEcccC
Q 043443          128 FAGREISVVLAAES  141 (299)
Q Consensus       128 l~Gr~i~V~~a~~~  141 (299)
                      |+|++|...+....
T Consensus       339 fdgRql~A~i~DG~  352 (382)
T KOG1548|consen  339 FDGRQLTASIWDGK  352 (382)
T ss_pred             ecceEEEEEEeCCc
Confidence            99999998887543

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

Probab=97.80  E-value=2e-05  Score=76.40  Aligned_cols=77  Identities=12%  Similarity=0.230  Sum_probs=65.3

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHh-cCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCcee---CCeeE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFE-RFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRF---AGREI  133 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~-~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l---~Gr~i  133 (299)
                      ....+.|||.||-.-+|..+|++++. .+|.|+++||-      +.+..|||.|.+.++|.+.+.+|||..|   +.+.|
T Consensus       441 ~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~WmD------kIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L  514 (718)
T KOG2416|consen  441 KEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWMD------KIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHL  514 (718)
T ss_pred             CCccceEeeecccccchHHHHHHHHhhccCchHHHHHH------HhhcceeEecccHHHHHHHHHHHhccccCCCCCcee
Confidence            34678999999988899999999999 56777777553      2367899999999999999999999987   57889


Q ss_pred             EEEEccc
Q 043443          134 SVVLAAE  140 (299)
Q Consensus       134 ~V~~a~~  140 (299)
                      .|.|+..
T Consensus       515 ~adf~~~  521 (718)
T KOG2416|consen  515 IADFVRA  521 (718)
T ss_pred             Eeeecch
Confidence            9998864

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

Probab=97.80  E-value=1.3e-05  Score=70.46  Aligned_cols=73  Identities=25%  Similarity=0.424  Sum_probs=62.0

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCC--------CCCc----cEEEEEEcCHHHHHHHHHhhCCce
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYT--------GEPR----GFAFVQFVDPYEAAEAQHHMNGKR  127 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~--------g~~~----g~afVeF~~~~~A~~Al~~lng~~  127 (299)
                      ....|||++||+.++..-|.++|..||+|-.|.|.....+        +.+.    -.++|||.+...|+.+...||++.
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~  152 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTP  152 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCc
Confidence            3478999999999999999999999999999988765443        2222    356899999999999999999999


Q ss_pred             eCCee
Q 043443          128 FAGRE  132 (299)
Q Consensus       128 l~Gr~  132 (299)
                      |+|++
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99875

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

Probab=97.76  E-value=1.1e-05  Score=70.86  Aligned_cols=65  Identities=20%  Similarity=0.409  Sum_probs=53.6

Q ss_pred             HHHHHHHh-cCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcccC
Q 043443           76 EELRAPFE-RFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAES  141 (299)
Q Consensus        76 ~dL~~~F~-~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~~  141 (299)
                      +||...|+ +||+|+++.|..+ ..-+..|-+||.|...++|++|++.||+-.|.|++|..++....
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~N-l~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pvT  148 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDN-LGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPVT  148 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcc-cchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCcC
Confidence            45555555 8999999876543 34456789999999999999999999999999999999998643

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

Probab=97.71  E-value=4e-05  Score=71.78  Aligned_cols=70  Identities=23%  Similarity=0.352  Sum_probs=57.8

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccC---CCC--CC--------CccEEEEEEcCHHHHHHHHHhhC
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKD---YYT--GE--------PRGFAFVQFVDPYEAAEAQHHMN  124 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d---~~~--g~--------~~g~afVeF~~~~~A~~Al~~ln  124 (299)
                      +....+|.|.|||.+-.-+.|.+||..||.|+.|.|+..   +.+  +.        .+-+|||||++.+.|.+|.+.|+
T Consensus       228 el~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~  307 (484)
T KOG1855|consen  228 ELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLN  307 (484)
T ss_pred             ccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhc
Confidence            346789999999999888999999999999999998765   221  11        25689999999999999999886


Q ss_pred             Cce
Q 043443          125 GKR  127 (299)
Q Consensus       125 g~~  127 (299)
                      ...
T Consensus       308 ~e~  310 (484)
T KOG1855|consen  308 PEQ  310 (484)
T ss_pred             hhh
Confidence            543

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

Probab=97.68  E-value=0.00013  Score=70.63  Aligned_cols=63  Identities=29%  Similarity=0.557  Sum_probs=51.7

Q ss_pred             HHHHHHhcCCCEeEEEeccCCC---CCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           77 ELRAPFERFGVVRDVYLPKDYY---TGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        77 dL~~~F~~~G~I~~v~i~~d~~---~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      +|+..+.+||.|..|.|..+..   ..-..|..||||.+.++|+.|++.|+|..|.+++|.+.|..
T Consensus       425 dvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYyd  490 (500)
T KOG0120|consen  425 DVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYD  490 (500)
T ss_pred             HHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecC
Confidence            3445567899999999887622   23346789999999999999999999999999999888764

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

Probab=97.64  E-value=0.00012  Score=68.38  Aligned_cols=77  Identities=19%  Similarity=0.240  Sum_probs=63.3

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCe-eEEEEEc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGR-EISVVLA  138 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr-~i~V~~a  138 (299)
                      +..+|++.|||..++|++|+++|..-|.+.......    ++.+.+|++.|++.++|..|+..|++..+.+. .|.|.|+
T Consensus       413 psatlHlsnip~svsee~lk~~f~~~g~~vkafkff----~kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSFS  488 (492)
T KOG1190|consen  413 PSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFF----QKDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSFS  488 (492)
T ss_pred             chhheeeccCCcccchhHHHHhhhcCCceEEeeeec----CCCcceeecccCChhHhhhhccccccccCCCCceEEEEee
Confidence            456999999999999999999999887664433221    23357999999999999999999999998754 8899998


Q ss_pred             cc
Q 043443          139 AE  140 (299)
Q Consensus       139 ~~  140 (299)
                      +.
T Consensus       489 ks  490 (492)
T KOG1190|consen  489 KS  490 (492)
T ss_pred             cc
Confidence            64

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

Probab=97.63  E-value=0.00016  Score=69.24  Aligned_cols=65  Identities=25%  Similarity=0.235  Sum_probs=59.6

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHh-cCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHh
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFE-RFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH  122 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~-~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~  122 (299)
                      -++..|||||+||--++.++|..||. -||.|+.+-|-.|+.-.-++|-|=|+|.+...-.+||.+
T Consensus       367 lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  367 IDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             cCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            45678999999999999999999998 799999999999977888999999999999999999963

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

Probab=97.63  E-value=0.00031  Score=57.29  Aligned_cols=75  Identities=21%  Similarity=0.278  Sum_probs=53.0

Q ss_pred             CCCEEEEeCCC------CCCCH---HHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCC
Q 043443           60 NHGSLLVRNIP------LDCRP---EELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAG  130 (299)
Q Consensus        60 ~~~~l~V~nLp------~~~te---~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~G  130 (299)
                      +..||.|.=+.      ..+.+   .+|.+.|..||+|.-|.++-        +..+|+|.+-+.|.+|+. |+|..|+|
T Consensus        26 pDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~--------~~mwVTF~dg~sALaals-~dg~~v~g   96 (146)
T PF08952_consen   26 PDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVG--------DTMWVTFRDGQSALAALS-LDGIQVNG   96 (146)
T ss_dssp             TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEET--------TCEEEEESSCHHHHHHHH-GCCSEETT
T ss_pred             CCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeC--------CeEEEEECccHHHHHHHc-cCCcEECC
Confidence            34577776554      12332   36788889999998888874        468999999999999998 89999999


Q ss_pred             eeEEEEEcccCCC
Q 043443          131 REISVVLAAESRK  143 (299)
Q Consensus       131 r~i~V~~a~~~~~  143 (299)
                      +.|+|.+..+...
T Consensus        97 ~~l~i~LKtpdW~  109 (146)
T PF08952_consen   97 RTLKIRLKTPDWL  109 (146)
T ss_dssp             EEEEEEE------
T ss_pred             EEEEEEeCCccHH
Confidence            9999999887553

; PDB: 1UFW_A 2DNR_A.

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

Probab=97.58  E-value=0.00038  Score=66.83  Aligned_cols=65  Identities=23%  Similarity=0.435  Sum_probs=49.5

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCC---CCCCCcc---EEEEEEcCHHHHHHHHHhh
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDY---YTGEPRG---FAFVQFVDPYEAAEAQHHM  123 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~---~~g~~~g---~afVeF~~~~~A~~Al~~l  123 (299)
                      ..-..+||||+||++++|++|...|..||.|. |++....   .--.++|   |+|+.|+++..+..-|.++
T Consensus       256 ~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC  326 (520)
T KOG0129|consen  256 PRYSRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSAC  326 (520)
T ss_pred             cccccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHH
Confidence            34568999999999999999999999999874 4554211   1123456   9999999988877766654

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

Probab=97.56  E-value=0.00017  Score=73.14  Aligned_cols=83  Identities=27%  Similarity=0.416  Sum_probs=72.7

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCC--eeEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAG--REIS  134 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~G--r~i~  134 (299)
                      .....+.|||++|..++....|..+|..||.|..|++-.      ..-||+|.|++...|+.|++.|-|..|++  +.|.
T Consensus       451 kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~h------gq~yayi~yes~~~aq~a~~~~rgap~G~P~~r~r  524 (975)
T KOG0112|consen  451 KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRH------GQPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLR  524 (975)
T ss_pred             ccccceeeccCCCCCCChHHHHHHHhhccCcceeeeccc------CCcceeeecccCccchhhHHHHhcCcCCCCCcccc
Confidence            566788999999999999999999999999999998853      35799999999999999999999999975  6799


Q ss_pred             EEEcccCCCCc
Q 043443          135 VVLAAESRKRP  145 (299)
Q Consensus       135 V~~a~~~~~~~  145 (299)
                      |.|+......+
T Consensus       525 vdla~~~~~~P  535 (975)
T KOG0112|consen  525 VDLASPPGATP  535 (975)
T ss_pred             cccccCCCCCh
Confidence            99988654443

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

Probab=97.54  E-value=0.00022  Score=63.88  Aligned_cols=66  Identities=26%  Similarity=0.316  Sum_probs=52.6

Q ss_pred             HHHHHHHHhcCCCEeEEEeccCCCCCC-CccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEccc
Q 043443           75 PEELRAPFERFGVVRDVYLPKDYYTGE-PRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAE  140 (299)
Q Consensus        75 e~dL~~~F~~~G~I~~v~i~~d~~~g~-~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~  140 (299)
                      ++++++.+++||+|..|.|...+..-. -.--.||+|+..+.|.+|+-.|||..|+|+.+..+|..-
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn~  366 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYNL  366 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheeccH
Confidence            356778889999999988776543221 123579999999999999999999999999998887653

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

Probab=97.25  E-value=0.00023  Score=67.52  Aligned_cols=79  Identities=22%  Similarity=0.302  Sum_probs=65.2

Q ss_pred             CCCCCCCCEEEEeCCCCCC-CHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeE
Q 043443           55 RRKEQNHGSLLVRNIPLDC-RPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREI  133 (299)
Q Consensus        55 ~~~~~~~~~l~V~nLp~~~-te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i  133 (299)
                      +.-..+.+.|-|.-++..+ +.++|..+|.+||+|..|.|-..      .-.|+|+|.+..+|-.|.. .++..|+++.|
T Consensus       366 g~~~~dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~------~~~a~vTF~t~aeag~a~~-s~~avlnnr~i  438 (526)
T KOG2135|consen  366 GHAVVDHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS------SLHAVVTFKTRAEAGEAYA-SHGAVLNNRFI  438 (526)
T ss_pred             cchhcccchhhhhccCCCCchHhhhhhhhhhcCccccccccCc------hhhheeeeeccccccchhc-cccceecCcee
Confidence            3345566777777777765 66899999999999999988654      3579999999999977775 69999999999


Q ss_pred             EEEEccc
Q 043443          134 SVVLAAE  140 (299)
Q Consensus       134 ~V~~a~~  140 (299)
                      +|.|-++
T Consensus       439 Kl~whnp  445 (526)
T KOG2135|consen  439 KLFWHNP  445 (526)
T ss_pred             EEEEecC
Confidence            9999876

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

Probab=97.22  E-value=0.00058  Score=67.63  Aligned_cols=82  Identities=24%  Similarity=0.154  Sum_probs=66.9

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeE-EEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRD-VYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV  135 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~-v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V  135 (299)
                      ......+|||..||..+++.++.++|.+.-.|++ |.|..-+ ++...+.|||+|.+++++..|+..-+.+.+..+.|.|
T Consensus       430 P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P-~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv  508 (944)
T KOG4307|consen  430 PGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLP-TDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRV  508 (944)
T ss_pred             CCCccceEEeccCCccccccchhhhhhhhhhhhheeEeccCC-cccccchhhheeccccccchhhhcccccccCceEEEe
Confidence            3445789999999999999999999999888877 5555443 6677899999999999998888766667778888888


Q ss_pred             EEcc
Q 043443          136 VLAA  139 (299)
Q Consensus       136 ~~a~  139 (299)
                      .-..
T Consensus       509 ~si~  512 (944)
T KOG4307|consen  509 DSIA  512 (944)
T ss_pred             echh
Confidence            7544

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

Probab=97.16  E-value=0.00035  Score=64.74  Aligned_cols=74  Identities=24%  Similarity=0.305  Sum_probs=55.3

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcC----CCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEE
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERF----GVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV  135 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~----G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V  135 (299)
                      +.-.|-+.+||+++++.||.+||..-    |.++.|.++.. .+|+..|-|||.|..+++|+.||.+ |...|+-+.|.|
T Consensus       160 ~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~r-pdgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYIEl  237 (508)
T KOG1365|consen  160 NQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTR-PDGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYIEL  237 (508)
T ss_pred             cceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEEC-CCCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHHHH
Confidence            34566778999999999999999632    23445555443 3688999999999999999999985 555555555544

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

Probab=97.12  E-value=0.0025  Score=44.44  Aligned_cols=55  Identities=18%  Similarity=0.212  Sum_probs=45.4

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcC---CCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhh
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFERF---GVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM  123 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~~~---G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~l  123 (299)
                      ...|+|.+|. +++.+||+.+|..|   .....|.++.|       .-|-|.|.+.+.|..||.+|
T Consensus         5 peavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdD-------tScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDD-------TSCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecC-------CcEEEEECCHHHHHHHHHcC
Confidence            4689999995 58889999999988   23557888877       36889999999999999865

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

Probab=97.06  E-value=0.03  Score=48.20  Aligned_cols=57  Identities=14%  Similarity=0.029  Sum_probs=35.2

Q ss_pred             CCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHH--hhCCceeC
Q 043443           73 CRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQH--HMNGKRFA  129 (299)
Q Consensus        73 ~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~--~lng~~l~  129 (299)
                      -+.--|.+-+...|.|---.-...++.....-+-|-.=.+.++|++||.  .|+|.+|-
T Consensus        28 d~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelr   86 (256)
T KOG4207|consen   28 DDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELR   86 (256)
T ss_pred             HHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceee
Confidence            3455677777777776432211112222223355666778999999995  68999984

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

Probab=96.98  E-value=4.6e-05  Score=76.72  Aligned_cols=69  Identities=23%  Similarity=0.285  Sum_probs=60.3

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeC
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFA  129 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~  129 (299)
                      ..++||.||+..+.+.+|...|..+|.|..|.+....+++..+|+|||+|...+++.+||...+...++
T Consensus       667 ~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g  735 (881)
T KOG0128|consen  667 LIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG  735 (881)
T ss_pred             HHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhh
Confidence            357899999999999999999999999888877666678899999999999999999999866665555

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

Probab=96.95  E-value=0.00041  Score=70.09  Aligned_cols=81  Identities=20%  Similarity=0.223  Sum_probs=72.2

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEccc
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAE  140 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~  140 (299)
                      ...|||.|+|+..|.++|+.+|.++|.++.+.++..+ .|+++|.|||.|.+..+|..++..++...+.-..+.|+++.+
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            4689999999999999999999999999998877664 789999999999999999999999999888888888888665


Q ss_pred             CC
Q 043443          141 SR  142 (299)
Q Consensus       141 ~~  142 (299)
                      ..
T Consensus       815 ~~  816 (881)
T KOG0128|consen  815 ER  816 (881)
T ss_pred             cc
Confidence            33

>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins []

Probab=96.88  E-value=0.0056  Score=44.31  Aligned_cols=67  Identities=18%  Similarity=0.302  Sum_probs=41.0

Q ss_pred             EEEEe-CCCCCCCHHHHHHHHhcCC-----CEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           63 SLLVR-NIPLDCRPEELRAPFERFG-----VVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        63 ~l~V~-nLp~~~te~dL~~~F~~~G-----~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      +|||. +--..++..+|..+|...+     .|-.|+|..        .|+||+... +.|+.++..|++..++|+.|.|+
T Consensus         2 rl~in~Gr~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~--------~~S~vev~~-~~a~~v~~~l~~~~~~gk~v~ve   72 (74)
T PF03880_consen    2 RLFINVGRKDGLTPRDIVGAICNEAGIPGRDIGRIDIFD--------NFSFVEVPE-EVAEKVLEALNGKKIKGKKVRVE   72 (74)
T ss_dssp             EEEES-SGGGT--HHHHHHHHHTCTTB-GGGEEEEEE-S--------S-EEEEE-T-T-HHHHHHHHTT--SSS----EE
T ss_pred             EEEEEcccccCCCHHHHHHHHHhccCCCHHhEEEEEEee--------eEEEEEECH-HHHHHHHHHhcCCCCCCeeEEEE
Confidence            45552 1145688999999998765     455777764        499999976 58899999999999999999998


Q ss_pred             Ec
Q 043443          137 LA  138 (299)
Q Consensus       137 ~a  138 (299)
                      .|
T Consensus        73 ~A   74 (74)
T PF03880_consen   73 RA   74 (74)
T ss_dssp             E-
T ss_pred             EC
Confidence            75

; PDB: 2G0C_A 3MOJ_B.

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

Probab=96.83  E-value=0.00093  Score=62.76  Aligned_cols=73  Identities=25%  Similarity=0.372  Sum_probs=58.9

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcC--CCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCc-eeCCeeEEEEEc
Q 043443           62 GSLLVRNIPLDCRPEELRAPFERF--GVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGK-RFAGREISVVLA  138 (299)
Q Consensus        62 ~~l~V~nLp~~~te~dL~~~F~~~--G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~-~l~Gr~i~V~~a  138 (299)
                      ..|||+||...++..||..+|...  +.-..+ |++       .||+||.+.+...|.+|++.|+|+ ++.|..+.|++.
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-LVK-------SGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHS   73 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcce-eee-------cceeeccCCchhhhhhhHHhhchhhhhcCceeeccch
Confidence            479999999999999999999754  211122 232       489999999999999999999997 588999999887


Q ss_pred             ccCC
Q 043443          139 AESR  142 (299)
Q Consensus       139 ~~~~  142 (299)
                      -++.
T Consensus        74 v~kk   77 (584)
T KOG2193|consen   74 VPKK   77 (584)
T ss_pred             hhHH
Confidence            6543

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

Probab=96.77  E-value=0.002  Score=62.51  Aligned_cols=56  Identities=25%  Similarity=0.409  Sum_probs=44.8

Q ss_pred             CCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeC----CeeEEEEEccc
Q 043443           85 FGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFA----GREISVVLAAE  140 (299)
Q Consensus        85 ~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~----Gr~i~V~~a~~  140 (299)
                      .|.-..+.++.|..+..+.|||||.|.+.+++..+.+++||+.|+    .+.+.|.||.-
T Consensus       413 ~gtYDFlYLPiDF~nkcNvGYAFINm~sp~ai~~F~kAFnGk~W~~FnS~Kia~itYArI  472 (549)
T KOG4660|consen  413 KGTYDFLYLPIDFKNKCNVGYAFINMTSPEAIIRFYKAFNGKKWEKFNSEKIASITYARI  472 (549)
T ss_pred             cCccceEEeccccccccccceeEEeecCHHHHHHHHHHHcCCchhhhcceeeeeeehhhh
Confidence            455556777778777889999999999999999999999999764    34556777764

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

Probab=96.70  E-value=0.0064  Score=44.84  Aligned_cols=56  Identities=18%  Similarity=0.281  Sum_probs=43.0

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCC
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNG  125 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng  125 (299)
                      .+.+||+ +|...-..||.++|..||.|. |.++.|       .-|||.+.+.+.|..|+..++-
T Consensus         9 dHVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~d-------TSAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen    9 DHVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWIND-------TSAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             CCEEEEE---TT--HHHHHHHCCCCCCEE-EEEECT-------TEEEEEECCCHHHHHHHHHHTT
T ss_pred             ceEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcC-------CcEEEEeecHHHHHHHHHHhcc
Confidence            4567776 999999999999999999985 545544       4899999999999999988753

; 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.

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=96.69  E-value=0.0022  Score=54.58  Aligned_cols=83  Identities=17%  Similarity=0.253  Sum_probs=51.9

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhc-CCCE---eEEE--eccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCC-
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFER-FGVV---RDVY--LPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAG-  130 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~-~G~I---~~v~--i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~G-  130 (299)
                      +...++|.|.+||+.+||+++.+.+.. ++..   .++.  +...........-|||.|.+.+++...+..++|..|-+ 
T Consensus         4 ~~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~   83 (176)
T PF03467_consen    4 EKEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDS   83 (176)
T ss_dssp             -----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-T
T ss_pred             cccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECC
Confidence            345679999999999999999987766 5555   3343  21111122234679999999999999999999988743 


Q ss_pred             ----eeEEEEEccc
Q 043443          131 ----REISVVLAAE  140 (299)
Q Consensus       131 ----r~i~V~~a~~  140 (299)
                          ....|++|.-
T Consensus        84 kg~~~~~~VE~Apy   97 (176)
T PF03467_consen   84 KGNEYPAVVEFAPY   97 (176)
T ss_dssp             TS-EEEEEEEE-SS
T ss_pred             CCCCcceeEEEcch
Confidence                2456777764

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=96.66  E-value=0.0084  Score=48.61  Aligned_cols=76  Identities=24%  Similarity=0.287  Sum_probs=57.7

Q ss_pred             CCCCCCCEEEEeCCCCCCC-HHH---HHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCe
Q 043443           56 RKEQNHGSLLVRNIPLDCR-PEE---LRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGR  131 (299)
Q Consensus        56 ~~~~~~~~l~V~nLp~~~t-e~d---L~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr  131 (299)
                      ..+.+..||.|.=|..++. .+|   |...+..||+|..|.+.-       +.-|+|.|.+...|-.|+.+++. ..-|.
T Consensus        81 ~kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG-------rqsavVvF~d~~SAC~Av~Af~s-~~pgt  152 (166)
T PF15023_consen   81 TKEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG-------RQSAVVVFKDITSACKAVSAFQS-RAPGT  152 (166)
T ss_pred             CCCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC-------CceEEEEehhhHHHHHHHHhhcC-CCCCc
Confidence            4567788999987766653 234   455667899999998764       46899999999999999998876 45566


Q ss_pred             eEEEEEcc
Q 043443          132 EISVVLAA  139 (299)
Q Consensus       132 ~i~V~~a~  139 (299)
                      .+.+.|-.
T Consensus       153 m~qCsWqq  160 (166)
T PF15023_consen  153 MFQCSWQQ  160 (166)
T ss_pred             eEEeeccc
Confidence            77777643

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

Probab=96.66  E-value=0.0019  Score=57.09  Aligned_cols=75  Identities=24%  Similarity=0.327  Sum_probs=60.0

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCce----eCCeeEEEEE
Q 043443           62 GSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKR----FAGREISVVL  137 (299)
Q Consensus        62 ~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~----l~Gr~i~V~~  137 (299)
                      ..|+|.||...++.+.|...|..||+|....++.| ..++..+-++|+|...-.|.+|+..++-.-    +.+..+.|..
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 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVD-DRGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGVEP  110 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeec-ccccccccchhhhhcchhHHHHHHHhccCccccCCCCCccCCCh
Confidence            68999999999999999999999999987666555 367888999999999999999998774332    3344544443

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

Probab=96.66  E-value=0.0088  Score=54.07  Aligned_cols=73  Identities=18%  Similarity=0.207  Sum_probs=56.0

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeE-EEEEcc
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREI-SVVLAA  139 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i-~V~~a~  139 (299)
                      .+=|.|.++|... ...|..+|.+||+|++.....      +-.|-+|.|.+..+|++||. .||++|+|..| -|..+.
T Consensus       197 D~WVTVfGFppg~-~s~vL~~F~~cG~Vvkhv~~~------ngNwMhirYssr~~A~KALs-kng~ii~g~vmiGVkpCt  268 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQ-VSIVLNLFSRCGEVVKHVTPS------NGNWMHIRYSSRTHAQKALS-KNGTIIDGDVMIGVKPCT  268 (350)
T ss_pred             cceEEEeccCccc-hhHHHHHHHhhCeeeeeecCC------CCceEEEEecchhHHHHhhh-hcCeeeccceEEeeeecC
Confidence            5667777887753 456788999999998776542      25699999999999999998 49999988654 465555


Q ss_pred             cC
Q 043443          140 ES  141 (299)
Q Consensus       140 ~~  141 (299)
                      ++
T Consensus       269 Dk  270 (350)
T KOG4285|consen  269 DK  270 (350)
T ss_pred             CH
Confidence            43

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

Probab=96.63  E-value=0.00041  Score=70.42  Aligned_cols=79  Identities=18%  Similarity=0.293  Sum_probs=65.4

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      ..+.+||++||+..+++.+|...|..+|.|..|+|...+ -+....||||.|.+...+..|+..|.+..|..-.+.+-+.
T Consensus       370 ~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~-~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG  448 (975)
T KOG0112|consen  370 RATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPH-IKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLG  448 (975)
T ss_pred             hhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCC-CCcccchhhhhhhccccCcccchhhcCCccccCccccccc
Confidence            357899999999999999999999999999999987653 2344569999999999999999999988876545444444

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=96.57  E-value=0.00087  Score=61.35  Aligned_cols=81  Identities=19%  Similarity=0.306  Sum_probs=61.7

Q ss_pred             CCEEEEeCCCCCCCHH-HHH--HHHhcCCCEeEEEeccCCC---CCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEE
Q 043443           61 HGSLLVRNIPLDCRPE-ELR--APFERFGVVRDVYLPKDYY---TGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREIS  134 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~-dL~--~~F~~~G~I~~v~i~~d~~---~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~  134 (299)
                      ..-+||-+|+..+..+ .|+  +.|.+||.|..|.+..+..   ......-++|+|+..++|..||...+|..++|+.|+
T Consensus        77 knlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lk  156 (327)
T KOG2068|consen   77 KNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALK  156 (327)
T ss_pred             hhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhH
Confidence            3567888888776444 443  6789999999998877652   111233489999999999999999999999999988


Q ss_pred             EEEcccC
Q 043443          135 VVLAAES  141 (299)
Q Consensus       135 V~~a~~~  141 (299)
                      +.+...+
T Consensus       157 a~~gttk  163 (327)
T KOG2068|consen  157 ASLGTTK  163 (327)
T ss_pred             HhhCCCc
Confidence            7776654

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=96.25  E-value=0.037  Score=43.30  Aligned_cols=68  Identities=19%  Similarity=0.155  Sum_probs=49.6

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCC-CEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCC
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFERFG-VVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAG  130 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~~~G-~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~G  130 (299)
                      ...+.+...|+.++.++|..+.+.+- .|..+.|+++.  ..++-.++|.|.+.++|..-.+.+||+.|+-
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            34455555566666677776666653 56678888763  2355678899999999999999999998763

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

>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=96.13  E-value=0.015  Score=49.70  Aligned_cols=62  Identities=21%  Similarity=0.274  Sum_probs=46.7

Q ss_pred             CHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhC--CceeCCeeEEEEEcccC
Q 043443           74 RPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMN--GKRFAGREISVVLAAES  141 (299)
Q Consensus        74 te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~ln--g~~l~Gr~i~V~~a~~~  141 (299)
                      ..+.|+++|..|+.+..+.+...      -+-.+|.|.+.++|..|...|+  +..|.|..|+|.++...
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s------FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~   71 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS------FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPT   71 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT------TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----S
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC------CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcccc
Confidence            45889999999999888776644      4678999999999999999999  99999999999998543

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.

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

Probab=96.02  E-value=0.01  Score=57.63  Aligned_cols=69  Identities=20%  Similarity=0.299  Sum_probs=54.0

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhc--CCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCC--ceeCCeeEEE
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFER--FGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNG--KRFAGREISV  135 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~--~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng--~~l~Gr~i~V  135 (299)
                      ..|.|+|.-||..+-+++|+.||..  |-.++.|.+..+       .--||+|++..||+.|++.|.-  ++|.|+.|..
T Consensus       174 kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N-------~nWyITfesd~DAQqAykylreevk~fqgKpImA  246 (684)
T KOG2591|consen  174 KRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHN-------DNWYITFESDTDAQQAYKYLREEVKTFQGKPIMA  246 (684)
T ss_pred             ceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeec-------CceEEEeecchhHHHHHHHHHHHHHhhcCcchhh
Confidence            4578889999999999999999975  667778877654       2579999999999999977643  3566665543

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

Probab=95.63  E-value=0.021  Score=56.62  Aligned_cols=74  Identities=15%  Similarity=0.186  Sum_probs=63.9

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      ...+..+|||+||...+..+-++.++..+|.|..+..+.         |+|.+|..+..+..|+..|+-..++|..|.+.
T Consensus        36 ~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~  106 (668)
T KOG2253|consen   36 PLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELNIDDQKLIEN  106 (668)
T ss_pred             CCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhcccCCCcchhhcc
Confidence            344567999999999999999999999999987765542         99999999999999999999999999988877


Q ss_pred             Ecc
Q 043443          137 LAA  139 (299)
Q Consensus       137 ~a~  139 (299)
                      ...
T Consensus       107 ~d~  109 (668)
T KOG2253|consen  107 VDE  109 (668)
T ss_pred             chh
Confidence            744

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

Probab=95.11  E-value=0.013  Score=59.65  Aligned_cols=74  Identities=20%  Similarity=0.255  Sum_probs=62.2

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCcee--CCeeEEEEEccc
Q 043443           63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRF--AGREISVVLAAE  140 (299)
Q Consensus        63 ~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l--~Gr~i~V~~a~~  140 (299)
                      +.++.|++-..+...|..+|.+||.|..++...+      ...|.|+|...+.|..|+++|+|+++  -|-+.+|.+|+.
T Consensus       300 ~~~~~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  300 KQSLENNAVNLTSSSLATLCSDYGSVASAWTLRD------LNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKT  373 (1007)
T ss_pred             hhhhhcccccchHHHHHHHHHhhcchhhheeccc------ccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccc
Confidence            4445556666777889999999999999998876      47899999999999999999999985  588899999885


Q ss_pred             CC
Q 043443          141 SR  142 (299)
Q Consensus       141 ~~  142 (299)
                      -.
T Consensus       374 ~~  375 (1007)
T KOG4574|consen  374 LP  375 (1007)
T ss_pred             cc
Confidence            43

>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=94.89  E-value=0.16  Score=35.99  Aligned_cols=56  Identities=16%  Similarity=0.287  Sum_probs=43.9

Q ss_pred             CCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           72 DCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        72 ~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      .++.+||+..|.+|+-. .|.  .++     .| -||.|.+..+|+.+....|+..+.+..|.++
T Consensus        11 ~~~v~d~K~~Lr~y~~~-~I~--~d~-----tG-fYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M~   66 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRWD-RIR--DDR-----TG-FYIVFNDSKEAERCFRAEDGTLFFTYRMQME   66 (66)
T ss_pred             CccHHHHHHHHhcCCcc-eEE--ecC-----CE-EEEEECChHHHHHHHHhcCCCEEEEEEEEeC
Confidence            46889999999999642 333  332     23 4899999999999999999999988887653

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

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=94.67  E-value=0.016  Score=53.09  Aligned_cols=81  Identities=14%  Similarity=0.046  Sum_probs=66.1

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      ..+++||+++.+.+.+.++..+|..+|.+..+.+.........+++++|.|...+.+..||.......+.+..+...+.+
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            47899999999999999999999999988877776656677889999999999999999998544456666666655554


Q ss_pred             c
Q 043443          140 E  140 (299)
Q Consensus       140 ~  140 (299)
                      .
T Consensus       167 ~  167 (285)
T KOG4210|consen  167 R  167 (285)
T ss_pred             c
Confidence            3

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.30  E-value=0.16  Score=49.97  Aligned_cols=81  Identities=19%  Similarity=0.256  Sum_probs=60.1

Q ss_pred             CCCCCEEEEeCCCCC-CCHHHHHHHHhcC----CCEeEEEeccCC----------CCCC---------------------
Q 043443           58 EQNHGSLLVRNIPLD-CRPEELRAPFERF----GVVRDVYLPKDY----------YTGE---------------------  101 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~-~te~dL~~~F~~~----G~I~~v~i~~d~----------~~g~---------------------  101 (299)
                      ...+.+|-|.||.|+ +...||..+|..|    |.|..|.|....          .+|.                     
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            456789999999997 6888999999876    578887765321          1111                     


Q ss_pred             ----------------CccEEEEEEcCHHHHHHHHHhhCCceeCCe--eEEEEEc
Q 043443          102 ----------------PRGFAFVQFVDPYEAAEAQHHMNGKRFAGR--EISVVLA  138 (299)
Q Consensus       102 ----------------~~g~afVeF~~~~~A~~Al~~lng~~l~Gr--~i~V~~a  138 (299)
                                      ..=||+|+|.+++.|.+.+..|+|++|...  .|-+.|.
T Consensus       251 ~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DLRFI  305 (650)
T KOG2318|consen  251 EDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLDLRFI  305 (650)
T ss_pred             hhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceeeeeec
Confidence                            012899999999999999999999999754  4444443

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

Probab=93.83  E-value=0.18  Score=48.19  Aligned_cols=69  Identities=20%  Similarity=0.297  Sum_probs=57.3

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcC-CCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCC
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERF-GVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAG  130 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~-G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~G  130 (299)
                      ..+.|+|-.+|..++..||..|+..| -.|..|.|++|.  -.+.=.++|.|.+.++|....+.+||+.|+.
T Consensus        73 ~~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~--~pnrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   73 SSTMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDG--MPNRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CCcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecC--CCceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            37899999999999999999998876 467889998853  2233456899999999999999999998864

>KOG4019 consensus Calcineurin-mediated signaling pathway inhibitor DSCR1 [Signal transduction mechanisms; General function prediction only]

Probab=91.90  E-value=0.19  Score=42.49  Aligned_cols=77  Identities=16%  Similarity=0.232  Sum_probs=57.8

Q ss_pred             CCCCEEEEeCCCCCCCH-----HHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCe-e
Q 043443           59 QNHGSLLVRNIPLDCRP-----EELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGR-E  132 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te-----~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr-~  132 (299)
                      +..++|++.+|+..+..     ...+.+|.+|.+...+.+.+.      .++.-|.|.+++.|..|..+++...|.|. .
T Consensus         8 dlp~~~~~c~i~~~VF~~~~~k~~~~~lFrq~n~~~~fq~lrs------frrvRi~f~~p~~a~~a~i~~~~~~f~~~~~   81 (193)
T KOG4019|consen    8 DLPTAIIACDIHEEVFVNREDKALFENLFRQINEDATFQLLRS------FRRVRINFSNPEAAADARIKLHSTSFNGKNE   81 (193)
T ss_pred             cccceeeeecccHHhhccHHHHHHHHhHHhhhCcchHHHHHHh------hceeEEeccChhHHHHHHHHhhhcccCCCce
Confidence            34567888998776532     234566777776666666543      46777899999999999999999999998 8


Q ss_pred             EEEEEcccC
Q 043443          133 ISVVLAAES  141 (299)
Q Consensus       133 i~V~~a~~~  141 (299)
                      |+..++...
T Consensus        82 ~k~yfaQ~~   90 (193)
T KOG4019|consen   82 LKLYFAQPG   90 (193)
T ss_pred             EEEEEccCC
Confidence            888888753

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

Probab=90.58  E-value=0.012  Score=55.41  Aligned_cols=78  Identities=18%  Similarity=0.311  Sum_probs=63.9

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      ....|.|.|||....|+.|..++.+||.|+.|..+..   ..-.-..-|+|...+.+..||.+|||..|....++|.|-.
T Consensus        79 rsrk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt---~~etavvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~YiP  155 (584)
T KOG2193|consen   79 RSRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNT---DSETAVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGYIP  155 (584)
T ss_pred             HhhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhcc---chHHHHHHHHHHHHHHHHHHHHhhcchHhhhhhhhcccCc
Confidence            3567899999999999999999999999998866432   1112334578899999999999999999999999998865


Q ss_pred             c
Q 043443          140 E  140 (299)
Q Consensus       140 ~  140 (299)
                      .
T Consensus       156 d  156 (584)
T KOG2193|consen  156 D  156 (584)
T ss_pred             h
Confidence            4

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

Probab=89.54  E-value=1.1  Score=40.47  Aligned_cols=47  Identities=15%  Similarity=0.273  Sum_probs=36.5

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCE-eEEEeccCCCCCCCccEEEEEEcCH
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFERFGVV-RDVYLPKDYYTGEPRGFAFVQFVDP  113 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~~~G~I-~~v~i~~d~~~g~~~g~afVeF~~~  113 (299)
                      .+-|+|+||+.++...||+..+.+.+.+ ..|.+.      .+.+-||+.|.+.
T Consensus       330 ~~di~~~nl~rd~rv~dlk~~lr~~~~~pm~iswk------g~~~k~flh~~~~  377 (396)
T KOG4410|consen  330 KTDIKLTNLSRDIRVKDLKSELRKRECTPMSISWK------GHFGKCFLHFGNR  377 (396)
T ss_pred             ccceeeccCccccchHHHHHHHHhcCCCceeEeee------cCCcceeEecCCc
Confidence            4569999999999999999999988754 344443      3367899999754

>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=89.43  E-value=0.82  Score=32.50  Aligned_cols=62  Identities=21%  Similarity=0.279  Sum_probs=46.2

Q ss_pred             HHHHHHHhcCC-CEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEccc
Q 043443           76 EELRAPFERFG-VVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAE  140 (299)
Q Consensus        76 ~dL~~~F~~~G-~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~  140 (299)
                      ++|.+.|...| +|..|.-+....+..+....||+++...+...   .|+=+.|++..|+|+....
T Consensus         2 ~~I~~~L~~~G~~v~~i~~~~~~~~k~pl~mf~veL~p~~~~k~---i~~Ik~l~~~~V~vE~~~k   64 (68)
T PF07530_consen    2 EEIKEELKDQGHPVRNIHNMHSRNTKKPLNMFFVELEPKPNNKE---IYKIKTLCGQRVKVERPRK   64 (68)
T ss_pred             HHHHHHHHHcCCceEEEEccccCCCCCCceEEEEeeccCccccc---eeehHhhCCeEEEEecCCC
Confidence            46777777766 77788777777777888899999987655333   4566788999999987654

These proteins are possibly involved in RNA binding or single strand DNA binding.

>smart00596 PRE_C2HC PRE_C2HC domain

Probab=89.27  E-value=0.67  Score=32.95  Aligned_cols=62  Identities=18%  Similarity=0.217  Sum_probs=47.1

Q ss_pred             HHHHHHHhcCC-CEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEccc
Q 043443           76 EELRAPFERFG-VVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAE  140 (299)
Q Consensus        76 ~dL~~~F~~~G-~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~  140 (299)
                      .+|++.|...| ++..|..+....+..+...-||+.....+...   .|+-+.|++..|.|+-...
T Consensus         2 ~~I~~~L~~~G~~v~~i~~m~~~~~r~P~nmf~vel~~~~~~~~---Il~ik~Lg~~~V~VEr~~k   64 (69)
T smart00596        2 SQIEEALKDIGFPVLFIHNMLNRDTKNPQNMFEVELVPAANGKE---ILNIKTLGGQRVTVERPHK   64 (69)
T ss_pred             HHHHHHHHHcCCceeEEEcccccCCCCcceeEEEEeeecCCCcc---eEeehhhCCeeEEEecCcc
Confidence            46788888887 67888888877777888899999987654444   4566788999999886543

>KOG4483 consensus Uncharacterized conserved protein [Function unknown]

Probab=89.24  E-value=0.87  Score=43.02  Aligned_cols=58  Identities=24%  Similarity=0.260  Sum_probs=48.0

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCE-eEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHh
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVV-RDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH  122 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I-~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~  122 (299)
                      .+-.+.|-|.++|...-.+||..+|..|+.- ..|.|+-+       ..||..|.+...|..||..
T Consensus       388 ~dlpHVlEIydfp~efkteDll~~f~~yq~kgfdIkWvDd-------thalaVFss~~~AaeaLt~  446 (528)
T KOG4483|consen  388 SDLPHVLEIYDFPDEFKTEDLLKAFETYQNKGFDIKWVDD-------THALAVFSSVNRAAEALTL  446 (528)
T ss_pred             ccccceeEeccCchhhccHHHHHHHHHhhcCCceeEEeec-------ceeEEeecchHHHHHHhhc
Confidence            3457899999999999999999999999753 45666655       4899999999999999873

>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=85.76  E-value=1.4  Score=34.84  Aligned_cols=57  Identities=26%  Similarity=0.251  Sum_probs=30.0

Q ss_pred             CEEEEeCCCCC---------CCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEc-CHHHHHHHHH
Q 043443           62 GSLLVRNIPLD---------CRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFV-DPYEAAEAQH  121 (299)
Q Consensus        62 ~~l~V~nLp~~---------~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~-~~~~A~~Al~  121 (299)
                      -+++|.|++..         ++.++|.+.|..|..++-..+ .++  ....++++|+|. +..-...|+.
T Consensus         9 wmgIi~N~~~~~~~~g~~~g~~~~~l~~~l~~f~p~kv~~l-~~~--~gh~g~aiv~F~~~w~Gf~~A~~   75 (116)
T PF03468_consen    9 WMGIIVNIPTEKDDDGRWVGMSNEELLDKLAEFNPLKVKPL-YGK--QGHTGFAIVEFNKDWSGFKNAMR   75 (116)
T ss_dssp             -EEEEE----EE-TTS-EE---SHHHHHHHHH---SEEEEE-EET--TEEEEEEEEE--SSHHHHHHHHH
T ss_pred             CEEEEEcCccccCCCCceeccCHHHHHHHHHhcCCceeEEC-cCC--CCCcEEEEEEECCChHHHHHHHH
Confidence            46778888554         355789999999987754333 332  255789999997 4455555554

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 Uncharacterized conserved protein [Function unknown]

Probab=82.12  E-value=0.24  Score=47.23  Aligned_cols=78  Identities=3%  Similarity=-0.148  Sum_probs=62.9

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEccc
Q 043443           62 GSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAE  140 (299)
Q Consensus        62 ~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~  140 (299)
                      ...|+..|+..+++.+|.-+|..||.|..+++...-+.+...-.+||...+ .+|..+|+.|.-..+.|..+.|.++..
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            456788899999999999999999999988887665566667788887765 677788877777777888888888763

>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=80.74  E-value=3.9  Score=37.30  Aligned_cols=82  Identities=15%  Similarity=0.278  Sum_probs=58.1

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCC-------CCCCCccEEEEEEcCHHHHHHHHH----hhCC-
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDY-------YTGEPRGFAFVQFVDPYEAAEAQH----HMNG-  125 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~-------~~g~~~g~afVeF~~~~~A~~Al~----~lng-  125 (299)
                      +--+..|.+.||...++-..+...|.+||.|+.|.++.+.       ...+....+.+-|-+.+.|.....    .|.- 
T Consensus        12 ~YrTRSLLfeNv~~sidLh~Fl~~fv~~~pIESiYL~~~~~~~~d~~~~d~~~~SilLSFlsr~~CLdFYNnvLQrLsEf   91 (309)
T PF10567_consen   12 EYRTRSLLFENVNNSIDLHSFLTKFVKFGPIESIYLIKSNDKPSDDYNDDKNNQSILLSFLSREICLDFYNNVLQRLSEF   91 (309)
T ss_pred             cceeHHHHHhhccccccHHHHHHHhhccCceeEEEEecCCCcccccccccccceEEEEeeechHHHHHHHHHHHHHHHHH
Confidence            3345678889999999999999999999999999998764       122345678899998888766542    2221 


Q ss_pred             -ceeCCeeEEEEEcc
Q 043443          126 -KRFAGREISVVLAA  139 (299)
Q Consensus       126 -~~l~Gr~i~V~~a~  139 (299)
                       +.|.-..|.|.+..
T Consensus        92 K~~L~S~~L~lsFV~  106 (309)
T PF10567_consen   92 KTKLKSESLTLSFVS  106 (309)
T ss_pred             HHhcCCcceeEEEEE
Confidence             23556666666554

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.

>COG5638 Uncharacterized conserved protein [Function unknown]

Probab=80.33  E-value=7.2  Score=37.19  Aligned_cols=73  Identities=19%  Similarity=0.263  Sum_probs=52.5

Q ss_pred             CCCCCEEEEeCCCCC-CCHHHHHHHHhcC----CCEeEEEeccCCC----------CC----------------------
Q 043443           58 EQNHGSLLVRNIPLD-CRPEELRAPFERF----GVVRDVYLPKDYY----------TG----------------------  100 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~-~te~dL~~~F~~~----G~I~~v~i~~d~~----------~g----------------------  100 (299)
                      ..++..|-|-||.|+ +...+|..+|..|    |.|..|.|.....          .|                      
T Consensus       143 G~~tkrLAvVnmDWd~v~a~DLf~~fsSf~P~ggkl~kV~iypsefGkeRm~~e~vqGpprdif~~~d~~~ssqk~~~dn  222 (622)
T COG5638         143 GNPTKRLAVVNMDWDRVDAKDLFKIFSSFLPYGGKLSKVKIYPSEFGKERMAAEHVQGPPRDIFTPADNQPSSQKFGDDN  222 (622)
T ss_pred             CCcccceeEeecccccchHHHHHHHHHhhCCCCCccceeEechhhhhHHHHhHhhccCCchhhccccccCcchhccCCcc
Confidence            456778999999886 6778899988865    5666665542100          00                      


Q ss_pred             ----CC-----------------------------ccEEEEEEcCHHHHHHHHHhhCCceeCC
Q 043443          101 ----EP-----------------------------RGFAFVQFVDPYEAAEAQHHMNGKRFAG  130 (299)
Q Consensus       101 ----~~-----------------------------~g~afVeF~~~~~A~~Al~~lng~~l~G  130 (299)
                          .-                             .=||+|+|.+...++..+..|+|.++..
T Consensus       223 ~~sd~d~g~d~~~Egd~g~e~d~~~lrqyqlerlryYyAvvec~d~~tsK~iY~~CDG~Eye~  285 (622)
T COG5638         223 VFSDRDAGEDALIEGDRGNEFDMVKLRQYQLERLRYYYAVVECEDIETSKNIYSACDGVEYEN  285 (622)
T ss_pred             chhhhhcchhhhhhcccccchhHHHHHHHHhhhheeEEEEEEeccchhhHHHHhccCcccccc
Confidence                00                             1289999999999999999999998764

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	299
2kn4_A	158	The Structure Of The Rrm Domain Of Sc35 Length = 15		4e-13
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		5e-13
2dnm_A	103	Solution Structure Of Rna Binding Domain In Srp46 S		3e-11
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		9e-09
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		1e-08
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		3e-08
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		4e-08
2cph_A	107	Solution Structure Of The C-Terminal Rna Recognitio		7e-08
1whw_A	99	Solution Structure Of The N-Terminal Rna Binding Do		9e-08
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		1e-07
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		4e-07
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		7e-07
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		1e-06
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		1e-06
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		1e-06
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		2e-06
3lpy_A	79	Crystal Structure Of The Rrm Domain Of Cyp33 Length		2e-06
2cq0_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		4e-06
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		5e-06
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		1e-05
3ucg_A	89	Crystal Structure Of A Rna Binding Domain Of Hypoth		1e-05
3b4d_A	96	Crystal Structure Of Human Pabpn1 Rrm Length = 96		2e-05
2dgs_A	99	Solution Structure Of The Second Rna Binding Domain		2e-05
3pgw_S	437	Crystal Structure Of Human U1 Snrnp Length = 437		3e-05
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		5e-05
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		5e-05
3cw1_K	216	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		5e-05
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		6e-05
2cqg_A	103	Solution Structure Of The Rna Binding Domain Of Tar		6e-05
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		6e-05
2i2y_A	150	Solution Structure Of The Rrm Of Srp20 Bound To The		7e-05
2i38_A	150	Solution Structure Of The Rrm Of Srp20 Length = 150		7e-05
2do4_A	100	Solution Structure Of The Rna Binding Domain Of Squ		8e-05
2d9p_A	103	Solution Structure Of Rna Binding Domain 4 In Polya		8e-05
2jvo_A	108	Segmental Isotope Labeling Of Npl3 Length = 108		9e-05
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		1e-04
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		1e-04
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		1e-04
2dnp_A	90	Solution Structure Of Rna Binding Domain 2 In Rna-B		1e-04
3bs9_A	87	X-Ray Structure Of Human Tia-1 Rrm2 Length = 87		1e-04
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		1e-04
1x4a_A	109	Solution Structure Of Rrm Domain In Splicing Factor		1e-04
1hl6_A	165	A Novel Mode Of Rbd-Protein Recognition In The Y14-		2e-04
2jwn_A	124	Solution Nmr Structure Of The Protease-Resistent Do		2e-04
2dgu_A	103	Solution Structure Of The Rna Binding Domain In Het		2e-04
1oo0_B	110	Crystal Structure Of The Drosophila Mago Nashi-Y14		3e-04
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		4e-04
2f9j_A	125	3.0 Angstrom Resolution Structure Of A Y22m Mutant		4e-04
2e5h_A	94	Solution Structure Of Rna Binding Domain In Zinc Fi		4e-04
2osq_A	74	Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein Length		4e-04
2cpe_A	113	Solution Structure Of The Rna Recognition Motif Of		4e-04
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		6e-04
1sxl_A	97	Resonance Assignments And Solution Structure Of The		6e-04
3lqv_A	115	Branch Recognition By Sf3b14 Length = 115		9e-04

>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35 Length = 158

Iteration: 1
 Score = 72.0 bits (175), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 36/76 (47%), Positives = 48/76 (63%)
Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           SL V N+     P+ LR  FE++G V DVY+P+D YT E RGFAFV+F D  +A +A   
Sbjct: 72  SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 131
Query: 123 MNGKRFAGREISVVLA 138
           M+G    GRE+ V +A
Sbjct: 132 MDGAVLDGRELRVQMA 147

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score = 71.6 bits (174), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 36/76 (47%), Positives = 48/76 (63%)
Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           SL V N+     P+ LR  FE++G V DVY+P+D YT E RGFAFV+F D  +A +A   
Sbjct: 49  SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 108
Query: 123 MNGKRFAGREISVVLA 138
           M+G    GRE+ V +A
Sbjct: 109 MDGAVLDGRELRVQMA 124

>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing Factor Length = 103

Iteration: 1
 Score = 65.9 bits (159), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 34/81 (41%), Positives = 51/81 (62%)
Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           +L V N+     P+ LR  FE++G V DVY+P++ +T  PRGFAFV+F D  +A +A+  
Sbjct: 15  TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74
Query: 123 MNGKRFAGREISVVLAAESRK 143
           M+G    GRE+ V +A   R+
Sbjct: 75  MDGAELDGRELRVQVARYGRR 95

>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 = 57.4 bits (137), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 41/74 (55%)
Query: 60  NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEA 119
           NH  + V ++  +   E+++A F  FG + D  + KD  TG+ +G+ FV F + ++A  A
Sbjct: 14  NHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENA 73
Query: 120 QHHMNGKRFAGREI 133
              M G+   GR+I
Sbjct: 74  IQQMGGQWLGGRQI 87

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 57.0 bits (136), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 29/82 (35%), Positives = 42/82 (51%)
Query: 60  NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEA 119
           + G L V  +  D   + L   F ++G + +V + KD  T   RGF FV F +  +A +A
Sbjct: 11  DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 70
Query: 120 QHHMNGKRFAGREISVVLAAES 141
              MNGK   GR+I V  A +S
Sbjct: 71  MMAMNGKSVDGRQIRVDQAGKS 92

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 55.5 bits (132), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 41/75 (54%)
Query: 59  QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAE 118
            NH  + V ++  +   E++++ F  FG + D  + KD  TG+ +G+ FV F +  +A  
Sbjct: 13  SNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAEN 72
Query: 119 AQHHMNGKRFAGREI 133
           A  HM G+   GR+I
Sbjct: 73  AIVHMGGQWLGGRQI 87

>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 = 55.5 bits (132), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 32/87 (36%), Positives = 48/87 (55%), Gaps = 1/87 (1%)
Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           S+ V NIP +   E+L+  F   G V    L  D  TG+P+G+ F ++ D   A  A  +
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 123 MNGKRFAGREISVVLAAESRKRPEEMR 149
           +NG+ F+GR + V  AA S K  EE++
Sbjct: 70  LNGREFSGRALRVDNAA-SEKNKEELK 95

>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 = 54.3 bits (129), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 33/90 (36%), Positives = 46/90 (51%), Gaps = 11/90 (12%)
Query: 57  KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYY-TGEPRGFAFVQFVDPYE 115
           K+Q    +LVRNIP      E+R  F  FG ++ V LPK    TG  RGF FV F+   +
Sbjct: 11  KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQD 70
Query: 116 AAEA------QHHMNGKR----FAGREISV 135
           A +A        H+ G+R    +A  E++V
Sbjct: 71  AKKAFNALCHSTHLYGRRLVLEWADSEVTV 100

>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain From Hypothetical Protein Bab23448 Length = 99

Iteration: 1
 Score = 53.9 bits (128), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 26/73 (35%), Positives = 42/73 (57%)
Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L VRN+      E+L   F  +G + +++ P D  T +P+GFAFV F+ P  A +A   +
Sbjct: 11  LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 124 NGKRFAGREISVV 136
           +G+ F GR + V+
Sbjct: 71  DGQVFQGRMLHVL 83

>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 = 1e-07,   Method: Compositional matrix adjust.
 Identities = 24/73 (32%), Positives = 40/73 (54%)
Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           +L+V  +P +   EE R+ F   G +    L +D  TG+  G+ FV ++DP +A +A + 
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 123 MNGKRFAGREISV 135
           +NG R   + I V
Sbjct: 64  LNGLRLQTKTIKV 76

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 52.0 bits (123), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 29/79 (36%), Positives = 43/79 (54%), Gaps = 2/79 (2%)
Query: 58  EQNH-GSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEA 116
           E +H G L +  +  +   + L+A F + G + +V L KD  T + RGFAF+ F +P +A
Sbjct: 3   EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADA 61
Query: 117 AEAQHHMNGKRFAGREISV 135
             A   MNGK   G+ I V
Sbjct: 62  KNAAKDMNGKSLHGKAIKV 80

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 51.2 bits (121), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 28/83 (33%), Positives = 42/83 (50%)
Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           +L+V  IP      +LR  FER+G +  V +  D  T + RG+ FV+F     A +A   
Sbjct: 44  NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103
Query: 123 MNGKRFAGREISVVLAAESRKRP 145
           +NG     + + V LAA   +RP
Sbjct: 104 LNGFNILNKRLKVALAASGHQRP 126

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 50.4 bits (119), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 28/61 (45%), Positives = 35/61 (57%)
Query: 78  LRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL 137
           L A F  FG + D+ +P DY T + RGFAFV+F    +AA A  +MN     GR I V L
Sbjct: 80  LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 139
Query: 138 A 138
           A
Sbjct: 140 A 140

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 50.1 bits (118), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 28/61 (45%), Positives = 35/61 (57%)
Query: 78  LRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL 137
           L A F  FG + D+ +P DY T + RGFAFV+F    +AA A  +MN     GR I V L
Sbjct: 24  LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 83
Query: 138 A 138
           A
Sbjct: 84  A 84

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 50.1 bits (118), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 30/75 (40%), Positives = 40/75 (53%)
Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L V  +  +   + L A F  FG + D+ +P DY T + RGFAFV+F    +AA A  +M
Sbjct: 15  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 124 NGKRFAGREISVVLA 138
           N     GR I V LA
Sbjct: 75  NESELFGRTIRVNLA 89

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 49.7 bits (117), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 28/61 (45%), Positives = 35/61 (57%)
Query: 78  LRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL 137
           L A F  FG + D+ +P DY T + RGFAFV+F    +AA A  +MN     GR I V L
Sbjct: 22  LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 81
Query: 138 A 138
           A
Sbjct: 82  A 82

>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33 Length = 79

Iteration: 1
 Score = 49.7 bits (117), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 28/61 (45%), Positives = 35/61 (57%)
Query: 78  LRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL 137
           L A F  FG + D+ +P DY T + RGFAFV+F    +AA A  +MN     GR I V L
Sbjct: 19  LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 78
Query: 138 A 138
           A
Sbjct: 79  A 79

>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 3 Subunit 4 Length = 103

Iteration: 1
 Score = 48.5 bits (114), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 23/69 (33%), Positives = 39/69 (56%)
Query: 57  KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEA 116
           +  ++ ++ V N+  D R  +L+  F  FG +  +YL KD  TG+ +GFAF+ F    +A
Sbjct: 11  RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDA 70
Query: 117 AEAQHHMNG 125
           A A   ++G
Sbjct: 71  ARAIAGVSG 79

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 48.1 bits (113), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 21/73 (28%), Positives = 39/73 (53%)
Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           +L+V  +P +   +E ++ F   G +    L +D  TG+  G+ FV + DP +A +A + 
Sbjct: 6   NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 123 MNGKRFAGREISV 135
           +NG +   + I V
Sbjct: 66  LNGLKLQTKTIKV 78

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 36/72 (50%)
Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L V ++  +   + LR  FE FG +  + L  D  TG  +G+ F+ F D   A +A   +
Sbjct: 29  LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 124 NGKRFAGREISV 135
           NG   AGR + V
Sbjct: 89  NGFELAGRPMKV 100

>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 = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           S+ V N+      EEL A F   G V  V +  D ++G P+GFA+++F D  E+      
Sbjct: 8   SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDK-ESVRTSLA 66
Query: 123 MNGKRFAGREISVV 136
           ++   F GR+I V+
Sbjct: 67  LDESLFRGRQIKVI 80

>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm Length = 96

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/79 (32%), Positives = 41/79 (51%), Gaps = 1/79 (1%)
Query: 58  EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAA 117
           E +  S+ V N+      EEL A F   G V  V +  D ++G P+GFA+++F D  E+ 
Sbjct: 2   EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDK-ESV 60
Query: 118 EAQHHMNGKRFAGREISVV 136
                ++   F GR+I V+
Sbjct: 61  RTSLALDESLFRGRQIKVI 79

>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In Daz- Associated Protein 1 Length = 99

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/68 (36%), Positives = 35/68 (51%), Gaps = 4/68 (5%)
Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQ--- 120
           + V  IP +C   ELR  F++FGVV +V +  D     PRGF F+ F D     +A    
Sbjct: 13  IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMH 72
Query: 121 -HHMNGKR 127
            H + GK+
Sbjct: 73  FHDIMGKK 80

>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp Length = 437

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 21/73 (28%), Positives = 40/73 (54%)
Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           +L V  +  D    +LR  FE +G ++ +++     +G+PRG+AF+++    +   A  H
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 123 MNGKRFAGREISV 135
            +GK+  GR + V
Sbjct: 164 ADGKKIDGRRVLV 176

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 45.1 bits (105), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 23/79 (29%), Positives = 41/79 (51%)
Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           +L+V  +P +   +E ++ F   G +    L +D  TG+  G+ FV + DP +A +A + 
Sbjct: 6   NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 123 MNGKRFAGREISVVLAAES 141
           +NG +   + I V  A  S
Sbjct: 66  LNGLKLQTKTIKVSYARPS 84

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 45.1 bits (105), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 27/80 (33%), Positives = 38/80 (47%)
Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
            L V  + L     +LR  F ++G + DV +  D  +   RGFAFV F +  +A EA+  
Sbjct: 48  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 107
Query: 123 MNGKRFAGREISVVLAAESR 142
            NG    GR I V  +   R
Sbjct: 108 ANGMELDGRRIRVDFSITKR 127

>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 216

Iteration: 1
 Score = 45.1 bits (105), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 21/73 (28%), Positives = 40/73 (54%)
Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           +L V  +  D    +LR  FE +G ++ +++     +G+PRG+AF+++    +   A  H
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 123 MNGKRFAGREISV 135
            +GK+  GR + V
Sbjct: 164 ADGKKIDGRRVLV 176

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 44.7 bits (104), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 25/72 (34%), Positives = 37/72 (51%)
Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L V ++  +   + LR  FE FG + ++ L KD  TG  +G+ F+ F D   A  A   +
Sbjct: 8   LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 124 NGKRFAGREISV 135
           NG   AGR + V
Sbjct: 68  NGFELAGRPMRV 79

>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna- Binding Protein-43 Length = 103

Iteration: 1
 Score = 44.7 bits (104), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 36/74 (48%), Gaps = 4/74 (5%)
Query: 59  QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEA-- 116
           Q    L+V  +P     ++L+  F  FG V  V + KD  TG  +GF FV+F + YE   
Sbjct: 13  QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTE-YETQV 71
Query: 117 -AEAQHHMNGKRFA 129
              +Q HM   R+ 
Sbjct: 72  KVMSQRHMIDGRWC 85

>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 = 44.7 bits (104), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 27/82 (32%), Positives = 39/82 (47%)
Query: 61  HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQ 120
           +  L V  + L     +LR  F ++G + DV +  D  +   RGFAFV F +  +A EA+
Sbjct: 15  NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74
Query: 121 HHMNGKRFAGREISVVLAAESR 142
              NG    GR I V  +   R
Sbjct: 75  ERANGMELDGRRIRVDFSITKR 96

>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna Cauc Length = 150

Iteration: 1
 Score = 44.7 bits (104), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 26/82 (31%), Positives = 42/82 (51%), Gaps = 16/82 (19%)
Query: 68  NIPLDCR-----------PEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEA 116
           + PLDC+             EL   F  +G +R V++ ++     P GFAFV+F DP +A
Sbjct: 69  SCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDA 123
Query: 117 AEAQHHMNGKRFAGREISVVLA 138
           A+A   ++G+   G  + V L+
Sbjct: 124 ADAVRELDGRTLCGCRVRVELS 145

>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20 Length = 150

Iteration: 1
 Score = 44.3 bits (103), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 26/82 (31%), Positives = 42/82 (51%), Gaps = 16/82 (19%)
Query: 68  NIPLDCR-----------PEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEA 116
           + PLDC+             EL   F  +G +R V++ ++     P GFAFV+F DP +A
Sbjct: 69  SCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDA 123
Query: 117 AEAQHHMNGKRFAGREISVVLA 138
           A+A   ++G+   G  + V L+
Sbjct: 124 ADAVRDLDGRTLCGCRVRVELS 145

>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous Cell Carcinoma Antigen Recognized By T Cells 3 Length = 100

Iteration: 1
 Score = 44.3 bits (103), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 21/75 (28%), Positives = 39/75 (52%), Gaps = 1/75 (1%)
Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L +  +P  C  EEL    +  G V+D+ L  +   G+P+G A+V++ +  +A++A   M
Sbjct: 20  LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKM 78
Query: 124 NGKRFAGREISVVLA 138
           +G       I V ++
Sbjct: 79  DGMTIKENIIKVAIS 93

>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In Polyadenylation Binding Protein 3 Length = 103

Iteration: 1
 Score = 44.3 bits (103), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 26/76 (34%), Positives = 37/76 (48%), Gaps = 2/76 (2%)
Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           +L V+N+      E LR  F  FG +    +  +   G  +GF FV F  P EA +A   
Sbjct: 17  NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTE 74
Query: 123 MNGKRFAGREISVVLA 138
           MNG+  A + + V LA
Sbjct: 75  MNGRIVATKPLYVALA 90

>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3 Length = 108

Iteration: 1
 Score = 44.3 bits (103), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 30/87 (34%), Positives = 45/87 (51%), Gaps = 8/87 (9%)
Query: 58  EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAA 117
           E ++  L VR  PLD +  EL   F  FG +++V +          GFAFV+F +   AA
Sbjct: 28  ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAA 79
Query: 118 EAQHHMNGKRFAGREISVVLAAESRKR 144
           +A   ++GK FA + + VV +    KR
Sbjct: 80  KAIEEVHGKSFANQPLEVVYSKLPAKR 106

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 26/73 (35%), Positives = 36/73 (49%)
Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
            L V  + L     +LR  F ++G + DV +  D  +   RGFAFV F +  +A EA+  
Sbjct: 17  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76
Query: 123 MNGKRFAGREISV 135
            NG    GR I V
Sbjct: 77  ANGMELDGRRIRV 89

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 27/82 (32%), Positives = 39/82 (47%)
Query: 61  HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQ 120
           +  L V  + L     +LR  F ++G + DV +  D  +   RGFAFV F +  +A EA+
Sbjct: 12  NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 71
Query: 121 HHMNGKRFAGREISVVLAAESR 142
              NG    GR I V  +   R
Sbjct: 72  ERANGMELDGRRIRVDFSITKR 93

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 23/72 (31%), Positives = 35/72 (48%), Gaps = 4/72 (5%)
Query: 58  EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAA 117
           +   G + V  I  D RP+E    F ++G + D  L  D  TG+ RGF FV     Y++A
Sbjct: 84  QDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFV----TYDSA 139
Query: 118 EAQHHMNGKRFA 129
           +A   +   +F 
Sbjct: 140 DAVDRVCQNKFI 151

>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding Protein 14 Length = 90

Iteration: 1
 Score = 43.5 bits (101), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 28/85 (32%), Positives = 42/85 (49%), Gaps = 8/85 (9%)
Query: 60  NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEA 119
           N   + V N+   C  +ELR+ FER G V +  + KDY        AFV      +A  A
Sbjct: 8   NTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKDY--------AFVHMEKEADAKAA 59
Query: 120 QHHMNGKRFAGREISVVLAAESRKR 144
              +NGK   G+ I+V L+ + +K+
Sbjct: 60  IAQLNGKEVKGKRINVELSTKGQKK 84

>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2 Length = 87

Iteration: 1
 Score = 43.5 bits (101), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 18/49 (36%), Positives = 28/49 (57%)
Query: 85  FGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREI 133
           FG + D  + KD  TG+ +G+ FV F + ++A  A   M G+   GR+I
Sbjct: 30  FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 78

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 43.5 bits (101), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/71 (32%), Positives = 33/71 (46%), Gaps = 4/71 (5%)
Query: 62  GSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQ- 120
           G L V  +      E LR+ F ++G V D  + KD  T + RGF FV+F DP        
Sbjct: 17  GKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLA 76
Query: 121 ---HHMNGKRF 128
              H ++G+  
Sbjct: 77  SRPHTLDGRNI 87

>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2 Length = 109

Iteration: 1
 Score = 43.5 bits (101), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 26/77 (33%), Positives = 43/77 (55%), Gaps = 3/77 (3%)
Query: 59  QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAE 118
            N   + V N+P D R +++   F ++G +RD+ L K+   G P  FAFV+F DP +A +
Sbjct: 20  NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL-KNRRGGPP--FAFVEFEDPRDAED 76
Query: 119 AQHHMNGKRFAGREISV 135
           A +  +G  + G  + V
Sbjct: 77  AVYGRDGYDYDGYRLRV 93

>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago Complex Length = 165

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/72 (27%), Positives = 40/72 (55%)
Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L V +I  + + +E++  F  +G +++++L  D  TG  +G+A V++    +A  A+  +
Sbjct: 75  LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 124 NGKRFAGREISV 135
           NG    G+ I V
Sbjct: 135 NGAEIMGQTIQV 146

>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of Xenopus Laevis Epabp2 Length = 124

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/80 (27%), Positives = 42/80 (52%), Gaps = 1/80 (1%)
Query: 57  KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEA 116
           KE +  S+ V N+      ++L A F   G +  + +  D ++G P+G+A+++F +   +
Sbjct: 32  KEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAE-RNS 90
Query: 117 AEAQHHMNGKRFAGREISVV 136
            +A   M+   F GR I V+
Sbjct: 91  VDAAVAMDETVFRGRTIKVL 110

>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein Q Length = 103

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 31/90 (34%), Positives = 39/90 (43%), Gaps = 9/90 (10%)
Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L VRN+      E L   F +FG +  V   KDY        AF+ F +   A +A   M
Sbjct: 14  LFVRNLANTVTEEILEKAFSQFGKLERVKKLKDY--------AFIHFDERDGAVKAMEEM 65
Query: 124 NGKRFAGREISVVLAA-ESRKRPEEMRQRH 152
           NGK   G  I +V A    +KR E   QR 
Sbjct: 66  NGKDLEGENIEIVFAKPPDQKRKERKAQRQ 95

>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex Length = 110

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 20/72 (27%), Positives = 40/72 (55%)
Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L V +I  + + +E++  F  +G +++++L  D  TG  +G+A V++    +A  A+  +
Sbjct: 29  LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 124 NGKRFAGREISV 135
           NG    G+ I V
Sbjct: 89  NGAEIMGQTIQV 100

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 42.0 bits (97), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 22/75 (29%), Positives = 35/75 (46%)
Query: 61  HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQ 120
           + +L+V  +P D    EL A F   G +    + +DY TG   G+AFV F    ++  A 
Sbjct: 3   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62
Query: 121 HHMNGKRFAGREISV 135
             +NG     + + V
Sbjct: 63  KVLNGITVRNKRLKV 77

>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 = 42.0 bits (97), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 22/73 (30%), Positives = 39/73 (53%), Gaps = 3/73 (4%)
Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L++RN+P     EE+   F ++G +R + +     T E RG A+V + D ++A  A  H+
Sbjct: 21  LMIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNACDHL 77
Query: 124 NGKRFAGREISVV 136
           +G     R + V+
Sbjct: 78  SGFNVCNRYLVVL 90

>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 = 42.0 bits (97), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 23/76 (30%), Positives = 37/76 (48%)
Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           ++ V N+P      +L   F ++G V  V + KD  T + +G AF+ F+D   A      
Sbjct: 18  TVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRA 77
Query: 123 MNGKRFAGREISVVLA 138
           +N K+  GR I   +A
Sbjct: 78  INNKQLFGRVIKASIA 93

>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein Length = 74

Iteration: 1
 Score = 42.0 bits (97), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 28/81 (34%), Positives = 43/81 (53%), Gaps = 8/81 (9%)
Query: 58  EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAA 117
           E ++  L VR  PLD +  EL   F  FG +++V +          GFAFV+F +   AA
Sbjct: 1   ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAA 52
Query: 118 EAQHHMNGKRFAGREISVVLA 138
           +A   ++GK FA + + VV +
Sbjct: 53  KAIEEVHGKSFANQPLEVVYS 73

>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing Sarcoma(Ews) Protein Length = 113

Iteration: 1
 Score = 42.0 bits (97), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 29/98 (29%), Positives = 50/98 (51%), Gaps = 15/98 (15%)
Query: 58  EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRD----------VYLPKDYYTGEPRGFAF 107
           + ++ ++ V+ +      ++L   F++ GVV+           +YL K+  TG+P+G A 
Sbjct: 12  DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE--TGKPKGDAT 69
Query: 108 VQFVDPYEAAEAQHHMNGKRFAGREISVVLAAESRKRP 145
           V + DP  A  A    +GK F G ++ V LA   RK+P
Sbjct: 70  VSYEDPPTAKAAVEWFDGKDFQGSKLKVSLA---RKKP 104

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 41.6 bits (96), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 22/75 (29%), Positives = 35/75 (46%)
Query: 61  HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQ 120
           + +L+V  +P D    EL A F   G +    + +DY TG   G+AFV F    ++  A 
Sbjct: 14  NTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAI 73
Query: 121 HHMNGKRFAGREISV 135
             +NG     + + V
Sbjct: 74  KVLNGITVRNKRLKV 88

>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 = 41.6 bits (96), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 21/62 (33%), Positives = 33/62 (53%)
Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           +L V N+P     ++L   F ++G +    + +D  TG PRG AFV++    EA EA   
Sbjct: 15  NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 74
Query: 123 MN 124
           +N
Sbjct: 75  LN 76

>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14 Length = 115

Iteration: 1
 Score = 40.8 bits (94), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 24/94 (25%), Positives = 48/94 (51%), Gaps = 11/94 (11%)
Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L +RN+P     EE+   F ++G +R + +     T E RG A+V + D ++A  A  H+
Sbjct: 11  LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNAVDHL 67
Query: 124 NGKRFAGREISVVL--------AAESRKRPEEMR 149
           +G   + R + V+           +++K+ E+++
Sbjct: 68  SGFNVSNRYLVVLYYNANRAFQKMDTKKKEEQLK 101

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	299
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.89
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.88
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.88
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.87
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.87
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.86
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.86
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.86
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.86
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.86
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.86
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.86
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.86
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.86
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.86
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.85
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.85
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.85
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.85
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.85
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.85
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.85
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.85
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.85
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.85
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.85
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.85
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.85
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.84
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.84
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.84
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.84
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.84
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.84
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.84
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.84
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.84
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.84
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.84
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.84
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.84
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.84
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.84
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.83
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.83
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.83
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.83
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.83
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.83
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.83
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.83
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.83
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.83
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.83
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.83
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.83
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.82
2div_A	99	TRNA selenocysteine associated protein; structural	99.82
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.82
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.82
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.82
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.82
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.82
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.82
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.82
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.82
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.82
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.82
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.81
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.81
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.81
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.81
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.81
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.81
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.81
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.81
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.81
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.81
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.81
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.81
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.81
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.81
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.81
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.81
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.81
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.8
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.8
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.8
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.8
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.8
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.8
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.8
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.8
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.8
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.8
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.79
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.79
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.79
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.79
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.79
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.79
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.79
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.79
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.79
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.79
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.79
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.79
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.79
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.79
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.79
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.78
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.78
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.78
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.78
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.78
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.78
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.78
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.78
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.78
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.77
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.77
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.77
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.77
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.77
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.77
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.77
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.76
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.76
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.76
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.76
1x5p_A	97	Negative elongation factor E; structure genomics,	99.76
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.76
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.76
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.76
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.76
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.76
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.76
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.76
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.75
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.75
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.61
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.75
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.75
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.74
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.74
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.73
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.73
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.73
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.73
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.73
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.72
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.72
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.72
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.72
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.72
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.72
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.71
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.71
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.71
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.7
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.7
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.7
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.7
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.7
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.69
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.69
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.69
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.69
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.68
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.68
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.68
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.67
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.67
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.67
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.66
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.66
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.65
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.64
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.64
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.64
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.64
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.64
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.63
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.63
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.62
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.62
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.6
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.59
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.58
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.58
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.57
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.57
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.57
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.57
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.57
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.56
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.54
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.54
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.53
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.53
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.52
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.49
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.49
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.42
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.36
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.3
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.09
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	99.0
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.82
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	98.27
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.01
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.92
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.79
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.78
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.52
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	97.41
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	97.32
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	96.57
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	96.06
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	95.92
4eyt_A	129	Telomerase associated protein P65; RNA, LA protein	93.26
2g0c_A	76	ATP-dependent RNA helicase DBPA; RNA recognition m	93.21
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	92.8
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	90.91

>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=99.89  E-value=4.4e-22  Score=190.62  Aligned_cols=85  Identities=25%  Similarity=0.513  Sum_probs=80.3

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      +.++|||+|||+.||+++|++||.+||.|+.|.|+.++.+++++|||||+|.+.++|++||+.|||++|+|+.|.|+|+.
T Consensus       101 ~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a~  180 (437)
T 3pgw_S          101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  180 (437)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            45799999999999999999999999999999999998899999999999999999999999999999999999999998


Q ss_pred             cCCCC
Q 043443          140 ESRKR  144 (299)
Q Consensus       140 ~~~~~  144 (299)
                      .....
T Consensus       181 ~~~~~  185 (437)
T 3pgw_S          181 GRTVK  185 (437)
T ss_pred             CCCCC
Confidence            75543

>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=99.88  E-value=1.7e-22  Score=154.90  Aligned_cols=81  Identities=30%  Similarity=0.509  Sum_probs=78.0

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      ..++|||+|||.++|+++|+++|++||+|..|.|+.++.++.++|||||+|.+.++|++||+.|||..|+|+.|.|+||+
T Consensus        18 ~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~Ak   97 (99)
T 4fxv_A           18 QGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR   97 (99)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            35799999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             c
Q 043443          140 E  140 (299)
Q Consensus       140 ~  140 (299)
                      +
T Consensus        98 P   98 (99)
T 4fxv_A           98 P   98 (99)
T ss_dssp             B
T ss_pred             C
Confidence            5

>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=99.88  E-value=1.2e-21  Score=152.23  Aligned_cols=77  Identities=18%  Similarity=0.283  Sum_probs=72.2

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCC-----e
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAG-----R  131 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~G-----r  131 (299)
                      .....++|||+|||+++++++|+++|.+||+|+.|.|+.+       |||||+|.+.++|++||+.||+++|+|     +
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~   83 (108)
T 1x4c_A           11 SRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETA   83 (108)
T ss_dssp             CCSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcce
Confidence            3456789999999999999999999999999999999875       899999999999999999999999999     9


Q ss_pred             eEEEEEccc
Q 043443          132 EISVVLAAE  140 (299)
Q Consensus       132 ~i~V~~a~~  140 (299)
                      .|.|+++++
T Consensus        84 ~i~V~~a~~   92 (108)
T 1x4c_A           84 YIRVKVDGP   92 (108)
T ss_dssp             EEEEEESSC
T ss_pred             EEEEEeCCC
Confidence            999999975

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.87  E-value=7.7e-22  Score=148.96  Aligned_cols=84  Identities=27%  Similarity=0.452  Sum_probs=79.2

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEE
Q 043443           56 RKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV  135 (299)
Q Consensus        56 ~~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V  135 (299)
                      ....+.++|||+|||..+++++|+++|.+||.|..|.|+.++.++.+++||||+|.+.++|++||+.||+..|+|+.|.|
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   90 (94)
T 2e5h_A           11 GLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKA   90 (94)
T ss_dssp             SCCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEE
Confidence            34456789999999999999999999999999999999999888999999999999999999999999999999999999


Q ss_pred             EEcc
Q 043443          136 VLAA  139 (299)
Q Consensus       136 ~~a~  139 (299)
                      +|++
T Consensus        91 ~~ak   94 (94)
T 2e5h_A           91 SIAI   94 (94)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9985

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.87  E-value=2.3e-21  Score=152.31  Aligned_cols=88  Identities=30%  Similarity=0.449  Sum_probs=82.0

Q ss_pred             CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCee
Q 043443           53 YGRRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGRE  132 (299)
Q Consensus        53 ~~~~~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~  132 (299)
                      .....+.+.++|||+|||+.+++++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|++||+.||+ +|+|+.
T Consensus         9 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~   87 (116)
T 2cqd_A            9 HGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRK   87 (116)
T ss_dssp             CCCCCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEE
T ss_pred             CCCcCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEE
Confidence            3455667789999999999999999999999999999999999998999999999999999999999999998 899999


Q ss_pred             EEEEEcccC
Q 043443          133 ISVVLAAES  141 (299)
Q Consensus       133 i~V~~a~~~  141 (299)
                      |.|+++...
T Consensus        88 l~V~~a~~~   96 (116)
T 2cqd_A           88 ANVNLAYLG   96 (116)
T ss_dssp             CEEEESTTT
T ss_pred             EEEEEcccC
Confidence            999999764

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.86  E-value=3.7e-21  Score=150.73  Aligned_cols=89  Identities=28%  Similarity=0.571  Sum_probs=82.7

Q ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEE
Q 043443           55 RRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREIS  134 (299)
Q Consensus        55 ~~~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~  134 (299)
                      .....+.++|||+|||..+++++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|++||+.||+..|+|+.|.
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            34556788999999999999999999999999999999999988999999999999999999999999999999999999


Q ss_pred             EEEcccCCC
Q 043443          135 VVLAAESRK  143 (299)
Q Consensus       135 V~~a~~~~~  143 (299)
                      |.|++.+..
T Consensus        89 V~~a~~~~~   97 (115)
T 2dgo_A           89 TNWATRKPP   97 (115)
T ss_dssp             EEESSCCCC
T ss_pred             EEEccCCCC
Confidence            999987544

>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=99.86  E-value=4.3e-22  Score=156.64  Aligned_cols=79  Identities=20%  Similarity=0.330  Sum_probs=65.7

Q ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCee-
Q 043443           54 GRRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGRE-  132 (299)
Q Consensus        54 ~~~~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~-  132 (299)
                      ++......++|||+|||+++++++|+++|.+||+|+.|.|+.+       |||||+|++.++|++||+.||+++|+|+. 
T Consensus         9 gpp~~r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~   81 (115)
T 3beg_B            9 GPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEG   81 (115)
T ss_dssp             --------CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTS
T ss_pred             CCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEe
Confidence            3334456789999999999999999999999999999999865       89999999999999999999999999998 


Q ss_pred             ----EEEEEcc
Q 043443          133 ----ISVVLAA  139 (299)
Q Consensus       133 ----i~V~~a~  139 (299)
                          |.|..+.
T Consensus        82 ~~~~i~v~~~~   92 (115)
T 3beg_B           82 ETAYIRVKVDG   92 (115)
T ss_dssp             CCCBCEEEECC
T ss_pred             eeEEEEeccCC
Confidence                5555543

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=1.5e-21  Score=150.06  Aligned_cols=86  Identities=30%  Similarity=0.508  Sum_probs=81.3

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      ...+.++|||+|||..+++++|+++|.+||+|..|.|+.++.++.++|||||+|.+.++|++||+.||+..|+|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   90 (103)
T 2cq0_A           11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVE   90 (103)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            45667999999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EcccCC
Q 043443          137 LAAESR  142 (299)
Q Consensus       137 ~a~~~~  142 (299)
                      +++++.
T Consensus        91 ~a~~~~   96 (103)
T 2cq0_A           91 WAKPST   96 (103)
T ss_dssp             ESSCCC
T ss_pred             ECCCCC
Confidence            998654

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=2.9e-21  Score=148.88  Aligned_cols=88  Identities=25%  Similarity=0.362  Sum_probs=82.3

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEE
Q 043443           56 RKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV  135 (299)
Q Consensus        56 ~~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V  135 (299)
                      ......++|||+|||..+++++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|++||+.||+..|+|+.|.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   89 (105)
T 1x5u_A           10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRV   89 (105)
T ss_dssp             CCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            34566789999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             EEcccCCC
Q 043443          136 VLAAESRK  143 (299)
Q Consensus       136 ~~a~~~~~  143 (299)
                      .++.....
T Consensus        90 ~~a~~~~~   97 (105)
T 1x5u_A           90 NKASAHNK   97 (105)
T ss_dssp             EETTTTSC
T ss_pred             EECCCCCc
Confidence            99987544

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.86  E-value=2e-21  Score=151.83  Aligned_cols=84  Identities=18%  Similarity=0.177  Sum_probs=79.5

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      .+..+|||+||++.+++++|+++|++||.|..|.|+.++.|+.++|||||+|.+.++|++||+.|||+.|+|+.|.|+++
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a   83 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLD   83 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            35679999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCC
Q 043443          139 AESR  142 (299)
Q Consensus       139 ~~~~  142 (299)
                      ....
T Consensus        84 ~~~~   87 (110)
T 3s8s_A           84 IKGQ   87 (110)
T ss_dssp             STTH
T ss_pred             CCCc
Confidence            7543

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=2.8e-21  Score=146.01  Aligned_cols=85  Identities=31%  Similarity=0.445  Sum_probs=79.9

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEE
Q 043443           56 RKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV  135 (299)
Q Consensus        56 ~~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V  135 (299)
                      ....+.++|||+|||..+++++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|++||+.||+..|+|+.|.|
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   89 (95)
T 2cqc_A           10 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   89 (95)
T ss_dssp             CSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            34556789999999999999999999999999999999999888999999999999999999999999999999999999


Q ss_pred             EEccc
Q 043443          136 VLAAE  140 (299)
Q Consensus       136 ~~a~~  140 (299)
                      ++++.
T Consensus        90 ~~a~~   94 (95)
T 2cqc_A           90 SGPSS   94 (95)
T ss_dssp             ECCSC
T ss_pred             EecCC
Confidence            99864

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.86  E-value=5.5e-21  Score=146.09  Aligned_cols=88  Identities=24%  Similarity=0.483  Sum_probs=81.4

Q ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeE
Q 043443           54 GRRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREI  133 (299)
Q Consensus        54 ~~~~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i  133 (299)
                      ......+.++|||+|||..+++++|+++|.+||.|..|.|+.+. ++.++|||||+|.+.++|++||+.||+..|+|+.|
T Consensus        10 ~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   88 (100)
T 2do4_A           10 RYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENII   88 (100)
T ss_dssp             CCSSCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEE
T ss_pred             CcccCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            34455678899999999999999999999999999999999987 88999999999999999999999999999999999


Q ss_pred             EEEEcccCC
Q 043443          134 SVVLAAESR  142 (299)
Q Consensus       134 ~V~~a~~~~  142 (299)
                      .|.+++++.
T Consensus        89 ~v~~a~~~~   97 (100)
T 2do4_A           89 KVAISNSGP   97 (100)
T ss_dssp             EEEECCCCS
T ss_pred             EEEECCCCC
Confidence            999998754

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A

Probab=99.86  E-value=3.9e-21  Score=150.72  Aligned_cols=87  Identities=23%  Similarity=0.352  Sum_probs=81.2

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      ...+.++|||+|||.++++++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|++||+.||+..|+|+.|.|+
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            34567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EcccCCC
Q 043443          137 LAAESRK  143 (299)
Q Consensus       137 ~a~~~~~  143 (299)
                      |++++..
T Consensus       101 ~a~~~~~  107 (115)
T 2cpz_A          101 LKRSKND  107 (115)
T ss_dssp             CCCCSCC
T ss_pred             EcCCCCc
Confidence            9986543

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.86  E-value=8.7e-21  Score=148.31  Aligned_cols=85  Identities=24%  Similarity=0.330  Sum_probs=78.8

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      .....++|||+|||..+++++|+++|.+||.|+.|.|+.++ ++.+++||||+|.+.++|++||+.||+..|+|+.|.|+
T Consensus        11 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   89 (114)
T 2do0_A           11 AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVK   89 (114)
T ss_dssp             CCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEE
Confidence            44567899999999999999999999999999999999887 58899999999999999999999999999999999999


Q ss_pred             EcccCC
Q 043443          137 LAAESR  142 (299)
Q Consensus       137 ~a~~~~  142 (299)
                      ++....
T Consensus        90 ~a~~~~   95 (114)
T 2do0_A           90 MDERAL   95 (114)
T ss_dssp             ECSCCC
T ss_pred             EcccCC
Confidence            997543

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.86  E-value=2.4e-21  Score=148.91  Aligned_cols=87  Identities=39%  Similarity=0.663  Sum_probs=81.7

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEE
Q 043443           56 RKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV  135 (299)
Q Consensus        56 ~~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V  135 (299)
                      ....+.++|||+|||..+++++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|++||+.||+..|+|+.|.|
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   87 (103)
T 2dnm_A            8 PDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRV   87 (103)
T ss_dssp             SCCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEE
T ss_pred             CCCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEE
Confidence            34566799999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             EEcccCC
Q 043443          136 VLAAESR  142 (299)
Q Consensus       136 ~~a~~~~  142 (299)
                      .+++...
T Consensus        88 ~~a~~~~   94 (103)
T 2dnm_A           88 QVARYGR   94 (103)
T ss_dssp             EECSSCC
T ss_pred             EECCcCC
Confidence            9998644

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=3.5e-21  Score=147.58  Aligned_cols=86  Identities=36%  Similarity=0.501  Sum_probs=80.9

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      ..+.++|||+|||..+++++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|++||+.||+..|+|+.|.|.+
T Consensus         9 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   88 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEe
Confidence            34678999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             cccCCC
Q 043443          138 AAESRK  143 (299)
Q Consensus       138 a~~~~~  143 (299)
                      +++...
T Consensus        89 a~~~~~   94 (102)
T 2cqb_A           89 AKPMRI   94 (102)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            987543

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.85  E-value=1.6e-21  Score=148.45  Aligned_cols=86  Identities=23%  Similarity=0.419  Sum_probs=79.4

Q ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCC--EeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCc----ee
Q 043443           55 RRKEQNHGSLLVRNIPLDCRPEELRAPFERFGV--VRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGK----RF  128 (299)
Q Consensus        55 ~~~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~--I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~----~l  128 (299)
                      ...+....+|||+|||+.+|+++|+++|++||.  |..|.|+.|+.++.++|||||+|.+.++|++||+.||+.    .|
T Consensus         3 ~~~~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i   82 (95)
T 2lkz_A            3 HHHHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKI   82 (95)
T ss_dssp             CCSSCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEE
T ss_pred             cccCCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceE
Confidence            445677899999999999999999999999995  678999999999999999999999999999999999997    58


Q ss_pred             CCeeEEEEEccc
Q 043443          129 AGREISVVLAAE  140 (299)
Q Consensus       129 ~Gr~i~V~~a~~  140 (299)
                      +|+.|.|+||+.
T Consensus        83 ~Gr~i~V~~Aks   94 (95)
T 2lkz_A           83 DGKTIGVDFAKS   94 (95)
T ss_dssp             TTEEEEEEECCC
T ss_pred             CCEEEEEEEccC
Confidence            999999999974

>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=99.85  E-value=7.3e-21  Score=147.93  Aligned_cols=89  Identities=24%  Similarity=0.381  Sum_probs=82.5

Q ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhC------Ccee
Q 043443           55 RRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMN------GKRF  128 (299)
Q Consensus        55 ~~~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~ln------g~~l  128 (299)
                      .....+.++|||+|||+.+++++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|++||+.||      +..|
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            3455668899999999999999999999999999999999999899999999999999999999999999      9999


Q ss_pred             CCeeEEEEEcccCCC
Q 043443          129 AGREISVVLAAESRK  143 (299)
Q Consensus       129 ~Gr~i~V~~a~~~~~  143 (299)
                      +|+.|.|.++.++..
T Consensus        89 ~g~~l~v~~a~~~~~  103 (111)
T 1x4h_A           89 DGRQLKVDLAVTRDE  103 (111)
T ss_dssp             SSCEEEEECCCCCCC
T ss_pred             cCEEEEEEECCCCcc
Confidence            999999999986543

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=3.2e-21  Score=147.79  Aligned_cols=85  Identities=34%  Similarity=0.560  Sum_probs=80.4

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      ..+.++|||+|||..+++++|+++|.+||+|..|.|+.++.++.++|||||+|.+.++|+.||+.||+..|+|+.|.|.+
T Consensus         9 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   88 (102)
T 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQ   88 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            44678999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             cccCC
Q 043443          138 AAESR  142 (299)
Q Consensus       138 a~~~~  142 (299)
                      ++...
T Consensus        89 a~~~~   93 (102)
T 1x5s_A           89 AGKSS   93 (102)
T ss_dssp             EECCC
T ss_pred             CCCCC
Confidence            98654

>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=99.85  E-value=1.4e-20  Score=144.50  Aligned_cols=87  Identities=30%  Similarity=0.460  Sum_probs=79.1

Q ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEE
Q 043443           55 RRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREIS  134 (299)
Q Consensus        55 ~~~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~  134 (299)
                      .....+.++|||+|||..+++++|+++|.+||.|..|.|+.+..  .+++||||+|.+.++|++||+.||+..|+|+.|.
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            34556789999999999999999999999999999999998753  3789999999999999999999999999999999


Q ss_pred             EEEcccCCC
Q 043443          135 VVLAAESRK  143 (299)
Q Consensus       135 V~~a~~~~~  143 (299)
                      |.++..+..
T Consensus        87 v~~a~~~~~   95 (103)
T 2cq3_A           87 VNNATARVM   95 (103)
T ss_dssp             EEECCSSCC
T ss_pred             EEEcccCCC
Confidence            999987544

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.85  E-value=9.9e-22  Score=148.22  Aligned_cols=84  Identities=23%  Similarity=0.425  Sum_probs=77.4

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCC-CEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhC-CceeCCeeEEEEEc
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFERFG-VVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMN-GKRFAGREISVVLA  138 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~~~G-~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~ln-g~~l~Gr~i~V~~a  138 (299)
                      +.+|||+|||..+|+++|+++|++|| +|..|.|+.++.++.++|||||+|.+.++|++||+.|+ +..|+|+.|.|+++
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a   80 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEc
Confidence            36899999999999999999999999 89999999999999999999999999999999999874 56799999999999


Q ss_pred             ccCCCC
Q 043443          139 AESRKR  144 (299)
Q Consensus       139 ~~~~~~  144 (299)
                      .++...
T Consensus        81 ~~~~~~   86 (91)
T 2lxi_A           81 DPKPKI   86 (91)
T ss_dssp             CSCCCC
T ss_pred             CCCCCC
Confidence            876544

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.85  E-value=7.9e-21  Score=144.83  Aligned_cols=86  Identities=31%  Similarity=0.587  Sum_probs=80.9

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      ..+.++|||+|||..+++++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|+.||+.||+..|+|+.|.|.+
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            34678999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             cccCCC
Q 043443          138 AAESRK  143 (299)
Q Consensus       138 a~~~~~  143 (299)
                      ++.+..
T Consensus        85 a~~~~~   90 (99)
T 1whw_A           85 STIKKE   90 (99)
T ss_dssp             CCCCST
T ss_pred             cCCCcc
Confidence            987543

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.85  E-value=8.8e-21  Score=146.52  Aligned_cols=89  Identities=34%  Similarity=0.571  Sum_probs=82.4

Q ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccC-CCCCCCccEEEEEEcCHHHHHHHHHhh-CCceeCCee
Q 043443           55 RRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKD-YYTGEPRGFAFVQFVDPYEAAEAQHHM-NGKRFAGRE  132 (299)
Q Consensus        55 ~~~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d-~~~g~~~g~afVeF~~~~~A~~Al~~l-ng~~l~Gr~  132 (299)
                      .......++|||+|||..+++++|+++|.+||.|..|.|+.+ +.++.++|||||+|.+.++|++||+.| |+..|+|+.
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~   88 (107)
T 2cph_A            9 VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRR   88 (107)
T ss_dssp             SCCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCB
T ss_pred             cccCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCE
Confidence            345567899999999999999999999999999999999998 788999999999999999999999999 999999999


Q ss_pred             EEEEEcccCCC
Q 043443          133 ISVVLAAESRK  143 (299)
Q Consensus       133 i~V~~a~~~~~  143 (299)
                      |.|.|++....
T Consensus        89 l~v~~a~~~~~   99 (107)
T 2cph_A           89 LVLEWADSEVT   99 (107)
T ss_dssp             CEEEECCCCCC
T ss_pred             EEEEeCCCCCC
Confidence            99999987543

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.85  E-value=5.3e-21  Score=146.95  Aligned_cols=86  Identities=30%  Similarity=0.466  Sum_probs=79.8

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEE
Q 043443           56 RKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV  135 (299)
Q Consensus        56 ~~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V  135 (299)
                      ....+.++|||+|||+.+++++|+++|.+||.|..|.|+.+  ++..++||||+|.+.++|++||+.||+..|+|+.|.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   87 (103)
T 2d9p_A           10 ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYV   87 (103)
T ss_dssp             CCCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            34557899999999999999999999999999999999987  7889999999999999999999999999999999999


Q ss_pred             EEcccCCC
Q 043443          136 VLAAESRK  143 (299)
Q Consensus       136 ~~a~~~~~  143 (299)
                      .+++.+..
T Consensus        88 ~~a~~~~~   95 (103)
T 2d9p_A           88 ALAQRKEE   95 (103)
T ss_dssp             EECSSCCC
T ss_pred             EEeccccc
Confidence            99987543

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.85  E-value=9.3e-21  Score=144.52  Aligned_cols=86  Identities=30%  Similarity=0.529  Sum_probs=80.4

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      ...+.++|||+|||..+++++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|++||+ ||+..|+|+.|.|.
T Consensus         6 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~   84 (99)
T 2dgs_A            6 SGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVK   84 (99)
T ss_dssp             CCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEE
Confidence            34567899999999999999999999999999999999998899999999999999999999999 99999999999999


Q ss_pred             EcccCCC
Q 043443          137 LAAESRK  143 (299)
Q Consensus       137 ~a~~~~~  143 (299)
                      ++.++..
T Consensus        85 ~a~~~~~   91 (99)
T 2dgs_A           85 RAEPRDS   91 (99)
T ss_dssp             ECCCCCC
T ss_pred             ECCCCcc
Confidence            9986543

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=7.1e-21  Score=148.66  Aligned_cols=89  Identities=27%  Similarity=0.438  Sum_probs=82.4

Q ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEe--------EEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCc
Q 043443           55 RRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVR--------DVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGK  126 (299)
Q Consensus        55 ~~~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~--------~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~  126 (299)
                      ...+.+.++|||+|||..+++++|+++|.+||.|.        .|.|+.++.++.++|||||+|.+.++|++||+.||+.
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~   88 (113)
T 2cpe_A            9 PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGK   88 (113)
T ss_dssp             CCCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             cccCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCC
Confidence            34566789999999999999999999999999999        6999999889999999999999999999999999999


Q ss_pred             eeCCeeEEEEEcccCCC
Q 043443          127 RFAGREISVVLAAESRK  143 (299)
Q Consensus       127 ~l~Gr~i~V~~a~~~~~  143 (299)
                      .|+|+.|.|.+++.+..
T Consensus        89 ~~~g~~l~V~~a~~~~~  105 (113)
T 2cpe_A           89 DFQGSKLKVSLARKKPP  105 (113)
T ss_dssp             EETTEECEEECSSCCCC
T ss_pred             ccCCCEEEEEECCCCCC
Confidence            99999999999987543

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.85  E-value=4e-21  Score=148.13  Aligned_cols=89  Identities=27%  Similarity=0.414  Sum_probs=82.3

Q ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeE
Q 043443           54 GRRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREI  133 (299)
Q Consensus        54 ~~~~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i  133 (299)
                      ......+.++|||+|||+.+++++|+++|.+||+|..|.|+.++.++.++|||||+|.+.++|++||+. |+..|+|+.|
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            344566789999999999999999999999999999999999988999999999999999999999998 9999999999


Q ss_pred             EEEEcccCCC
Q 043443          134 SVVLAAESRK  143 (299)
Q Consensus       134 ~V~~a~~~~~  143 (299)
                      .|.++.++..
T Consensus        88 ~V~~a~~~~~   97 (105)
T 2dh8_A           88 DPKPCTPRGM   97 (105)
T ss_dssp             BCCCSCCSSC
T ss_pred             EEEEccCCCC
Confidence            9999987544

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=1.3e-20  Score=145.05  Aligned_cols=86  Identities=20%  Similarity=0.369  Sum_probs=79.4

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCC-CCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEE
Q 043443           56 RKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYT-GEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREIS  134 (299)
Q Consensus        56 ~~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~-g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~  134 (299)
                      ....+.++|||+|||+.+++++|+++|.+|| |..|.|+.++.+ +.++|||||+|.+.++|++|| .||+..|+|+.|.
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~   87 (104)
T 1wi8_A           10 LPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIR   87 (104)
T ss_dssp             CCSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECE
T ss_pred             CCCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEE
Confidence            3445678999999999999999999999999 999999999887 899999999999999999999 8999999999999


Q ss_pred             EEEcccCCC
Q 043443          135 VVLAAESRK  143 (299)
Q Consensus       135 V~~a~~~~~  143 (299)
                      |+++..+..
T Consensus        88 V~~a~~~~~   96 (104)
T 1wi8_A           88 VDVADQAQD   96 (104)
T ss_dssp             EEECCCCCC
T ss_pred             EEEccCCCC
Confidence            999987543

>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=99.84  E-value=1.1e-20  Score=139.25  Aligned_cols=81  Identities=28%  Similarity=0.441  Sum_probs=77.7

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEccc
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAE  140 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~  140 (299)
                      +++|||+|||..+++++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|+.||+.|||..|+|+.|.|.++.+
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   80 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK   80 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCc
Confidence            36899999999999999999999999999999999988999999999999999999999999999999999999999986


Q ss_pred             C
Q 043443          141 S  141 (299)
Q Consensus       141 ~  141 (299)
                      +
T Consensus        81 ~   81 (83)
T 3md1_A           81 L   81 (83)
T ss_dssp             C
T ss_pred             C
Confidence            4

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*

Probab=99.84  E-value=6.2e-21  Score=151.87  Aligned_cols=87  Identities=23%  Similarity=0.375  Sum_probs=81.4

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      ...+.++|||+|||+.+++++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|++||+.||+..|+|+.|.|+
T Consensus        18 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   97 (126)
T 3ex7_B           18 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   97 (126)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            44567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EcccCCC
Q 043443          137 LAAESRK  143 (299)
Q Consensus       137 ~a~~~~~  143 (299)
                      |+..+..
T Consensus        98 ~a~~~~~  104 (126)
T 3ex7_B           98 WCFVRGP  104 (126)
T ss_dssp             ESEESSS
T ss_pred             EecCCCC
Confidence            9986543

>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=99.84  E-value=8.9e-21  Score=140.90  Aligned_cols=83  Identities=28%  Similarity=0.540  Sum_probs=76.9

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      .+.++|||+|||..+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|+.||+.||+..|+|+.|.|.++
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA   83 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEec
Confidence            35679999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             ccC
Q 043443          139 AES  141 (299)
Q Consensus       139 ~~~  141 (299)
                      +++
T Consensus        84 ~~k   86 (87)
T 3bs9_A           84 TRK   86 (87)
T ss_dssp             C--
T ss_pred             CCC
Confidence            753

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.84  E-value=1.7e-20  Score=144.18  Aligned_cols=84  Identities=24%  Similarity=0.390  Sum_probs=78.6

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      ...+.++|||+|||+.+++++|+++|.+|| |..|.|+.++.++.++|||||+|.+.++|++|| .||+..|+|+.|.|.
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            445678999999999999999999999997 999999999989999999999999999999999 899999999999999


Q ss_pred             EcccCC
Q 043443          137 LAAESR  142 (299)
Q Consensus       137 ~a~~~~  142 (299)
                      ++.+..
T Consensus        89 ~a~~~~   94 (103)
T 2dng_A           89 IAEGRK   94 (103)
T ss_dssp             ECCCCC
T ss_pred             EecCCC
Confidence            998643

>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=99.84  E-value=9.6e-21  Score=140.13  Aligned_cols=82  Identities=37%  Similarity=0.522  Sum_probs=78.0

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      ..+.++|||+|||..+++++|+++|.+||.|..|.|+.++.++..+|||||+|.+.++|+.||+.|||..|+|+.|.|+|
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   83 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   83 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            35678999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             cc
Q 043443          138 AA  139 (299)
Q Consensus       138 a~  139 (299)
                      ++
T Consensus        84 ak   85 (85)
T 3mdf_A           84 AK   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            84

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.84  E-value=1.4e-20  Score=142.22  Aligned_cols=83  Identities=31%  Similarity=0.506  Sum_probs=79.2

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      +.++|||+|||..+++++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|++||+.||+..|+|+.|.|.++.
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            56899999999999999999999999999999999998899999999999999999999999999999999999999998


Q ss_pred             cCC
Q 043443          140 ESR  142 (299)
Q Consensus       140 ~~~  142 (299)
                      .+.
T Consensus        84 ~~~   86 (95)
T 2dnz_A           84 ERL   86 (95)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            643

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A

Probab=99.84  E-value=1.1e-20  Score=145.87  Aligned_cols=88  Identities=26%  Similarity=0.445  Sum_probs=81.7

Q ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCcee---CCe
Q 043443           55 RRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRF---AGR  131 (299)
Q Consensus        55 ~~~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l---~Gr  131 (299)
                      ...+.+.++|||+|||..+++++|+++|.+||+|..|.|+.++.++.++|||||+|.+.++|++||+.||+..|   .|+
T Consensus         7 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~   86 (106)
T 2dgp_A            7 GMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNR   86 (106)
T ss_dssp             SCCCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSS
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCc
Confidence            34556778999999999999999999999999999999999998999999999999999999999999999988   899


Q ss_pred             eEEEEEcccCC
Q 043443          132 EISVVLAAESR  142 (299)
Q Consensus       132 ~i~V~~a~~~~  142 (299)
                      .|.|.++....
T Consensus        87 ~l~v~~a~~~~   97 (106)
T 2dgp_A           87 PIQVKPADSES   97 (106)
T ss_dssp             CCEEEECCCCS
T ss_pred             eEEEEECCccc
Confidence            99999998654

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=3.5e-20  Score=142.34  Aligned_cols=87  Identities=22%  Similarity=0.356  Sum_probs=78.6

Q ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEE
Q 043443           55 RRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREIS  134 (299)
Q Consensus        55 ~~~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~  134 (299)
                      .......++|||+|||..+++++|+++|.+||.|..|.|+.+..+  .+|||||+|.+.++|++||+.||+..|.|+.|.
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            345567899999999999999999999999999999999987533  689999999999999999999999999999999


Q ss_pred             EEEcccCCC
Q 043443          135 VVLAAESRK  143 (299)
Q Consensus       135 V~~a~~~~~  143 (299)
                      |.+++....
T Consensus        87 V~~a~~~~~   95 (103)
T 2cqi_A           87 VNWATTPSS   95 (103)
T ss_dssp             EEECCCTTC
T ss_pred             EEECCCCcc
Confidence            999987543

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens}

Probab=99.84  E-value=7.4e-21  Score=143.80  Aligned_cols=85  Identities=31%  Similarity=0.427  Sum_probs=77.8

Q ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEE
Q 043443           55 RRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREIS  134 (299)
Q Consensus        55 ~~~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~  134 (299)
                      .......++|||+|||..+++++|+++|.+||+|..|.|+.++. +.++|||||+|.+.++|++||+.||+..|+|+.|.
T Consensus        10 ~~~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   88 (95)
T 2ywk_A           10 PAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPIN   88 (95)
T ss_dssp             --CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEE
Confidence            34456678999999999999999999999999999999999875 88999999999999999999999999999999999


Q ss_pred             EEEccc
Q 043443          135 VVLAAE  140 (299)
Q Consensus       135 V~~a~~  140 (299)
                      |.+++.
T Consensus        89 V~~a~~   94 (95)
T 2ywk_A           89 VSGPSS   94 (95)
T ss_dssp             EECCCC
T ss_pred             EEEcCC
Confidence            999863

>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=99.84  E-value=4.6e-20  Score=143.19  Aligned_cols=84  Identities=29%  Similarity=0.512  Sum_probs=76.5

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEE
Q 043443           56 RKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV  135 (299)
Q Consensus        56 ~~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V  135 (299)
                      ....+.++|||+|||.++++++|+++|.+||.|..|.|+.+   +.+++||||+|.+.++|++||+.||+..|+|+.|.|
T Consensus        17 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   93 (109)
T 1x4a_A           17 PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRV   93 (109)
T ss_dssp             CCCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            34556789999999999999999999999999999999754   457899999999999999999999999999999999


Q ss_pred             EEcccCC
Q 043443          136 VLAAESR  142 (299)
Q Consensus       136 ~~a~~~~  142 (299)
                      +|++...
T Consensus        94 ~~a~~~~  100 (109)
T 1x4a_A           94 EFPRSGR  100 (109)
T ss_dssp             ECCCCCC
T ss_pred             EEcccCC
Confidence            9998654

>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=99.84  E-value=2.8e-20  Score=143.26  Aligned_cols=86  Identities=23%  Similarity=0.388  Sum_probs=79.5

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCC---eeE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAG---REI  133 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~G---r~i  133 (299)
                      ...+.++|||+|||..+++++|+++|.+||.|..|.|+.++ ++.++|||||+|.+.++|++||+.||+..|.|   +.|
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l   89 (105)
T 2dnh_A           11 RGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSL   89 (105)
T ss_dssp             SCCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccE
Confidence            34567899999999999999999999999999999999987 78899999999999999999999999999998   999


Q ss_pred             EEEEcccCCC
Q 043443          134 SVVLAAESRK  143 (299)
Q Consensus       134 ~V~~a~~~~~  143 (299)
                      .|.+++....
T Consensus        90 ~V~~a~~~~~   99 (105)
T 2dnh_A           90 VVKFADTDKE   99 (105)
T ss_dssp             EEEESCSSCC
T ss_pred             EEEECccCcc
Confidence            9999987544

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X

Probab=99.84  E-value=1.9e-20  Score=154.62  Aligned_cols=86  Identities=22%  Similarity=0.349  Sum_probs=80.8

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      ..+.++|||+|||..+++++|+++|.+||+|+.|.|+.++.++.+++||||+|.+.++|++||+.||+..|+|+.|.|+|
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            34678999999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             cccCCC
Q 043443          138 AAESRK  143 (299)
Q Consensus       138 a~~~~~  143 (299)
                      ++....
T Consensus       116 a~~~~~  121 (156)
T 1h2v_Z          116 DAGFKE  121 (156)
T ss_dssp             ESCCCT
T ss_pred             CCCCCC
Confidence            986443

>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=99.84  E-value=2.6e-20  Score=141.32  Aligned_cols=83  Identities=24%  Similarity=0.366  Sum_probs=79.3

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEccc
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAE  140 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~  140 (299)
                      .++|||+|||..+++++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|++||+.|||..|+|+.|.|.++.+
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            57999999999999999999999999999999999988999999999999999999999999999999999999999987


Q ss_pred             CCC
Q 043443          141 SRK  143 (299)
Q Consensus       141 ~~~  143 (299)
                      ...
T Consensus        82 ~~~   84 (96)
T 2x1f_A           82 SDI   84 (96)
T ss_dssp             SSG
T ss_pred             CCC
Confidence            554

>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=99.84  E-value=9.4e-21  Score=152.10  Aligned_cols=86  Identities=31%  Similarity=0.473  Sum_probs=81.0

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      ...+.++|||+|||.++++++|+++|.+||+|..|.|+.++.++..+|||||+|.+.++|++||+.||+..|+|+.|.|+
T Consensus        42 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~  121 (129)
T 2kxn_B           42 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVD  121 (129)
T ss_dssp             CCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEES
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EcccCC
Q 043443          137 LAAESR  142 (299)
Q Consensus       137 ~a~~~~  142 (299)
                      |++++.
T Consensus       122 ~a~~~~  127 (129)
T 2kxn_B          122 FSITKR  127 (129)
T ss_dssp             CCSSSS
T ss_pred             EecCCC
Confidence            998654

>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=99.84  E-value=8.3e-21  Score=144.45  Aligned_cols=83  Identities=24%  Similarity=0.329  Sum_probs=77.7

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      ....++|||+|||+.+++++|+++|.+||.|..|.++.++.++.++|||||+|.+.++|++||+.||+..|+|+.|.|++
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            34568999999999999999999999999999888888888899999999999999999999999999999999999999


Q ss_pred             ccc
Q 043443          138 AAE  140 (299)
Q Consensus       138 a~~  140 (299)
                      +..
T Consensus        92 a~~   94 (98)
T 2cqp_A           92 GSG   94 (98)
T ss_dssp             SSC
T ss_pred             cCC
Confidence            875

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=1.3e-20  Score=142.70  Aligned_cols=83  Identities=25%  Similarity=0.436  Sum_probs=79.0

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEE-EeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDV-YLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v-~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      +.++|||+|||..+++++|+++|.+||.|..| .|+.++.++.++|||||+|.+.++|++||+.||+..|+|+.|.|.++
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (96)
T 1x5t_A            4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYA   83 (96)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            56899999999999999999999999999999 99999889999999999999999999999999999999999999999


Q ss_pred             ccCC
Q 043443          139 AESR  142 (299)
Q Consensus       139 ~~~~  142 (299)
                      .++.
T Consensus        84 ~~~~   87 (96)
T 1x5t_A           84 FKKD   87 (96)
T ss_dssp             CCCC
T ss_pred             cccC
Confidence            8654

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=1.7e-20  Score=144.76  Aligned_cols=86  Identities=23%  Similarity=0.382  Sum_probs=80.8

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      ...+.++|||+|||..+++++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|+.||+.|||..|+|+.|.|.
T Consensus        19 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   98 (106)
T 1p27_B           19 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   98 (106)
T ss_dssp             CBTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEE
Confidence            34567899999999999999999999999999999999999899999999999999999999999999999999999999


Q ss_pred             EcccCC
Q 043443          137 LAAESR  142 (299)
Q Consensus       137 ~a~~~~  142 (299)
                      ++.++.
T Consensus        99 ~a~~~~  104 (106)
T 1p27_B           99 WCFVRG  104 (106)
T ss_dssp             ESEESS
T ss_pred             eecCCC
Confidence            998653

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}

Probab=99.83  E-value=2.5e-20  Score=146.82  Aligned_cols=84  Identities=33%  Similarity=0.584  Sum_probs=79.1

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      ..+.++|||+|||.++++++|+++|++||.|+.|.|+.+. ++.++|||||+|.+.++|++||+.|||..|+|+.|.|++
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~   82 (116)
T 2fy1_A            4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQ   82 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4567899999999999999999999999999999999987 899999999999999999999999999999999999999


Q ss_pred             cccCC
Q 043443          138 AAESR  142 (299)
Q Consensus       138 a~~~~  142 (299)
                      ++...
T Consensus        83 a~~~~   87 (116)
T 2fy1_A           83 AKKPS   87 (116)
T ss_dssp             CCCSS
T ss_pred             CCCCC
Confidence            98643

>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=99.83  E-value=3.1e-20  Score=144.35  Aligned_cols=86  Identities=23%  Similarity=0.392  Sum_probs=81.0

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      ...+.++|||+|||..+++++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|+.||..|||..|+|+.|.|.
T Consensus        22 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  101 (110)
T 1oo0_B           22 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD  101 (110)
T ss_dssp             CBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            44567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EcccCC
Q 043443          137 LAAESR  142 (299)
Q Consensus       137 ~a~~~~  142 (299)
                      ++..+.
T Consensus       102 ~a~~~~  107 (110)
T 1oo0_B          102 WCFVKG  107 (110)
T ss_dssp             ESEESS
T ss_pred             EcccCC
Confidence            998654

>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=99.83  E-value=2.7e-20  Score=143.83  Aligned_cols=82  Identities=26%  Similarity=0.434  Sum_probs=77.8

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      ...+.++|||+|||+.+++++|+++|.+||.|+.|.|+.+. ++.++|||||+|.+.++|++||+.||+..|+|+.|.|+
T Consensus        25 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~  103 (107)
T 3ulh_A           25 GVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQ  103 (107)
T ss_dssp             CCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            34567899999999999999999999999999999999988 89999999999999999999999999999999999999


Q ss_pred             Ecc
Q 043443          137 LAA  139 (299)
Q Consensus       137 ~a~  139 (299)
                      +++
T Consensus       104 ~a~  106 (107)
T 3ulh_A          104 LVT  106 (107)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            985

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.83  E-value=5.3e-20  Score=148.66  Aligned_cols=82  Identities=37%  Similarity=0.524  Sum_probs=77.3

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      ...+..+|||+|||..+++++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|++||+.||+..|+|+.|.|.
T Consensus        59 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  138 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN  138 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEE
T ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             Ec
Q 043443          137 LA  138 (299)
Q Consensus       137 ~a  138 (299)
                      +|
T Consensus       139 ~A  140 (140)
T 2ku7_A          139 LA  140 (140)
T ss_dssp             C-
T ss_pred             eC
Confidence            86

>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=99.83  E-value=4.3e-21  Score=144.12  Aligned_cols=82  Identities=15%  Similarity=0.240  Sum_probs=72.8

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCC--CEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           62 GSLLVRNIPLDCRPEELRAPFERFG--VVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        62 ~~l~V~nLp~~~te~dL~~~F~~~G--~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      .+|||+|||+++++++|+++|.+||  .|..|.|+.++.++.++|||||+|.+.++|++||+.|||.+|+|+.|.|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            5799999999999999999999999  99999999999999999999999999999999999999999999999999998


Q ss_pred             cCCC
Q 043443          140 ESRK  143 (299)
Q Consensus       140 ~~~~  143 (299)
                      +...
T Consensus        82 ~~~~   85 (90)
T 3p5t_L           82 KLEH   85 (90)
T ss_dssp             ----
T ss_pred             CCcc
Confidence            7543

>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=99.83  E-value=6.8e-20  Score=139.25  Aligned_cols=80  Identities=25%  Similarity=0.356  Sum_probs=73.7

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeC--CeeEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFA--GREIS  134 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~--Gr~i~  134 (299)
                      ...+.++|||+|||.++++++|+++|.+||.|..|.|+.+      ++||||+|.+.++|++||+.||+..|+  |+.|.
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~   86 (97)
T 1why_A           13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLR   86 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEE
Confidence            4456789999999999999999999999999999999864      689999999999999999999999999  99999


Q ss_pred             EEEcccCC
Q 043443          135 VVLAAESR  142 (299)
Q Consensus       135 V~~a~~~~  142 (299)
                      |+|++++.
T Consensus        87 V~~a~~~~   94 (97)
T 1why_A           87 VDFAKSGP   94 (97)
T ss_dssp             EEECCCCC
T ss_pred             EEECCCCC
Confidence            99998643

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.83  E-value=2.1e-20  Score=142.20  Aligned_cols=85  Identities=21%  Similarity=0.468  Sum_probs=78.2

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCC---CCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEE
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYY---TGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV  135 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~---~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V  135 (299)
                      .+.++|||+|||+.+++++|+++|.+||.|..|.|+.++.   ++.++|||||+|.+.++|++||+.||+..|+|+.|.|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   82 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEV   82 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            3568999999999999999999999999999999998776   5688999999999999999999999999999999999


Q ss_pred             EEcccCCC
Q 043443          136 VLAAESRK  143 (299)
Q Consensus       136 ~~a~~~~~  143 (299)
                      .+++....
T Consensus        83 ~~a~~~~~   90 (98)
T 2cpf_A           83 RISERATK   90 (98)
T ss_dssp             ECSSCSSC
T ss_pred             EEccCCCC
Confidence            99986543

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A

Probab=99.83  E-value=7.2e-21  Score=143.85  Aligned_cols=81  Identities=22%  Similarity=0.285  Sum_probs=75.7

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      ...++|||+|||+.+++++|+++|.+||.|..|.++.++.++.++|||||+|.+.++|++||+.||+..|+|+.|.|+++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a   92 (95)
T 2ek1_A           13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGP   92 (95)
T ss_dssp             --CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEec
Confidence            34589999999999999999999999999998888888888999999999999999999999999999999999999997


Q ss_pred             c
Q 043443          139 A  139 (299)
Q Consensus       139 ~  139 (299)
                      .
T Consensus        93 ~   93 (95)
T 2ek1_A           93 S   93 (95)
T ss_dssp             C
T ss_pred             c
Confidence            6

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.83  E-value=3.9e-20  Score=149.73  Aligned_cols=87  Identities=30%  Similarity=0.459  Sum_probs=81.6

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      .....++|||+|||.++++++|+++|..||+|+.|.|+.++.++.++|||||+|.+.++|++||+.||+..|+|+.|.|.
T Consensus        38 ~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  117 (139)
T 1u6f_A           38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA  117 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            44567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EcccCCC
Q 043443          137 LAAESRK  143 (299)
Q Consensus       137 ~a~~~~~  143 (299)
                      +++....
T Consensus       118 ~a~~~~~  124 (139)
T 1u6f_A          118 LAASGHQ  124 (139)
T ss_dssp             ESSCCCC
T ss_pred             ECCCCCC
Confidence            9987544

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

Probab=99.83  E-value=8.2e-20  Score=143.69  Aligned_cols=83  Identities=25%  Similarity=0.362  Sum_probs=78.3

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      ...+.++|||+|||+++++++|+++|.+||+|..|.|+.++.++.++|||||+|.+.++|+.||+.||+..|+|+.|.|+
T Consensus        36 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~  115 (118)
T 2khc_A           36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQ  115 (118)
T ss_dssp             CCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            44567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             Ecc
Q 043443          137 LAA  139 (299)
Q Consensus       137 ~a~  139 (299)
                      |++
T Consensus       116 ~ak  118 (118)
T 2khc_A          116 LKK  118 (118)
T ss_dssp             EC-
T ss_pred             ecC
Confidence            974

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens}

Probab=99.83  E-value=3.1e-20  Score=138.13  Aligned_cols=83  Identities=20%  Similarity=0.462  Sum_probs=77.1

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCC-CccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGE-PRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~-~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      ..++|||+|||.++++++|+++|.+||.|..|.|+.+..++. .+|||||+|.+.++|++||+.|||..|+|+.|.|+++
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            457999999999999999999999999999999998876655 8999999999999999999999999999999999999


Q ss_pred             ccCC
Q 043443          139 AESR  142 (299)
Q Consensus       139 ~~~~  142 (299)
                      .+..
T Consensus        83 ~~~~   86 (88)
T 4a8x_A           83 LAPW   86 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7643

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=9.4e-20  Score=139.92  Aligned_cols=87  Identities=26%  Similarity=0.432  Sum_probs=79.4

Q ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEE
Q 043443           55 RRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREIS  134 (299)
Q Consensus        55 ~~~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~  134 (299)
                      .....+.++|||+|||+.+++++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|++||.  ++..|+|+.|.
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            3445667899999999999999999999999999999999998899999999999999999999998  57899999999


Q ss_pred             EEEcccCCC
Q 043443          135 VVLAAESRK  143 (299)
Q Consensus       135 V~~a~~~~~  143 (299)
                      |.++..+..
T Consensus        87 v~~a~~~~~   95 (103)
T 2cqg_A           87 CKLPNSKQS   95 (103)
T ss_dssp             EECCCTTCC
T ss_pred             EEecCCCCc
Confidence            999987543

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.82  E-value=3.1e-20  Score=141.49  Aligned_cols=83  Identities=25%  Similarity=0.388  Sum_probs=79.0

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEe-EEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCee----E
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVR-DVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGRE----I  133 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~-~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~----i  133 (299)
                      .+.++|||+|||.++++++|+++|.+||.|. .|.|+.++.++.++|||||+|.+.++|++||+.||+..|.|+.    |
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            4578999999999999999999999999999 9999999889999999999999999999999999999999999    9


Q ss_pred             EEEEcccC
Q 043443          134 SVVLAAES  141 (299)
Q Consensus       134 ~V~~a~~~  141 (299)
                      .|+|++..
T Consensus        87 ~v~~a~~~   94 (99)
T 2div_A           87 KLNYATYS   94 (99)
T ss_dssp             CEEETTCC
T ss_pred             EEeecCCC
Confidence            99999864

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A

Probab=99.82  E-value=1.1e-19  Score=139.77  Aligned_cols=79  Identities=29%  Similarity=0.474  Sum_probs=72.5

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      ..+.++|||+|||.++++++|+++|.+||.|..|.|+        ++||||+|.+.++|++||+.||+..|+|+.|.|.+
T Consensus         8 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   79 (103)
T 2dgu_A            8 MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVF   79 (103)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEE
Confidence            3456899999999999999999999999999999987        35999999999999999999999999999999999


Q ss_pred             cccCCCC
Q 043443          138 AAESRKR  144 (299)
Q Consensus       138 a~~~~~~  144 (299)
                      +++....
T Consensus        80 a~~~~~~   86 (103)
T 2dgu_A           80 AKPPDQK   86 (103)
T ss_dssp             CCCCCCC
T ss_pred             cCCCccc
Confidence            9875543

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.82  E-value=7.9e-21  Score=145.65  Aligned_cols=83  Identities=22%  Similarity=0.350  Sum_probs=78.7

Q ss_pred             CCCCEEEEeCCCC------CCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCC-e
Q 043443           59 QNHGSLLVRNIPL------DCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAG-R  131 (299)
Q Consensus        59 ~~~~~l~V~nLp~------~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~G-r  131 (299)
                      ...++|||+|||+      .+++++|+++|.+||.|..|.|+.++.|+.++|||||+|.+.++|++||+.|||..|+| +
T Consensus         4 ~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r   83 (100)
T 3ns6_A            4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKH   83 (100)
T ss_dssp             CGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSC
T ss_pred             CcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCe
Confidence            3467999999999      99999999999999999999999999999999999999999999999999999999999 9


Q ss_pred             eEEEEEcccC
Q 043443          132 EISVVLAAES  141 (299)
Q Consensus       132 ~i~V~~a~~~  141 (299)
                      .|.|.++.+.
T Consensus        84 ~l~V~~a~~~   93 (100)
T 3ns6_A           84 RLFLYTMKDV   93 (100)
T ss_dssp             BCEEEESHHH
T ss_pred             EEEEEECchh
Confidence            9999999753

>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=99.82  E-value=3.8e-20  Score=145.44  Aligned_cols=81  Identities=22%  Similarity=0.375  Sum_probs=74.8

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEccc
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAE  140 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~  140 (299)
                      .++|||+|||+.+++++|+++|.+||.|..|.|+.+.  +.++|||||+|.+.++|+.||+.||+.+|+|+.|.|.++..
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            4689999999999999999999999999999999875  44789999999999999999999999999999999999986


Q ss_pred             CCC
Q 043443          141 SRK  143 (299)
Q Consensus       141 ~~~  143 (299)
                      +..
T Consensus        83 ~~~   85 (115)
T 4f25_A           83 RKE   85 (115)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            543

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.82  E-value=4e-20  Score=141.04  Aligned_cols=83  Identities=28%  Similarity=0.472  Sum_probs=78.5

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeE--------EEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCcee
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRD--------VYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRF  128 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~--------v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l  128 (299)
                      .....++|||+|||.++++++|+++|.+||.|..        |.|+.++.++.++|||||+|.+.++|+.||+.|||..|
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~   88 (99)
T 2la6_A            9 SHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEF   88 (99)
T ss_dssp             SCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEe
Confidence            3456789999999999999999999999999999        99999988999999999999999999999999999999


Q ss_pred             CCeeEEEEEcc
Q 043443          129 AGREISVVLAA  139 (299)
Q Consensus       129 ~Gr~i~V~~a~  139 (299)
                      +|+.|.|++|+
T Consensus        89 ~g~~l~V~~A~   99 (99)
T 2la6_A           89 SGNPIKVSFAT   99 (99)
T ss_dssp             SSSBCEEEECC
T ss_pred             CCcEEEEEecC
Confidence            99999999974

>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=99.82  E-value=6.1e-20  Score=141.59  Aligned_cols=83  Identities=29%  Similarity=0.509  Sum_probs=76.4

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeE-EEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRD-VYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV  135 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~-v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V  135 (299)
                      .....++|||+|||+.+++++|+++|.+||.|.. |.|+.+ .++.++|||||+|.+.++|++||+. |+..|+|+.|.|
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            4456789999999999999999999999999987 888888 7899999999999999999999997 999999999999


Q ss_pred             EEcccC
Q 043443          136 VLAAES  141 (299)
Q Consensus       136 ~~a~~~  141 (299)
                      .++...
T Consensus        89 ~~~~~~   94 (104)
T 1wg5_A           89 FKSSRA   94 (104)
T ss_dssp             EEECTT
T ss_pred             EECCHH
Confidence            998753

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.82  E-value=1.3e-20  Score=152.33  Aligned_cols=88  Identities=42%  Similarity=0.698  Sum_probs=81.9

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEE
Q 043443           56 RKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV  135 (299)
Q Consensus        56 ~~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V  135 (299)
                      ....+.++|||+|||..+++++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|++||+.||+..|+|+.|.|
T Consensus        42 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V  121 (135)
T 2lea_A           42 PDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRV  121 (135)
T ss_dssp             SSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            34556789999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             EEcccCCC
Q 043443          136 VLAAESRK  143 (299)
Q Consensus       136 ~~a~~~~~  143 (299)
                      .|++....
T Consensus       122 ~~a~~~~~  129 (135)
T 2lea_A          122 QMARYGRP  129 (135)
T ss_dssp             EECCCCCC
T ss_pred             EECCCCCC
Confidence            99986543

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=3.1e-20  Score=145.64  Aligned_cols=84  Identities=23%  Similarity=0.265  Sum_probs=77.8

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCE-eEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVV-RDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV  135 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I-~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V  135 (299)
                      ...+.++|||+|||+.+++++|+++|.+||.| ..|.|+.++ ++.++|||||+|.+.++|++||+. |+..|+|+.|.|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v   88 (114)
T 2cpy_A           11 VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFV   88 (114)
T ss_dssp             CCSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEE
T ss_pred             CCCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEE
Confidence            34567899999999999999999999999999 889999998 899999999999999999999986 999999999999


Q ss_pred             EEcccCC
Q 043443          136 VLAAESR  142 (299)
Q Consensus       136 ~~a~~~~  142 (299)
                      .++..+.
T Consensus        89 ~~a~~~~   95 (114)
T 2cpy_A           89 HVVTLED   95 (114)
T ss_dssp             EEECHHH
T ss_pred             EECCHHH
Confidence            9997643

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.82  E-value=5.6e-20  Score=138.10  Aligned_cols=83  Identities=29%  Similarity=0.480  Sum_probs=77.1

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      ..+.++|||+|||..+++++|+++|.+||.|..|.|+.+  ++.++|||||+|.+.++|++||+.||+..|+|+.|.|.+
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            345689999999999999999999999999999999874  788899999999999999999999999999999999999


Q ss_pred             cccCC
Q 043443          138 AAESR  142 (299)
Q Consensus       138 a~~~~  142 (299)
                      +++..
T Consensus        83 a~~~~   87 (92)
T 2dgv_A           83 DRNAS   87 (92)
T ss_dssp             CSCCS
T ss_pred             cCCCC
Confidence            98654

>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=99.82  E-value=3.1e-20  Score=142.99  Aligned_cols=81  Identities=16%  Similarity=0.210  Sum_probs=74.3

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      ....++|||+|||+++|+++|+++|.+||. +.|.|+.++ +++++|||||+|.+.++|++||+ ||+..|+|+.|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~   88 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFL   88 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEECC-CCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEE
Confidence            455689999999999999999999999995 499999987 89999999999999999999995 799999999999999


Q ss_pred             cccC
Q 043443          138 AAES  141 (299)
Q Consensus       138 a~~~  141 (299)
                      +...
T Consensus        89 ~~~~   92 (102)
T 1wez_A           89 NSTA   92 (102)
T ss_dssp             ECCC
T ss_pred             CCCC
Confidence            8753

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A

Probab=99.82  E-value=8.7e-20  Score=136.10  Aligned_cols=81  Identities=30%  Similarity=0.532  Sum_probs=77.2

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      +.++|||+|||..+++++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|++|| .||+..|+|+.|.|.+++
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~   83 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKR   83 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETT
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEcc
Confidence            4579999999999999999999999999999999999889999999999999999999999 899999999999999997


Q ss_pred             cC
Q 043443          140 ES  141 (299)
Q Consensus       140 ~~  141 (299)
                      +.
T Consensus        84 ~~   85 (89)
T 3ucg_A           84 TN   85 (89)
T ss_dssp             TT
T ss_pred             CC
Confidence            64

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=4.4e-20  Score=142.49  Aligned_cols=85  Identities=14%  Similarity=0.291  Sum_probs=78.6

Q ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeE
Q 043443           54 GRRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREI  133 (299)
Q Consensus        54 ~~~~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i  133 (299)
                      .-..+....+|||+|||+++|+++|+++|++||+|..|.|+.++. +.++|||||+|.+.++|+.||. ||+..|+|+.|
T Consensus         4 ~~~~~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l   81 (103)
T 1s79_A            4 ILKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDL   81 (103)
T ss_dssp             CCSSCSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTC
T ss_pred             cccccCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEE
Confidence            334556678999999999999999999999999999999999886 8999999999999999999999 89999999999


Q ss_pred             EEEEccc
Q 043443          134 SVVLAAE  140 (299)
Q Consensus       134 ~V~~a~~  140 (299)
                      .|.++..
T Consensus        82 ~V~~~~~   88 (103)
T 1s79_A           82 LILFKDD   88 (103)
T ss_dssp             EEEEHHH
T ss_pred             EEEEchH
Confidence            9999874

>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=99.81  E-value=1.2e-19  Score=135.04  Aligned_cols=82  Identities=29%  Similarity=0.515  Sum_probs=76.1

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEE
Q 043443           56 RKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV  135 (299)
Q Consensus        56 ~~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V  135 (299)
                      ..+.+.++|||+|||+.+++++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|++||+ +++..|+|+.|.|
T Consensus         6 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v   84 (87)
T 3s7r_A            6 KNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDP   84 (87)
T ss_dssp             -CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEE
Confidence            345677899999999999999999999999999999999998899999999999999999999996 5889999999999


Q ss_pred             EEc
Q 043443          136 VLA  138 (299)
Q Consensus       136 ~~a  138 (299)
                      ++|
T Consensus        85 ~~A   87 (87)
T 3s7r_A           85 KKA   87 (87)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            885

>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=99.81  E-value=5.8e-20  Score=142.85  Aligned_cols=84  Identities=30%  Similarity=0.468  Sum_probs=79.5

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      ..+.++|||+|||..+++++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|+.||+.|||..|+|+.|.|.+
T Consensus        23 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~  102 (108)
T 2jrs_A           23 SAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGH  102 (108)
T ss_dssp             CSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34568999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             cccC
Q 043443          138 AAES  141 (299)
Q Consensus       138 a~~~  141 (299)
                      ++++
T Consensus       103 a~~k  106 (108)
T 2jrs_A          103 VTER  106 (108)
T ss_dssp             SCSS
T ss_pred             cccC
Confidence            9764

>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=99.81  E-value=1.5e-19  Score=137.25  Aligned_cols=80  Identities=26%  Similarity=0.291  Sum_probs=74.7

Q ss_pred             CCCEEEEeCCCCCCCHHHHH----HHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEE
Q 043443           60 NHGSLLVRNIPLDCRPEELR----APFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV  135 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~----~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V  135 (299)
                      +.++|||+|||+.+++++|+    ++|.+||+|..|.|+.++.+   ++||||+|.+.++|++||+.|||..|+|+.|.|
T Consensus         8 ~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V   84 (96)
T 2dgx_A            8 NGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILV   84 (96)
T ss_dssp             SCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            45799999999999999999    99999999999999988655   789999999999999999999999999999999


Q ss_pred             EEcccCC
Q 043443          136 VLAAESR  142 (299)
Q Consensus       136 ~~a~~~~  142 (299)
                      +++++..
T Consensus        85 ~~a~~~~   91 (96)
T 2dgx_A           85 SLATGAS   91 (96)
T ss_dssp             EECCCSS
T ss_pred             EEcCCCC
Confidence            9998643

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.81  E-value=6e-20  Score=145.01  Aligned_cols=83  Identities=18%  Similarity=0.236  Sum_probs=76.8

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCC---EeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGV---VRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREI  133 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~---I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i  133 (299)
                      ...+.++|||+|||+++|+++|+++|..||.   |..|.|+.++. ++++|||||+|.+.++|++||+ ||++.|+|+.|
T Consensus        13 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i   90 (118)
T 2db1_A           13 EGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRESMGHRYI   90 (118)
T ss_dssp             CBCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEE
Confidence            4456789999999999999999999999999   89999998876 8999999999999999999999 99999999999


Q ss_pred             EEEEcccC
Q 043443          134 SVVLAAES  141 (299)
Q Consensus       134 ~V~~a~~~  141 (299)
                      .|.++..+
T Consensus        91 ~V~~a~~~   98 (118)
T 2db1_A           91 EVFKSHRT   98 (118)
T ss_dssp             EEEEECHH
T ss_pred             EEEECCHH
Confidence            99998643

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.81  E-value=7.4e-20  Score=142.79  Aligned_cols=86  Identities=17%  Similarity=0.280  Sum_probs=77.9

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHH---HHHhcCCCEeEEEeccCCCCC---CCccEEEEEEcCHHHHHHHHHhhCCceeCC
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELR---APFERFGVVRDVYLPKDYYTG---EPRGFAFVQFVDPYEAAEAQHHMNGKRFAG  130 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~---~~F~~~G~I~~v~i~~d~~~g---~~~g~afVeF~~~~~A~~Al~~lng~~l~G  130 (299)
                      .....++|||+|||+.+++++|+   ++|.+||+|..|.|+.+..++   .++|||||+|.+.++|++||+.||+..|+|
T Consensus        11 r~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~g   90 (111)
T 2cpi_A           11 RVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDG   90 (111)
T ss_dssp             CCCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             cccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECC
Confidence            34557899999999999999999   999999999999999887644   456999999999999999999999999999


Q ss_pred             eeEEEEEcccCC
Q 043443          131 REISVVLAAESR  142 (299)
Q Consensus       131 r~i~V~~a~~~~  142 (299)
                      +.|.|++++++.
T Consensus        91 r~l~V~~a~~k~  102 (111)
T 2cpi_A           91 RTLKASLGTTKY  102 (111)
T ss_dssp             EEEEEESCCCCS
T ss_pred             EEEEEEeccccc
Confidence            999999998754

>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=99.81  E-value=3.4e-20  Score=150.19  Aligned_cols=83  Identities=17%  Similarity=0.209  Sum_probs=77.1

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCC---EeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCee
Q 043443           56 RKEQNHGSLLVRNIPLDCRPEELRAPFERFGV---VRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGRE  132 (299)
Q Consensus        56 ~~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~---I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~  132 (299)
                      ....+.++|||+|||+++|+++|+++|.+||.   |..|.|+.++. +.++|||||+|.+.++|++||+ ||+.+|+|+.
T Consensus        39 ~~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~  116 (136)
T 2hgl_A           39 PEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRY  116 (136)
T ss_dssp             SSCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEE
Confidence            34556789999999999999999999999999   88999999876 9999999999999999999999 9999999999


Q ss_pred             EEEEEccc
Q 043443          133 ISVVLAAE  140 (299)
Q Consensus       133 i~V~~a~~  140 (299)
                      |.|.++..
T Consensus       117 i~V~~a~~  124 (136)
T 2hgl_A          117 IEVFKSHR  124 (136)
T ss_dssp             EEEEECCH
T ss_pred             EEEEECCh
Confidence            99999864

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.81  E-value=7.1e-20  Score=151.74  Aligned_cols=83  Identities=16%  Similarity=0.250  Sum_probs=77.6

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCC--CEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFG--VVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G--~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      ...++|||+|||+++++++|+++|.+||  .|..|.|+.++.++.++|||||+|.+.++|++||+.|||..|+|+.|.|.
T Consensus        53 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~  132 (156)
T 3n9u_C           53 NRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVR  132 (156)
T ss_dssp             ---CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEE
Confidence            3568999999999999999999999999  99999999999999999999999999999999999999999999999999


Q ss_pred             EcccC
Q 043443          137 LAAES  141 (299)
Q Consensus       137 ~a~~~  141 (299)
                      ++.++
T Consensus       133 ~a~~~  137 (156)
T 3n9u_C          133 PATRQ  137 (156)
T ss_dssp             ECCHH
T ss_pred             EcCCC
Confidence            99754

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.81  E-value=7e-20  Score=140.80  Aligned_cols=84  Identities=23%  Similarity=0.331  Sum_probs=79.0

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhc-CCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCce-eCCeeEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFER-FGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKR-FAGREISV  135 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~-~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~-l~Gr~i~V  135 (299)
                      ..+.++|||+|||.++++++|+++|.+ ||.|..|.|+.+. ++.++|||||+|.+.++|++||+.||+.. |+|+.|.|
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v   84 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRL   84 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEE
Confidence            456789999999999999999999999 9999999999998 89999999999999999999999999999 99999999


Q ss_pred             EEcccCC
Q 043443          136 VLAAESR  142 (299)
Q Consensus       136 ~~a~~~~  142 (299)
                      .++..+.
T Consensus        85 ~~a~~~~   91 (104)
T 2dhg_A           85 SVAIPKA   91 (104)
T ss_dssp             CBCCCCC
T ss_pred             EEccCCC
Confidence            9997644

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.81  E-value=5.1e-19  Score=149.52  Aligned_cols=83  Identities=24%  Similarity=0.403  Sum_probs=78.2

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      ...++|||+|||+.+++++|+++|.+||+|+.|.|+.+. ++.++|||||+|.+.++|++||+.||+..|+|+.|.|+|+
T Consensus        86 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a  164 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV  164 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            346899999999999999999999999999999999988 8999999999999999999999999999999999999999


Q ss_pred             ccCC
Q 043443          139 AESR  142 (299)
Q Consensus       139 ~~~~  142 (299)
                      ....
T Consensus       165 ~~~~  168 (177)
T 2f3j_A          165 ASQI  168 (177)
T ss_dssp             SSGG
T ss_pred             cCCC
Confidence            8643

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A

Probab=99.81  E-value=1.1e-19  Score=151.68  Aligned_cols=87  Identities=23%  Similarity=0.393  Sum_probs=80.7

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEE
Q 043443           56 RKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV  135 (299)
Q Consensus        56 ~~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V  135 (299)
                      ....+.++|||+|||+.+++++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|+.||+.|||..|+|+.|.|
T Consensus        67 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  146 (165)
T 1rk8_A           67 QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQV  146 (165)
T ss_dssp             CCCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            34456789999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             EEcccCC
Q 043443          136 VLAAESR  142 (299)
Q Consensus       136 ~~a~~~~  142 (299)
                      .|+..+.
T Consensus       147 ~~a~~~~  153 (165)
T 1rk8_A          147 DWCFVKG  153 (165)
T ss_dssp             EESEECC
T ss_pred             EEecCCC
Confidence            9998643

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=6.9e-20  Score=141.54  Aligned_cols=81  Identities=16%  Similarity=0.247  Sum_probs=73.3

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhC--CceeCCeeEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMN--GKRFAGREISV  135 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~ln--g~~l~Gr~i~V  135 (299)
                      ..+.++|||+|||+.+++++|+++|++||+|+.|.|+.+      +|||||+|++.++|+.||+.|+  +.+|+|+.|.|
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V   86 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI   86 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCB
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            345789999999999999999999999999999999875      6999999999999999999886  47899999999


Q ss_pred             EEcccCCCC
Q 043443          136 VLAAESRKR  144 (299)
Q Consensus       136 ~~a~~~~~~  144 (299)
                      +|++.+...
T Consensus        87 ~~A~~~~~~   95 (105)
T 1sjq_A           87 QFSNHKELK   95 (105)
T ss_dssp             CCCSSSSCC
T ss_pred             EEcCCCCCC
Confidence            999876544

>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=99.81  E-value=1.7e-19  Score=139.73  Aligned_cols=86  Identities=24%  Similarity=0.288  Sum_probs=79.1

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCC-EeEEEec-cCCCCCCCccEEEEEEcCHHHHHHHHHhhC--CceeCCeeE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGV-VRDVYLP-KDYYTGEPRGFAFVQFVDPYEAAEAQHHMN--GKRFAGREI  133 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~-I~~v~i~-~d~~~g~~~g~afVeF~~~~~A~~Al~~ln--g~~l~Gr~i  133 (299)
                      ..+.++|||+|||+.+++++|+++|.+||. |..|.|+ .+..++.++|||||+|.+.++|+.||+.||  +..|+|+.|
T Consensus         5 s~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l   84 (109)
T 2dis_A            5 SSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQI   84 (109)
T ss_dssp             CCCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCC
T ss_pred             ccCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeE
Confidence            345789999999999999999999999998 9999998 788888999999999999999999999996  589999999


Q ss_pred             EEEEcccCCC
Q 043443          134 SVVLAAESRK  143 (299)
Q Consensus       134 ~V~~a~~~~~  143 (299)
                      .|.|+++...
T Consensus        85 ~V~~a~~~~~   94 (109)
T 2dis_A           85 AVDWAEPEID   94 (109)
T ss_dssp             EEEESCSSCS
T ss_pred             EEEEcCCCCC
Confidence            9999987554

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.81  E-value=2e-19  Score=134.94  Aligned_cols=83  Identities=17%  Similarity=0.295  Sum_probs=77.2

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      .....++|||+|||+.+++++|+++|.+| .|..|.|+.+ .++.++|||||+|.+.++|++||+ ||+..|+|+.|.|.
T Consensus         6 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~   82 (91)
T 2dgw_A            6 SGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVF   82 (91)
T ss_dssp             CCCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEE
T ss_pred             CCCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEE
Confidence            34567899999999999999999999999 9999999998 789999999999999999999999 99999999999999


Q ss_pred             EcccCC
Q 043443          137 LAAESR  142 (299)
Q Consensus       137 ~a~~~~  142 (299)
                      ++..+.
T Consensus        83 ~a~~~~   88 (91)
T 2dgw_A           83 REKSGP   88 (91)
T ss_dssp             EESSCC
T ss_pred             ECCcCC
Confidence            998653

>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=99.81  E-value=8e-20  Score=142.97  Aligned_cols=82  Identities=24%  Similarity=0.415  Sum_probs=77.9

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      ...++|||+|||..+++++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|++|| .||+..|+|+.|.|.++
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a  101 (114)
T 2cq4_A           23 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQAS  101 (114)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEec
Confidence            34689999999999999999999999999999999999989999999999999999999999 89999999999999999


Q ss_pred             ccC
Q 043443          139 AES  141 (299)
Q Consensus       139 ~~~  141 (299)
                      +..
T Consensus       102 ~~~  104 (114)
T 2cq4_A          102 QAE  104 (114)
T ss_dssp             HHH
T ss_pred             CCC
Confidence            763

>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=99.81  E-value=9e-20  Score=140.43  Aligned_cols=78  Identities=15%  Similarity=0.187  Sum_probs=71.3

Q ss_pred             CCCCCEEEEeCCCC-CCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCc--eeCCeeEE
Q 043443           58 EQNHGSLLVRNIPL-DCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGK--RFAGREIS  134 (299)
Q Consensus        58 ~~~~~~l~V~nLp~-~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~--~l~Gr~i~  134 (299)
                      ..+.++|||+|||+ .+++++|+++|.+||.|..|.|+.+      ++||||+|++.++|+.||+.||+.  +|.|+.|.
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            34678999999999 9999999999999999999999876      589999999999999999999864  59999999


Q ss_pred             EEEcccC
Q 043443          135 VVLAAES  141 (299)
Q Consensus       135 V~~a~~~  141 (299)
                      |++++..
T Consensus        86 V~~a~~~   92 (102)
T 1x4d_A           86 VHLSQKY   92 (102)
T ss_dssp             EEEECCC
T ss_pred             EEECCCC
Confidence            9999854

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.81  E-value=2.9e-19  Score=136.68  Aligned_cols=81  Identities=25%  Similarity=0.470  Sum_probs=73.6

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      ...+.++|||+|||..+++++|+++|.+||.|   .|+.+ .++..+|||||+|.+.++|++||+.||+..|+|+.|.|+
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            45568999999999999999999999999987   45555 578899999999999999999999999999999999999


Q ss_pred             EcccC
Q 043443          137 LAAES  141 (299)
Q Consensus       137 ~a~~~  141 (299)
                      +++++
T Consensus        87 ~a~~~   91 (101)
T 2fc9_A           87 LQGPR   91 (101)
T ss_dssp             ECSSC
T ss_pred             EcCCC
Confidence            99864

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.80  E-value=3.9e-20  Score=148.59  Aligned_cols=85  Identities=26%  Similarity=0.408  Sum_probs=79.3

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeE--EEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCc----eeCC
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRD--VYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGK----RFAG  130 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~--v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~----~l~G  130 (299)
                      .+....+|||+|||+++++++|+++|.+||.|..  |.|+.++.++.++|||||+|.+. +|++||+.||+.    .|+|
T Consensus        19 ~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~g   97 (131)
T 2m2b_A           19 SENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDG   97 (131)
T ss_dssp             CSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGG
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCC
Confidence            3456789999999999999999999999999976  99999999999999999999999 999999999999    9999


Q ss_pred             eeEEEEEcccCC
Q 043443          131 REISVVLAAESR  142 (299)
Q Consensus       131 r~i~V~~a~~~~  142 (299)
                      +.|.|+++++..
T Consensus        98 r~l~V~~a~~~~  109 (131)
T 2m2b_A           98 KTINVEFAKGSK  109 (131)
T ss_dssp             CCCCCEECCCSC
T ss_pred             EEEEEEECCCCC
Confidence            999999998643

>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=99.80  E-value=3.1e-20  Score=142.65  Aligned_cols=85  Identities=33%  Similarity=0.565  Sum_probs=79.9

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      ...++|||+|||..+++++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|+.||+.|||..|+|+.|.|.++
T Consensus         6 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   85 (104)
T 1p1t_A            6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNA   85 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEET
T ss_pred             CCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeC
Confidence            34689999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             ccCCC
Q 043443          139 AESRK  143 (299)
Q Consensus       139 ~~~~~  143 (299)
                      .....
T Consensus        86 ~~~~~   90 (104)
T 1p1t_A           86 ASEKN   90 (104)
T ss_dssp             TCTTH
T ss_pred             CCccc
Confidence            86543

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.80  E-value=9.3e-19  Score=138.98  Aligned_cols=85  Identities=24%  Similarity=0.388  Sum_probs=79.8

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      ....++|||+|||..+++++|+++|.+||+|..|.|+.+. ++.++|||||+|.+.++|+.||+.||+..|+|+.|.|++
T Consensus        32 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  110 (124)
T 2kt5_A           32 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  110 (124)
T ss_dssp             CSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            3567899999999999999999999999999999999988 899999999999999999999999999999999999999


Q ss_pred             cccCCC
Q 043443          138 AAESRK  143 (299)
Q Consensus       138 a~~~~~  143 (299)
                      +.....
T Consensus       111 a~~~~~  116 (124)
T 2kt5_A          111 VASQID  116 (124)
T ss_dssp             ECCTTC
T ss_pred             eCCCCC
Confidence            987544

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.80  E-value=2.5e-19  Score=139.41  Aligned_cols=86  Identities=22%  Similarity=0.377  Sum_probs=76.4

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      ...+.++|||+|||..+++++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|++||+.| +..|+|+.|.|.
T Consensus        21 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~   99 (109)
T 2rs2_A           21 MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPK   99 (109)
T ss_dssp             -----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEE
Confidence            3445789999999999999999999999999999999999889999999999999999999999976 599999999999


Q ss_pred             EcccCCC
Q 043443          137 LAAESRK  143 (299)
Q Consensus       137 ~a~~~~~  143 (299)
                      ++.....
T Consensus       100 ~a~~~~~  106 (109)
T 2rs2_A          100 VAFPRRA  106 (109)
T ss_dssp             ECCCCCC
T ss_pred             EccCCCC
Confidence            9986543

>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=99.80  E-value=5.5e-20  Score=146.27  Aligned_cols=84  Identities=15%  Similarity=0.228  Sum_probs=76.3

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      ...+.++|||+|||+++++++|+++|.+||.|..|.++.+..++.++|||||+|.+.++|++||+ ||+..|+|+.|.|.
T Consensus        21 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~   99 (124)
T 1wel_A           21 PHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVH   99 (124)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEE
Confidence            34567899999999999999999999999999886666666789999999999999999999999 99999999999999


Q ss_pred             EcccC
Q 043443          137 LAAES  141 (299)
Q Consensus       137 ~a~~~  141 (299)
                      ++..+
T Consensus       100 ~a~~~  104 (124)
T 1wel_A          100 PITKK  104 (124)
T ss_dssp             EECHH
T ss_pred             ECCHH
Confidence            99754

>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=99.80  E-value=2.5e-19  Score=136.60  Aligned_cols=80  Identities=29%  Similarity=0.532  Sum_probs=74.0

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      ...+.++|||+|||..+++++|+++|.+||+|..|.|+.+      ++||||+|.+.++|++||+.||+..|+|+.|.|.
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            4456789999999999999999999999999999999865      6999999999999999999999999999999999


Q ss_pred             EcccCC
Q 043443          137 LAAESR  142 (299)
Q Consensus       137 ~a~~~~  142 (299)
                      +++++.
T Consensus        85 ~a~~~~   90 (99)
T 2cpj_A           85 FACHSA   90 (99)
T ss_dssp             ESSCCS
T ss_pred             EcCCCC
Confidence            998643

>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=99.80  E-value=7.1e-19  Score=135.20  Aligned_cols=81  Identities=16%  Similarity=0.194  Sum_probs=72.8

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhh--CCceeCCeeEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM--NGKRFAGREIS  134 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~l--ng~~l~Gr~i~  134 (299)
                      ...+.++|||+|||+.+++++|+++|.+||.|..|.|+.+      +|||||+|++.++|+.||+.|  ++.+|.|+.|.
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            3456789999999999999999999999999999998865      699999999999999999977  46789999999


Q ss_pred             EEEcccCCC
Q 043443          135 VVLAAESRK  143 (299)
Q Consensus       135 V~~a~~~~~  143 (299)
                      |+|++.+..
T Consensus        85 V~~a~~~~~   93 (101)
T 2cq1_A           85 IQYSNHKEL   93 (101)
T ss_dssp             EEECSCSSC
T ss_pred             EEEcCcccC
Confidence            999986544

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.80  E-value=9.3e-20  Score=131.75  Aligned_cols=75  Identities=24%  Similarity=0.373  Sum_probs=72.2

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        63 ~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      +|||+|||.++++++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|++||+ ||+..|+|+.|.|.+|
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            59999999999999999999999999999999998899999999999999999999998 9999999999999875

>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=99.80  E-value=7.8e-19  Score=137.21  Aligned_cols=86  Identities=24%  Similarity=0.432  Sum_probs=79.0

Q ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCcee------
Q 043443           55 RRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRF------  128 (299)
Q Consensus        55 ~~~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l------  128 (299)
                      ...+.+.++|||+|||..+++++|+++|.+||.|..|.|+.+. ++.++|||||+|.+.++|+.||+.|||..|      
T Consensus        19 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~   97 (114)
T 1x5o_A           19 KQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGV   97 (114)
T ss_dssp             SCCCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTS
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccc
Confidence            3455678999999999999999999999999999999999987 899999999999999999999999999999      


Q ss_pred             --CCeeEEEEEcccC
Q 043443          129 --AGREISVVLAAES  141 (299)
Q Consensus       129 --~Gr~i~V~~a~~~  141 (299)
                        .++.|.|.|+.+.
T Consensus        98 ~~~~~~l~v~~a~p~  112 (114)
T 1x5o_A           98 SAPTEPLLCKFSGPS  112 (114)
T ss_dssp             CCCSSCBEEEECCCS
T ss_pred             cCCCCceeEEccCCC
Confidence              5788999999753

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=2.8e-19  Score=140.26  Aligned_cols=83  Identities=23%  Similarity=0.385  Sum_probs=78.3

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      +.++|||+|||+++++++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|++||+. |+..|+|+.|.|.++.
T Consensus        26 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~  104 (116)
T 1x4b_A           26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAV  104 (116)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECC
Confidence            468999999999999999999999999999999999988999999999999999999999997 9999999999999998


Q ss_pred             cCCC
Q 043443          140 ESRK  143 (299)
Q Consensus       140 ~~~~  143 (299)
                      ++..
T Consensus       105 ~~~~  108 (116)
T 1x4b_A          105 AREE  108 (116)
T ss_dssp             SCCC
T ss_pred             CCcc
Confidence            7543

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=4.2e-20  Score=136.85  Aligned_cols=81  Identities=16%  Similarity=0.240  Sum_probs=75.9

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      .+.++|||+|||..+++++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|+.||+.|||..|+|+.|+|.++
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            35689999999999999999999999999999999999889999999999999999999999999999999999987765


Q ss_pred             c
Q 043443          139 A  139 (299)
Q Consensus       139 ~  139 (299)
                      .
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=5e-19  Score=130.91  Aligned_cols=78  Identities=23%  Similarity=0.339  Sum_probs=72.2

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhh-CCceeCCeeEE
Q 043443           56 RKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM-NGKRFAGREIS  134 (299)
Q Consensus        56 ~~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~l-ng~~l~Gr~i~  134 (299)
                      ..+...++|||+|||..+++++|+++|.+||.|..|.|+.+      +|||||+|.+.++|+.||+.| |+..|+|+.|.
T Consensus         7 ~~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~   80 (85)
T 2ytc_A            7 GEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLN   80 (85)
T ss_dssp             CSCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEECC
T ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEE
Confidence            34556789999999999999999999999999999999875      699999999999999999999 99999999999


Q ss_pred             EEEcc
Q 043443          135 VVLAA  139 (299)
Q Consensus       135 V~~a~  139 (299)
                      |+|++
T Consensus        81 v~~ak   85 (85)
T 2ytc_A           81 VKWGR   85 (85)
T ss_dssp             EEECC
T ss_pred             EEecC
Confidence            99974

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=4.5e-19  Score=132.81  Aligned_cols=78  Identities=23%  Similarity=0.440  Sum_probs=72.4

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      ..+.++|||+|||.++++++|+++|.+||+|..|.|+        ++||||+|.+.++|++||+.||+..|+|+.|.|++
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   76 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEA   76 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEE
Confidence            3567899999999999999999999999999999987        47999999999999999999999999999999999


Q ss_pred             cccCCC
Q 043443          138 AAESRK  143 (299)
Q Consensus       138 a~~~~~  143 (299)
                      ++.+..
T Consensus        77 a~~~~~   82 (90)
T 2dnq_A           77 SKNKSK   82 (90)
T ss_dssp             SSCCCC
T ss_pred             CCCCCC
Confidence            987543

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

Probab=99.79  E-value=4.3e-19  Score=134.86  Aligned_cols=81  Identities=27%  Similarity=0.434  Sum_probs=72.6

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      .....++|||+|||+.+++++|+++|.+||.|. +.++.+    .++|||||+|.+.++|+.||+.|||..|+|+.|.|.
T Consensus        15 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   89 (97)
T 2e5j_A           15 GAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVA   89 (97)
T ss_dssp             SSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE----TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC----CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            445678999999999999999999999999996 666543    678999999999999999999999999999999999


Q ss_pred             EcccCC
Q 043443          137 LAAESR  142 (299)
Q Consensus       137 ~a~~~~  142 (299)
                      +++++.
T Consensus        90 ~a~~~~   95 (97)
T 2e5j_A           90 LARQQR   95 (97)
T ss_dssp             ECCCCC
T ss_pred             EcCCCC
Confidence            998653

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.79  E-value=4.4e-19  Score=135.77  Aligned_cols=77  Identities=18%  Similarity=0.226  Sum_probs=71.0

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCce--eCCeeEEEE
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKR--FAGREISVV  136 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~--l~Gr~i~V~  136 (299)
                      .+..+|||+|||..+|+++|.++|.+||.|+.|.|+..      +|||||+|++.++|++||+.||+..  |.|+.|.|+
T Consensus        19 ~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~------kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~   92 (100)
T 3r27_A           19 PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVN   92 (100)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEE
Confidence            45789999999999999999999999999999999854      6999999999999999999999875  789999999


Q ss_pred             EcccC
Q 043443          137 LAAES  141 (299)
Q Consensus       137 ~a~~~  141 (299)
                      +++.+
T Consensus        93 ~S~~k   97 (100)
T 3r27_A           93 YSTSQ   97 (100)
T ss_dssp             ECSCS
T ss_pred             ecccc
Confidence            99864

>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=99.79  E-value=4e-19  Score=146.72  Aligned_cols=85  Identities=44%  Similarity=0.731  Sum_probs=80.4

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      ...++|||+|||+.+++++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|+.||+.|||..|+|+.|.|.++
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            45789999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             ccCCC
Q 043443          139 AESRK  143 (299)
Q Consensus       139 ~~~~~  143 (299)
                      ++...
T Consensus       148 ~~~~~  152 (158)
T 2kn4_A          148 RYGRP  152 (158)
T ss_dssp             CCSSC
T ss_pred             CCCCC
Confidence            86543

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=4.5e-19  Score=135.75  Aligned_cols=83  Identities=24%  Similarity=0.398  Sum_probs=75.0

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      ...+.++|||+|||..+++++|+++|.+|+   .|.++.++.++.++|||||+|.+.++|++||+.||+..|+|+.|.|+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   87 (102)
T 2fc8_A           11 RSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLD   87 (102)
T ss_dssp             SSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            456678999999999999999999999874   56677777788999999999999999999999999999999999999


Q ss_pred             EcccCC
Q 043443          137 LAAESR  142 (299)
Q Consensus       137 ~a~~~~  142 (299)
                      +++++.
T Consensus        88 ~a~~~~   93 (102)
T 2fc8_A           88 WAKPKG   93 (102)
T ss_dssp             ECCCCC
T ss_pred             EecCCC
Confidence            998643

>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=99.79  E-value=5.9e-19  Score=136.38  Aligned_cols=80  Identities=19%  Similarity=0.180  Sum_probs=71.8

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCc--eeCCeeEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGK--RFAGREISV  135 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~--~l~Gr~i~V  135 (299)
                      ..+..+|||+|||+.+++++|+++|.+||.|..|.|+.+      +|||||+|++.++|++||+.||+.  .|+|+.|.|
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V   85 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFF   85 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            455789999999999999999999999999999998864      699999999999999999988764  599999999


Q ss_pred             EEcccCCC
Q 043443          136 VLAAESRK  143 (299)
Q Consensus       136 ~~a~~~~~  143 (299)
                      +|++.+..
T Consensus        86 ~~a~~~~~   93 (104)
T 1wex_A           86 NYSTSKRI   93 (104)
T ss_dssp             EECSSSSC
T ss_pred             EEccCccc
Confidence            99986543

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=8.1e-19  Score=131.96  Aligned_cols=79  Identities=30%  Similarity=0.505  Sum_probs=72.8

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      .....++|||+|||..+++++|+++|.+||.|..|.|+.        +||||+|.+.++|++||+.||+..|+|+.|.|+
T Consensus         6 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   77 (92)
T 2dgt_A            6 SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQ   77 (92)
T ss_dssp             CCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS--------SEEEEEESCHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Confidence            445678999999999999999999999999999999984        499999999999999999999999999999999


Q ss_pred             EcccCCC
Q 043443          137 LAAESRK  143 (299)
Q Consensus       137 ~a~~~~~  143 (299)
                      +++++..
T Consensus        78 ~a~~~~~   84 (92)
T 2dgt_A           78 LSTSRLR   84 (92)
T ss_dssp             ESSCCCS
T ss_pred             EccCCCC
Confidence            9986543

>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=99.79  E-value=1.2e-19  Score=138.96  Aligned_cols=82  Identities=22%  Similarity=0.399  Sum_probs=74.8

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCC-CCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDY-YTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~-~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      ....++|||+|||.++++++|+++|.+|| |..|.|+.++ .++.++|||||+|.+.++|++|| .|||..|+|+.|.|+
T Consensus        16 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V~   93 (100)
T 2j76_E           16 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVD   93 (100)
T ss_dssp             ----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCCE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEEE
Confidence            45578999999999999999999999999 9999999987 68999999999999999999999 899999999999999


Q ss_pred             EcccC
Q 043443          137 LAAES  141 (299)
Q Consensus       137 ~a~~~  141 (299)
                      +++..
T Consensus        94 ~a~~~   98 (100)
T 2j76_E           94 VADQA   98 (100)
T ss_dssp             ECCCS
T ss_pred             eccCC
Confidence            99764

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.79  E-value=3.3e-19  Score=141.43  Aligned_cols=81  Identities=25%  Similarity=0.515  Sum_probs=77.2

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      +.++|||+|||..+++++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|+.|| .||+..|+|+.|.|++++
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~  113 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKR  113 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            4689999999999999999999999999999999999889999999999999999999999 799999999999999997


Q ss_pred             cC
Q 043443          140 ES  141 (299)
Q Consensus       140 ~~  141 (299)
                      ..
T Consensus       114 ~~  115 (124)
T 2jwn_A          114 TN  115 (124)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.79  E-value=2.8e-19  Score=139.81  Aligned_cols=77  Identities=17%  Similarity=0.203  Sum_probs=71.4

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCC-CEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFG-VVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G-~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      ..++|||+|||+++++++|+++|.+|| +|..|.|+.+    .++|||||+|.+.++|++||+.|||.+|+|+.|.|+++
T Consensus        27 ~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~----~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a  102 (111)
T 2jvr_A           27 KRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR----DFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERD  102 (111)
T ss_dssp             CCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC----SSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC----CCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            457999999999999999999999999 9999988643    46899999999999999999999999999999999998


Q ss_pred             cc
Q 043443          139 AE  140 (299)
Q Consensus       139 ~~  140 (299)
                      +.
T Consensus       103 ~~  104 (111)
T 2jvr_A          103 DN  104 (111)
T ss_dssp             CC
T ss_pred             CC
Confidence            74

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=4e-19  Score=138.21  Aligned_cols=83  Identities=31%  Similarity=0.501  Sum_probs=76.6

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      .....++|||+|||..+++++|+++|.+||.|..|.|+.+.  +.++|||||+|.+.++|++||+.|||..|+|+.|.|+
T Consensus        25 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  102 (109)
T 2err_A           25 NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN  102 (109)
T ss_dssp             CTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            44567899999999999999999999999999999999874  3488999999999999999999999999999999999


Q ss_pred             EcccC
Q 043443          137 LAAES  141 (299)
Q Consensus       137 ~a~~~  141 (299)
                      +++.+
T Consensus       103 ~a~~~  107 (109)
T 2err_A          103 NATAR  107 (109)
T ss_dssp             ECCCS
T ss_pred             ECCCC
Confidence            99764

>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=99.79  E-value=4.4e-19  Score=140.15  Aligned_cols=81  Identities=16%  Similarity=0.253  Sum_probs=73.4

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCC--ceeCCeeEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNG--KRFAGREISV  135 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng--~~l~Gr~i~V  135 (299)
                      ..+..+|||+|||+.+++++|+++|++||.|+.|.|+.+      +|||||+|++.++|++||+.|++  .+|.|+.|.|
T Consensus        28 ~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V  101 (119)
T 2ad9_A           28 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI  101 (119)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEE
Confidence            345789999999999999999999999999999999876      69999999999999999999884  6899999999


Q ss_pred             EEcccCCCC
Q 043443          136 VLAAESRKR  144 (299)
Q Consensus       136 ~~a~~~~~~  144 (299)
                      ++++.+...
T Consensus       102 ~~a~~k~~~  110 (119)
T 2ad9_A          102 QFSNHKELK  110 (119)
T ss_dssp             EECSSSSCC
T ss_pred             EEccCCCCC
Confidence            999875543

>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=99.79  E-value=1.9e-19  Score=158.24  Aligned_cols=82  Identities=15%  Similarity=0.246  Sum_probs=77.6

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCC--CEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFG--VVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G--~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      ..++|||+||+++||+++|+++|.+||  .|+.|.|+.++.+++++|||||+|.+.++|++||+.||+++|+|+.|.|.+
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            567999999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             cccC
Q 043443          138 AAES  141 (299)
Q Consensus       138 a~~~  141 (299)
                      ++..
T Consensus       147 a~~~  150 (229)
T 3q2s_C          147 VNKQ  150 (229)
T ss_dssp             CCHH
T ss_pred             CCCC
Confidence            9754

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=9.3e-19  Score=131.10  Aligned_cols=78  Identities=32%  Similarity=0.517  Sum_probs=72.1

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      ...+.++|||+|||..+++++|+++|.+||.|..|.|+.        +||||+|.+.++|+.||+.||+..|+|+.|.|.
T Consensus         5 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   76 (90)
T 2dnp_A            5 SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVE   76 (90)
T ss_dssp             SSCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            345678999999999999999999999999999999984        499999999999999999999999999999999


Q ss_pred             EcccCC
Q 043443          137 LAAESR  142 (299)
Q Consensus       137 ~a~~~~  142 (299)
                      ++++..
T Consensus        77 ~a~~~~   82 (90)
T 2dnp_A           77 LSTKGQ   82 (90)
T ss_dssp             ESCCCC
T ss_pred             ECCCCC
Confidence            998653

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.78  E-value=1.2e-19  Score=131.65  Aligned_cols=76  Identities=24%  Similarity=0.437  Sum_probs=73.3

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           62 GSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        62 ~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      ++|||+|||.++++++|+++|++||+|..|.|+.++.++.++|||||+|.+.++|++||+.|+ ..|+|+.|.|++|
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            479999999999999999999999999999999998899999999999999999999999999 9999999999987

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.78  E-value=4.9e-19  Score=136.72  Aligned_cols=81  Identities=20%  Similarity=0.437  Sum_probs=74.9

Q ss_pred             CCCCEEEEeCCCCCC------CHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCe-
Q 043443           59 QNHGSLLVRNIPLDC------RPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGR-  131 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~------te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr-  131 (299)
                      ...++|||+|||+.+      ++++|+++|.+||.|..|.|+  ..++.++|||||+|.+.++|+.||..|||..|+|+ 
T Consensus        13 ~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~   90 (105)
T 2nlw_A           13 GIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQH   90 (105)
T ss_dssp             SCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTC
T ss_pred             CCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCc
Confidence            346899999999999      789999999999999999988  35789999999999999999999999999999998 


Q ss_pred             eEEEEEcccC
Q 043443          132 EISVVLAAES  141 (299)
Q Consensus       132 ~i~V~~a~~~  141 (299)
                      .|.|.++...
T Consensus        91 ~l~V~~a~~~  100 (105)
T 2nlw_A           91 TFRVNLFTDF  100 (105)
T ss_dssp             EEEEECSCCC
T ss_pred             eEEEEEcchH
Confidence            9999999754

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.78  E-value=6.3e-19  Score=130.96  Aligned_cols=73  Identities=21%  Similarity=0.204  Sum_probs=69.3

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      ..-|||+||++.+|+++|+++|.+||+|..|.|+.      ++|||||+|.+.++|+.||+.||+..|.|++|.|++|.
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            46899999999999999999999999999999976      47999999999999999999999999999999999984

>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=99.78  E-value=7.7e-20  Score=148.60  Aligned_cols=83  Identities=18%  Similarity=0.210  Sum_probs=74.5

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      .....++|||+|||+++|+++|+++|++|| |+.|.|+.++. ++++|||||+|++.++|++|| .||+.+|+|+.|.|.
T Consensus        42 ~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~  118 (139)
T 2hgn_A           42 QSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELF  118 (139)
T ss_dssp             ---CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEE
Confidence            345678999999999999999999999999 77999999975 999999999999999999999 689999999999999


Q ss_pred             EcccCC
Q 043443          137 LAAESR  142 (299)
Q Consensus       137 ~a~~~~  142 (299)
                      ++....
T Consensus       119 ~a~~~~  124 (139)
T 2hgn_A          119 LNSTTG  124 (139)
T ss_dssp             ECCCSC
T ss_pred             ECCCCC
Confidence            987644

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=6.4e-19  Score=137.31  Aligned_cols=79  Identities=27%  Similarity=0.346  Sum_probs=73.3

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      .+.++|||+|||+++++++|+++|.+| .|..|.|+.++. +.++|||||+|.+.++|++|| .||+..|+|+.|.|..+
T Consensus        14 ~~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a   90 (109)
T 2dnn_A           14 PDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPA   90 (109)
T ss_dssp             HHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEEC
Confidence            345799999999999999999999999 899999999875 899999999999999999999 59999999999999888


Q ss_pred             cc
Q 043443          139 AE  140 (299)
Q Consensus       139 ~~  140 (299)
                      ..
T Consensus        91 ~~   92 (109)
T 2dnn_A           91 TE   92 (109)
T ss_dssp             CH
T ss_pred             Cc
Confidence            64

>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=99.78  E-value=9e-20  Score=136.49  Aligned_cols=81  Identities=30%  Similarity=0.489  Sum_probs=74.1

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcccC
Q 043443           62 GSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAES  141 (299)
Q Consensus        62 ~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~~  141 (299)
                      ++|||+|||..+++++|+++|.+||+|..|.|+.++.++.++|||||+|.+.+ |+.||..|||..|+|+.|.|++|...
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            58999999999999999999999999999999999889999999999999999 99999999999999999999999865


Q ss_pred             CC
Q 043443          142 RK  143 (299)
Q Consensus       142 ~~  143 (299)
                      ..
T Consensus        81 ~~   82 (90)
T 2ki2_A           81 KS   82 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            43

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=4.2e-18  Score=129.75  Aligned_cols=77  Identities=34%  Similarity=0.460  Sum_probs=71.0

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcC--CCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERF--GVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV  135 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~--G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V  135 (299)
                      ....++|||+|||+.+++++|+++|.+|  |.|..|.++        ++||||+|.+.++|++||+.||+..|+|+.|.|
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            3457899999999999999999999999  999999876        479999999999999999999999999999999


Q ss_pred             EEcccCC
Q 043443          136 VLAAESR  142 (299)
Q Consensus       136 ~~a~~~~  142 (299)
                      .++++..
T Consensus        84 ~~a~~~~   90 (99)
T 2cpd_A           84 TLAKPVD   90 (99)
T ss_dssp             ECCCCCC
T ss_pred             EECCCCC
Confidence            9998643

>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=99.78  E-value=1.2e-18  Score=135.16  Aligned_cols=79  Identities=22%  Similarity=0.384  Sum_probs=73.7

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      ....++|||+|||..+++++|+++|.+||.|..|.|+.+      ++||||+|.+.++|+.||+.||+..|+|+.|.|.|
T Consensus        22 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   95 (109)
T 1x4g_A           22 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYW   95 (109)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEe
Confidence            445789999999999999999999999999999999876      69999999999999999999999999999999999


Q ss_pred             cccCC
Q 043443          138 AAESR  142 (299)
Q Consensus       138 a~~~~  142 (299)
                      ++...
T Consensus        96 a~~~~  100 (109)
T 1x4g_A           96 GKESP  100 (109)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            98643

>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=99.77  E-value=3.6e-19  Score=142.17  Aligned_cols=81  Identities=30%  Similarity=0.437  Sum_probs=73.4

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEe--EEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVR--DVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREIS  134 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~--~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~  134 (299)
                      .....++|||+|||+++|+++|+++|.+| .|+  .|.|+.++. |.++|||||+|.+.++|++||+. ++..|+|+.|.
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-GKITGEAFVQFASQELAEKALGK-HKERIGHRYIE  114 (126)
T ss_dssp             CSSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHHH-CCCEECCEEEE
Confidence            34567899999999999999999999999 677  899999876 99999999999999999999984 77999999999


Q ss_pred             EEEccc
Q 043443          135 VVLAAE  140 (299)
Q Consensus       135 V~~a~~  140 (299)
                      |.++..
T Consensus       115 V~~a~~  120 (126)
T 2hgm_A          115 VFKSSQ  120 (126)
T ss_dssp             CEEECH
T ss_pred             EEECCH
Confidence            998864

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.77  E-value=1.5e-19  Score=138.29  Aligned_cols=83  Identities=20%  Similarity=0.273  Sum_probs=75.3

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      ...++|||+|||.++++++|+++|.+||.|.. .++.+..++.++|||||+|.+.++|++||+ ||+..|.|+.|.|.++
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            45789999999999999999999999999887 566666778899999999999999999999 9999999999999999


Q ss_pred             ccCCC
Q 043443          139 AESRK  143 (299)
Q Consensus       139 ~~~~~  143 (299)
                      +++..
T Consensus        93 ~~~~~   97 (101)
T 1fj7_A           93 KGRDG   97 (101)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            86543

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

Probab=99.77  E-value=1.4e-18  Score=131.47  Aligned_cols=80  Identities=24%  Similarity=0.312  Sum_probs=72.2

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEE-EeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDV-YLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v-~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      ....++|||+|||+.+++++|+++|.+||.|..| .|+.++.+    +.|||+|.+.++|+.||+.|||..|+|+.|.|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~----~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~   87 (96)
T 2e44_A           12 RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET----AVVNVTYSSKDQARQALDKLNGFQLENFTLKVA   87 (96)
T ss_dssp             CCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSS----EEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEE
T ss_pred             CCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCC----CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            3456899999999999999999999999999999 58877543    349999999999999999999999999999999


Q ss_pred             EcccC
Q 043443          137 LAAES  141 (299)
Q Consensus       137 ~a~~~  141 (299)
                      ++.++
T Consensus        88 ~a~~~   92 (96)
T 2e44_A           88 YIPDE   92 (96)
T ss_dssp             ECCCC
T ss_pred             EcCcc
Confidence            99875

>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=99.77  E-value=2e-19  Score=140.66  Aligned_cols=82  Identities=23%  Similarity=0.391  Sum_probs=73.2

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEe----EEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVR----DVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREI  133 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~----~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i  133 (299)
                      ..+.++|||+|||..+++++|+++|.+||.|.    .+.+.    ++.++|||||+|.+.++|+.||+.||+..|+|+.|
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~----~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l   97 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM----TGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKIL   97 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEE----CSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcC----CCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEE
Confidence            34578999999999999999999999999984    44444    67889999999999999999999999999999999


Q ss_pred             EEEEcccCCC
Q 043443          134 SVVLAAESRK  143 (299)
Q Consensus       134 ~V~~a~~~~~  143 (299)
                      .|.+++....
T Consensus        98 ~v~~a~~~~~  107 (115)
T 2cpx_A           98 VIEFGKNKKQ  107 (115)
T ss_dssp             EEEECCCCSC
T ss_pred             EEEEccCCCC
Confidence            9999987543

>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=99.77  E-value=6.8e-19  Score=137.43  Aligned_cols=77  Identities=27%  Similarity=0.466  Sum_probs=71.5

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      ...++|||+|||+.+++++|+++|.+||.|..|.|+..      ++||||+|.+.++|+.||+.|||..|+|+.|.|+|+
T Consensus         8 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   81 (111)
T 1whx_A            8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG------GITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWA   81 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCSS------SSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            34679999999999999999999999999999998753      689999999999999999999999999999999999


Q ss_pred             ccC
Q 043443          139 AES  141 (299)
Q Consensus       139 ~~~  141 (299)
                      ...
T Consensus        82 ~~~   84 (111)
T 1whx_A           82 PIG   84 (111)
T ss_dssp             ETT
T ss_pred             CCC
Confidence            754

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

Probab=99.77  E-value=1.6e-18  Score=138.64  Aligned_cols=81  Identities=19%  Similarity=0.313  Sum_probs=73.3

Q ss_pred             CCCCEEEEeCCCCCCCHHHHH----HHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEE
Q 043443           59 QNHGSLLVRNIPLDCRPEELR----APFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREIS  134 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~----~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~  134 (299)
                      .+.++|||+|||+.+++++|+    ++|++||.|..|.|..   ++.++|||||+|.+.++|+.||..|||..|.|+.|.
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~  103 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLV  103 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEE
Confidence            456899999999999999876    6999999999998864   578899999999999999999999999999999999


Q ss_pred             EEEcccCC
Q 043443          135 VVLAAESR  142 (299)
Q Consensus       135 V~~a~~~~  142 (299)
                      |.|++.+.
T Consensus       104 V~~a~~~~  111 (127)
T 2a3j_A          104 ITFSETPQ  111 (127)
T ss_dssp             EEECCCCC
T ss_pred             EEEccCcc
Confidence            99998643

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

Probab=99.77  E-value=1.5e-18  Score=134.81  Aligned_cols=79  Identities=37%  Similarity=0.590  Sum_probs=72.3

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      .+...++|||+|||.++++++|+++|.+||.|..|.|+        +|||||+|.+.++|++||+.|||..|+|+.|.|.
T Consensus        27 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   98 (108)
T 2jvo_A           27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVV   98 (108)
T ss_dssp             -CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            44567899999999999999999999999999999987        5899999999999999999999999999999999


Q ss_pred             EcccCCC
Q 043443          137 LAAESRK  143 (299)
Q Consensus       137 ~a~~~~~  143 (299)
                      +++....
T Consensus        99 ~a~~~~~  105 (108)
T 2jvo_A           99 YSKLPAK  105 (108)
T ss_dssp             SCSCCC-
T ss_pred             EecCCCC
Confidence            9986543

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.76  E-value=6.5e-19  Score=129.43  Aligned_cols=72  Identities=21%  Similarity=0.507  Sum_probs=67.5

Q ss_pred             CEEEEeCCCCCC------CHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCe-eEE
Q 043443           62 GSLLVRNIPLDC------RPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGR-EIS  134 (299)
Q Consensus        62 ~~l~V~nLp~~~------te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr-~i~  134 (299)
                      ++|||+|||..+      ++++|+++|.+||.|..|.|+  +.++.++|||||+|.+.++|++||+.|||..|+|+ .|.
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            689999999999      789999999999999999987  35789999999999999999999999999999999 887


Q ss_pred             E
Q 043443          135 V  135 (299)
Q Consensus       135 V  135 (299)
                      |
T Consensus        80 V   80 (81)
T 2krb_A           80 V   80 (81)
T ss_dssp             C
T ss_pred             e
Confidence            6

>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=99.76  E-value=5.2e-19  Score=137.02  Aligned_cols=82  Identities=13%  Similarity=0.191  Sum_probs=76.3

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCC---EeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGV---VRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREI  133 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~---I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i  133 (299)
                      .....++|||+|||+++|+++|+++|..||.   |..|.|+.++. +.++|||||+|.+.++|++||+ ||+..|+|+.|
T Consensus         7 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i   84 (107)
T 2lmi_A            7 EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMGQRYV   84 (107)
T ss_dssp             CCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCC
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEE
Confidence            3456789999999999999999999999998   89999999876 9999999999999999999999 99999999999


Q ss_pred             EEEEccc
Q 043443          134 SVVLAAE  140 (299)
Q Consensus       134 ~V~~a~~  140 (299)
                      .|.++..
T Consensus        85 ~V~~a~~   91 (107)
T 2lmi_A           85 EVYEINN   91 (107)
T ss_dssp             CCEECCH
T ss_pred             EEEECCH
Confidence            9999875

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.76  E-value=1.3e-18  Score=132.93  Aligned_cols=76  Identities=21%  Similarity=0.309  Sum_probs=71.0

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      ...++|||+|||..+++++|+++|.+||.|..|.|+.      .+|||||+|.+.++|+.||..||+..|+|+.|.|.|+
T Consensus        25 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   98 (101)
T 2la4_A           25 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP------EKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWG   98 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBC
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEec
Confidence            3468999999999999999999999999999999984      3799999999999999999999999999999999998


Q ss_pred             cc
Q 043443          139 AE  140 (299)
Q Consensus       139 ~~  140 (299)
                      ++
T Consensus        99 ~~  100 (101)
T 2la4_A           99 KE  100 (101)
T ss_dssp             CC
T ss_pred             cC
Confidence            75

>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=99.76  E-value=1.5e-18  Score=130.72  Aligned_cols=77  Identities=21%  Similarity=0.345  Sum_probs=69.0

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCC-EeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCC-ceeCCeeEEEE
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGV-VRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNG-KRFAGREISVV  136 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~-I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng-~~l~Gr~i~V~  136 (299)
                      ...++|||+|||.++++++|+++|.+||. |..+.+.       .+|||||+|.+.++|++||+.||+ ..|+|+.|.|+
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            45689999999999999999999999999 6655553       268999999999999999999999 99999999999


Q ss_pred             EcccCC
Q 043443          137 LAAESR  142 (299)
Q Consensus       137 ~a~~~~  142 (299)
                      +++++.
T Consensus        79 ~a~~~~   84 (93)
T 2cqh_A           79 YSVSKK   84 (93)
T ss_dssp             ECCCCC
T ss_pred             EccCcc
Confidence            998653

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=8.4e-18  Score=127.68  Aligned_cols=78  Identities=27%  Similarity=0.427  Sum_probs=70.7

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      ...+.++|||+||  ++++++|+++|.+||+|..|.|.      ..+|||||+|.+.++|++||+.||+..|+|+.|.|.
T Consensus        11 ~~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~   82 (97)
T 1x5p_A           11 APRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVN   82 (97)
T ss_dssp             CCCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            3446789999996  89999999999999999999985      347999999999999999999999999999999999


Q ss_pred             EcccCC
Q 043443          137 LAAESR  142 (299)
Q Consensus       137 ~a~~~~  142 (299)
                      |+..+.
T Consensus        83 ~a~~~~   88 (97)
T 1x5p_A           83 IARKQP   88 (97)
T ss_dssp             CCSSCC
T ss_pred             ECCCCC
Confidence            998654

>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=99.76  E-value=4.4e-18  Score=129.59  Aligned_cols=77  Identities=19%  Similarity=0.421  Sum_probs=70.9

Q ss_pred             CCCCCCEEEEeCCCC-CCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEE
Q 043443           57 KEQNHGSLLVRNIPL-DCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV  135 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~-~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V  135 (299)
                      ...+.++|||+|||. .+++++|+++|.+||.|..|.|.        +|||||+|.+.++|++||+.|||..|+|+.|.|
T Consensus        18 ~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V   89 (97)
T 2xnq_A           18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLIL   89 (97)
T ss_dssp             -CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEE
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            344678999999998 99999999999999999999884        589999999999999999999999999999999


Q ss_pred             EEcccC
Q 043443          136 VLAAES  141 (299)
Q Consensus       136 ~~a~~~  141 (299)
                      ++++..
T Consensus        90 ~~a~~~   95 (97)
T 2xnq_A           90 EVSSSN   95 (97)
T ss_dssp             EECCCC
T ss_pred             EecCCC
Confidence            999753

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.76  E-value=8.9e-19  Score=133.93  Aligned_cols=76  Identities=32%  Similarity=0.589  Sum_probs=71.7

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcccC
Q 043443           62 GSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAES  141 (299)
Q Consensus        62 ~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~~  141 (299)
                      ++|||+|||.++++++|+++|++||+|..|.|+.+     ++|||||+|.+.++|++||+.||+..|+|+.|.|.+++..
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   75 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGM   75 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCC
Confidence            58999999999999999999999999999999876     5799999999999999999999999999999999999865


Q ss_pred             C
Q 043443          142 R  142 (299)
Q Consensus       142 ~  142 (299)
                      .
T Consensus        76 ~   76 (101)
T 2hvz_A           76 P   76 (101)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.76  E-value=1.4e-18  Score=131.67  Aligned_cols=84  Identities=25%  Similarity=0.438  Sum_probs=75.1

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHH----HHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCee
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELR----APFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGRE  132 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~----~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~  132 (299)
                      ...+.++|||+|||..+++++|+    ++|.+||.|..|.|+.   ++.++|||||+|.+.++|+.||+.|||..|+|+.
T Consensus         4 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   80 (97)
T 1nu4_A            4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKP   80 (97)
T ss_dssp             --CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcE
Confidence            34567899999999999999999    9999999999998873   4567899999999999999999999999999999


Q ss_pred             EEEEEcccCCC
Q 043443          133 ISVVLAAESRK  143 (299)
Q Consensus       133 i~V~~a~~~~~  143 (299)
                      |.|+++++...
T Consensus        81 l~v~~a~~~~~   91 (97)
T 1nu4_A           81 MRIQYAKTDSD   91 (97)
T ss_dssp             CEEEECSSCCT
T ss_pred             EEEEEccCCCc
Confidence            99999987543

>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=99.76  E-value=8e-19  Score=137.23  Aligned_cols=80  Identities=19%  Similarity=0.275  Sum_probs=71.6

Q ss_pred             CCCCCCEEEEeCCCCC-CCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCC--ceeCCeeE
Q 043443           57 KEQNHGSLLVRNIPLD-CRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNG--KRFAGREI  133 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~-~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng--~~l~Gr~i  133 (299)
                      ...+.++|||+|||++ +++++|+++|.+||+|..|.|+..      +|||||+|++.++|+.||+.||+  .+|.|+.|
T Consensus        21 ~~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l   94 (112)
T 1x4f_A           21 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCV   94 (112)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCC
T ss_pred             cCCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEE
Confidence            3456789999999998 999999999999999999999754      69999999999999999998864  56999999


Q ss_pred             EEEEcccCC
Q 043443          134 SVVLAAESR  142 (299)
Q Consensus       134 ~V~~a~~~~  142 (299)
                      .|++++...
T Consensus        95 ~V~~a~~~~  103 (112)
T 1x4f_A           95 KVDLSEKYK  103 (112)
T ss_dssp             EEEEECSCS
T ss_pred             EEEECcccc
Confidence            999998643

>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=99.76  E-value=5e-19  Score=127.76  Aligned_cols=75  Identities=24%  Similarity=0.391  Sum_probs=71.6

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        63 ~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      +|||+|||..+++++|+++|.+||+|..|.|+.++.++.++|||||+|.+.++|++||+ +++..|+|+.|.|.+|
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            59999999999999999999999999999999998899999999999999999999998 4899999999999875

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=3.8e-18  Score=128.85  Aligned_cols=79  Identities=22%  Similarity=0.268  Sum_probs=69.5

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      .....+|||+|||+++++++|+++|.+||.|..|  +.++.++.   ||||+|.+.++|++||+ ||+..|+|+.|.|.+
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  44444544   99999999999999999 999999999999998


Q ss_pred             cccCC
Q 043443          138 AAESR  142 (299)
Q Consensus       138 a~~~~  142 (299)
                      +....
T Consensus        79 a~~~~   83 (94)
T 2e5g_A           79 REQKE   83 (94)
T ss_dssp             SCCSC
T ss_pred             CCcCC
Confidence            87543

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=9.6e-19  Score=139.21  Aligned_cols=81  Identities=22%  Similarity=0.293  Sum_probs=73.8

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCE----eEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVV----RDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREI  133 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I----~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i  133 (299)
                      ..+.++|||+|||+++|+++|++||.+||.|    ..|.|+.+. +++++|||||+|.+.++|++||+. |++.|+|+.|
T Consensus        20 ~~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~-~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i   97 (123)
T 2dha_A           20 KENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP-DGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYI   97 (123)
T ss_dssp             CCSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECT-TSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECC-CCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEE
Confidence            3567899999999999999999999999976    689898884 899999999999999999999996 9999999999


Q ss_pred             EEEEccc
Q 043443          134 SVVLAAE  140 (299)
Q Consensus       134 ~V~~a~~  140 (299)
                      .|..+..
T Consensus        98 ~V~~a~~  104 (123)
T 2dha_A           98 ELFRSTA  104 (123)
T ss_dssp             CCEEECH
T ss_pred             EEEECCH
Confidence            9998864

>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=99.75  E-value=4e-18  Score=133.32  Aligned_cols=80  Identities=26%  Similarity=0.495  Sum_probs=74.1

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      ...++|||+|||..+++++|+++|.+||.|..|.|+.+   +..+|||||+|.+.++|+.||+.|||..|+|+.|.|.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   82 (115)
T 3lqv_A            6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYY   82 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEe
Confidence            45689999999999999999999999999999999865   455899999999999999999999999999999999999


Q ss_pred             ccC
Q 043443          139 AES  141 (299)
Q Consensus       139 ~~~  141 (299)
                      .+.
T Consensus        83 ~~~   85 (115)
T 3lqv_A           83 NAN   85 (115)
T ss_dssp             CHH
T ss_pred             cCC
Confidence            853

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.75  E-value=2.2e-18  Score=130.78  Aligned_cols=78  Identities=19%  Similarity=0.406  Sum_probs=70.8

Q ss_pred             CCCCCCEEEEeCCCC-CCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEE
Q 043443           57 KEQNHGSLLVRNIPL-DCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV  135 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~-~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V  135 (299)
                      ...+.++|||+|||+ .+++++|+++|.+||.|..|.|.        +|||||+|.+.++|+.||+.||+..|.|+.|.|
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 99999999999999999999985        589999999999999999999999999999999


Q ss_pred             EEcccCC
Q 043443          136 VLAAESR  142 (299)
Q Consensus       136 ~~a~~~~  142 (299)
                      ++++...
T Consensus        78 ~~a~~~~   84 (96)
T 2kvi_A           78 EVSSSNA   84 (96)
T ss_dssp             EEEECCC
T ss_pred             EEcCcCC
Confidence            9998654

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.61  E-value=6.9e-20  Score=143.86  Aligned_cols=85  Identities=27%  Similarity=0.461  Sum_probs=79.7

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeE--------EEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeC
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRD--------VYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFA  129 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~--------v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~  129 (299)
                      ..+.++|||+|||..+++++|+++|.+||.|..        |.|+.++.++.++|||||+|.+.++|++||+.||+..|+
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            456789999999999999999999999999998        889998888999999999999999999999999999999


Q ss_pred             CeeEEEEEcccCC
Q 043443          130 GREISVVLAAESR  142 (299)
Q Consensus       130 Gr~i~V~~a~~~~  142 (299)
                      |+.|.|.+++.+.
T Consensus        84 g~~l~V~~a~~~~   96 (116)
T 2lcw_A           84 GNPIKVSFATRRA   96 (116)
Confidence            9999999998654

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.75  E-value=1.6e-18  Score=131.24  Aligned_cols=81  Identities=25%  Similarity=0.437  Sum_probs=72.8

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      .+.+.++|||+|||..+++++|+++|.+||.|..|     ..++.++|||||+|.+.++|+.||+.||+..|+|+.|.|.
T Consensus        12 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   86 (96)
T 1fjc_A           12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLY   86 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34567899999999999999999999999988766     2367889999999999999999999999999999999999


Q ss_pred             EcccCC
Q 043443          137 LAAESR  142 (299)
Q Consensus       137 ~a~~~~  142 (299)
                      ++.++.
T Consensus        87 ~a~~~~   92 (96)
T 1fjc_A           87 YTGEKG   92 (96)
T ss_dssp             ECSSSC
T ss_pred             EcCCCC
Confidence            997643

>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=99.75  E-value=4.1e-18  Score=132.39  Aligned_cols=74  Identities=23%  Similarity=0.470  Sum_probs=69.4

Q ss_pred             CCCEEEEeCCCCC-CCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           60 NHGSLLVRNIPLD-CRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        60 ~~~~l~V~nLp~~-~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      ..++|||+|||+. +++++|+++|.+||.|..|.|.        ++||||+|.+.++|+.||+.||+..|+|+.|.|+++
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 INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH--------KGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMA   97 (110)
T ss_dssp             CSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEEE--------TTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEES
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            4589999999999 9999999999999999999982        689999999999999999999999999999999999


Q ss_pred             ccC
Q 043443          139 AES  141 (299)
Q Consensus       139 ~~~  141 (299)
                      +..
T Consensus        98 ~~~  100 (110)
T 1wf1_A           98 GEP  100 (110)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            753

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.74  E-value=7.3e-18  Score=145.99  Aligned_cols=84  Identities=23%  Similarity=0.352  Sum_probs=77.9

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      ..+.++|||+|||+++|+++|+++|++||+|+.|.|+.++.++.++|||||+|.+.++|+.||+.||+..+.|+.|.|.+
T Consensus        12 ~~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~   91 (213)
T 4f02_A           12 SYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMW   91 (213)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccccc
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccC
Q 043443          138 AAES  141 (299)
Q Consensus       138 a~~~  141 (299)
                      +...
T Consensus        92 ~~~~   95 (213)
T 4f02_A           92 SQRD   95 (213)
T ss_dssp             CCCC
T ss_pred             cccc
Confidence            8653

>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=99.74  E-value=1.4e-18  Score=141.27  Aligned_cols=86  Identities=22%  Similarity=0.336  Sum_probs=73.1

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEE--eccC---CCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeE
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVY--LPKD---YYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREI  133 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~--i~~d---~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i  133 (299)
                      .+.++|||+|||+.+++++|+++|.+||.|..|.  ++.+   ..++.++|||||+|.+.++|+.||..|||..|.|+.|
T Consensus        43 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l  122 (143)
T 3egn_A           43 EPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPM  122 (143)
T ss_dssp             SCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcEE
Confidence            4568999999999999999999999999987641  1111   2367889999999999999999999999999999999


Q ss_pred             EEEEcccCCCC
Q 043443          134 SVVLAAESRKR  144 (299)
Q Consensus       134 ~V~~a~~~~~~  144 (299)
                      .|.+++.....
T Consensus       123 ~V~~a~~~~~~  133 (143)
T 3egn_A          123 VVQFARSARPK  133 (143)
T ss_dssp             EEEECCCSCC-
T ss_pred             EEEECCCCCCc
Confidence            99999865443

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.73  E-value=2.3e-18  Score=131.84  Aligned_cols=81  Identities=23%  Similarity=0.450  Sum_probs=75.9

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      ...++|||+|||..+++++|+++|.+||.|..|.|+.++ ++.++|||||+|.+.++|++||+  ++..|+|+.|.|.++
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a   83 (102)
T 2xs2_A            7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPA   83 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEEC
Confidence            456899999999999999999999999999999999998 89999999999999999999998  999999999999999


Q ss_pred             ccCC
Q 043443          139 AESR  142 (299)
Q Consensus       139 ~~~~  142 (299)
                      ..+.
T Consensus        84 ~~~~   87 (102)
T 2xs2_A           84 IRKQ   87 (102)
T ss_dssp             EECC
T ss_pred             CcCc
Confidence            8643

>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=99.73  E-value=6.8e-18  Score=132.17  Aligned_cols=77  Identities=18%  Similarity=0.333  Sum_probs=70.1

Q ss_pred             CCCCCEEEE--eCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCcee-----CC
Q 043443           58 EQNHGSLLV--RNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRF-----AG  130 (299)
Q Consensus        58 ~~~~~~l~V--~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l-----~G  130 (299)
                      ..++.+|||  +||++.+++++|+++|++||+|..|.|+.+      +|||||+|.+.++|++||+.|||.+|     .|
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            345789999  779999999999999999999999988753      68999999999999999999999998     68


Q ss_pred             eeEEEEEccc
Q 043443          131 REISVVLAAE  140 (299)
Q Consensus       131 r~i~V~~a~~  140 (299)
                      ..|.|.++..
T Consensus        96 ~~l~v~~a~~  105 (114)
T 2cq2_A           96 ITLYLNFVEK  105 (114)
T ss_dssp             EECEEEEESC
T ss_pred             cEEEEEeccc
Confidence            9999999875

>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=99.73  E-value=9.6e-18  Score=137.45  Aligned_cols=80  Identities=30%  Similarity=0.561  Sum_probs=74.3

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      .....++|||+|||+.+++++|+++|.+||.|..|.|+.+     ++|||||+|.+.++|+.||+.|||..|+|+.|.|.
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            3456789999999999999999999999999999999876     47999999999999999999999999999999999


Q ss_pred             EcccC
Q 043443          137 LAAES  141 (299)
Q Consensus       137 ~a~~~  141 (299)
                      +++++
T Consensus       144 ~a~~~  148 (150)
T 2i2y_A          144 LSNGE  148 (150)
T ss_dssp             ECCCC
T ss_pred             EcCCC
Confidence            99864

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.73  E-value=1.8e-17  Score=136.26  Aligned_cols=82  Identities=28%  Similarity=0.453  Sum_probs=78.2

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      ....++|||+|||..+++++|+++|.+||.|..|.|+.+..++.++|||||+|.+.++|++||..|||..|+|+.|.|.|
T Consensus        84 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  163 (166)
T 3md3_A           84 SDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINW  163 (166)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEe
Confidence            34568999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             cc
Q 043443          138 AA  139 (299)
Q Consensus       138 a~  139 (299)
                      |+
T Consensus       164 a~  165 (166)
T 3md3_A          164 AA  165 (166)
T ss_dssp             SC
T ss_pred             cC
Confidence            86

>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=99.73  E-value=1e-17  Score=124.99  Aligned_cols=75  Identities=21%  Similarity=0.416  Sum_probs=69.5

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      ..++|||+|||+.+++++|+++|.+| .|..|.|.      .++|||||+|.+.++|++||+.|||..|+|+.|.|+++.
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            45789999999999999999999999 99999885      458999999999999999999999999999999999997


Q ss_pred             cC
Q 043443          140 ES  141 (299)
Q Consensus       140 ~~  141 (299)
                      ..
T Consensus        77 ~~   78 (88)
T 1wg1_A           77 TD   78 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.72  E-value=2.6e-17  Score=135.42  Aligned_cols=81  Identities=32%  Similarity=0.576  Sum_probs=77.7

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEccc
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAE  140 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~  140 (299)
                      .++|||+|||..+++++|+++|.+||+|..|.|+.++.++.++|||||+|.+.++|+.||+.||+..|.|+.|.|.++.+
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            57999999999999999999999999999999999988999999999999999999999999999999999999999975


Q ss_pred             C
Q 043443          141 S  141 (299)
Q Consensus       141 ~  141 (299)
                      .
T Consensus        82 ~   82 (167)
T 1fxl_A           82 S   82 (167)
T ss_dssp             C
T ss_pred             C
Confidence            4

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.72  E-value=2e-17  Score=136.64  Aligned_cols=83  Identities=28%  Similarity=0.470  Sum_probs=78.7

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      +.++|||+|||.++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|+.||+.||+..|.|+.|.|.++.
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            45899999999999999999999999999999999998889999999999999999999999999999999999999998


Q ss_pred             cCC
Q 043443          140 ESR  142 (299)
Q Consensus       140 ~~~  142 (299)
                      +..
T Consensus        82 ~~~   84 (168)
T 1b7f_A           82 PGG   84 (168)
T ss_dssp             CCS
T ss_pred             CCc
Confidence            644

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.72  E-value=2.5e-17  Score=131.88  Aligned_cols=78  Identities=19%  Similarity=0.330  Sum_probs=70.5

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccE-EEEEEcCHHHHHHHHHhhCCceeCC--eeEEEE
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGF-AFVQFVDPYEAAEAQHHMNGKRFAG--REISVV  136 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~-afVeF~~~~~A~~Al~~lng~~l~G--r~i~V~  136 (299)
                      ....|||+||++.+|+++|.++|++||+|..|.|+..     .++| |||+|.+.++|+.||+.|||..|.|  +.|+|+
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            3457889999999999999999999999999988754     2577 9999999999999999999999998  999999


Q ss_pred             EcccCC
Q 043443          137 LAAESR  142 (299)
Q Consensus       137 ~a~~~~  142 (299)
                      |++...
T Consensus       102 ~ak~~~  107 (130)
T 3zzy_A          102 FSKLTS  107 (130)
T ss_dssp             ECSCSS
T ss_pred             ecCCCc
Confidence            998654

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.72  E-value=1.4e-17  Score=130.36  Aligned_cols=79  Identities=23%  Similarity=0.358  Sum_probs=69.1

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCC---CCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEE
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYT---GEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV  135 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~---g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V  135 (299)
                      ...++|||+|||+++++++|+++|.+||+|. +.++.+..+   +.++|||||+|.+.++|++||+.|+  .|+|+.|.|
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            4468999999999999999999999999999 888888776   7999999999999999999999884  477777777


Q ss_pred             EEccc
Q 043443          136 VLAAE  140 (299)
Q Consensus       136 ~~a~~  140 (299)
                      ..+..
T Consensus        83 ~~~~~   87 (114)
T 2dnl_A           83 VSSPT   87 (114)
T ss_dssp             ECCSS
T ss_pred             ccCCC
Confidence            65543

>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=99.72  E-value=1.7e-17  Score=137.76  Aligned_cols=80  Identities=18%  Similarity=0.274  Sum_probs=71.6

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCC--eeEEEE
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAG--REISVV  136 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~G--r~i~V~  136 (299)
                      ....+|||+||++.+++++|+++|++||+|+.|.|+.+    ..++||||+|.+.++|+.||+.|||..|.|  +.|+|+
T Consensus        44 s~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k----~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~  119 (164)
T 1sjr_A           44 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID  119 (164)
T ss_dssp             CCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEE
T ss_pred             CceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEE
Confidence            34567999999999999999999999999999998643    347899999999999999999999999965  999999


Q ss_pred             EcccCC
Q 043443          137 LAAESR  142 (299)
Q Consensus       137 ~a~~~~  142 (299)
                      |++.+.
T Consensus       120 ~Ak~~~  125 (164)
T 1sjr_A          120 FSKLTS  125 (164)
T ss_dssp             ECSSSS
T ss_pred             EecCCc
Confidence            998753

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.72  E-value=3e-17  Score=141.11  Aligned_cols=84  Identities=21%  Similarity=0.425  Sum_probs=79.5

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      ...++|||+|||..+++++|+++|.+||.|+.|.|+.+..++.++|||||+|.+.++|++||+.|||..|+|+.|.|.++
T Consensus       123 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a  202 (216)
T 2qfj_A          123 RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA  202 (216)
T ss_dssp             TTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEEC
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEe
Confidence            34589999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             ccCC
Q 043443          139 AESR  142 (299)
Q Consensus       139 ~~~~  142 (299)
                      ....
T Consensus       203 ~~~~  206 (216)
T 2qfj_A          203 VTPP  206 (216)
T ss_dssp             SSCS
T ss_pred             cCCC
Confidence            8653

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.71  E-value=1.5e-17  Score=131.70  Aligned_cols=79  Identities=14%  Similarity=0.217  Sum_probs=72.6

Q ss_pred             CEEEEeCC----CCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcC----HHH----HHHHHH--hhCCce
Q 043443           62 GSLLVRNI----PLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVD----PYE----AAEAQH--HMNGKR  127 (299)
Q Consensus        62 ~~l~V~nL----p~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~----~~~----A~~Al~--~lng~~  127 (299)
                      +.|||+||    |+.|++++|+++|..||+|..|.++.|+.||.++|||||+|.+    +++    |..||.  .|||..
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            68999999    9999999999999999999999999999999999999999996    333    889988  789999


Q ss_pred             eCCeeEEEEEccc
Q 043443          128 FAGREISVVLAAE  140 (299)
Q Consensus       128 l~Gr~i~V~~a~~  140 (299)
                      |+|+.|.|.+...
T Consensus        83 I~Gr~irV~ln~~   95 (136)
T 2j8a_A           83 IMGFKFEVILNKH   95 (136)
T ss_dssp             ETTEEEEEEECCT
T ss_pred             ecCcEEEEEECcc
Confidence            9999999999764

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.71  E-value=6e-17  Score=128.85  Aligned_cols=75  Identities=21%  Similarity=0.243  Sum_probs=67.5

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccE-EEEEEcCHHHHHHHHHhhCCceeCC--eeEEEEEc
Q 043443           62 GSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGF-AFVQFVDPYEAAEAQHHMNGKRFAG--REISVVLA  138 (299)
Q Consensus        62 ~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~-afVeF~~~~~A~~Al~~lng~~l~G--r~i~V~~a  138 (299)
                      ..|||+||++.+++++|+++|++||+|..|.|+..      .|| |||+|.+.++|+.||+.|||..|.|  +.|.|++|
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            45689999999999999999999999999998642      286 9999999999999999999999987  69999999


Q ss_pred             ccCC
Q 043443          139 AESR  142 (299)
Q Consensus       139 ~~~~  142 (299)
                      +...
T Consensus       100 k~~~  103 (124)
T 2e5i_A          100 RPTR  103 (124)
T ss_dssp             SCSC
T ss_pred             cCCc
Confidence            8654

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=4.6e-17  Score=122.12  Aligned_cols=74  Identities=27%  Similarity=0.399  Sum_probs=65.4

Q ss_pred             CCCE-EEEeCCCCCCCHHH----HHHHHhcC-CCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeE
Q 043443           60 NHGS-LLVRNIPLDCRPEE----LRAPFERF-GVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREI  133 (299)
Q Consensus        60 ~~~~-l~V~nLp~~~te~d----L~~~F~~~-G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i  133 (299)
                      +..| |||+|||+.+++++    |.++|.+| |+|..|       ++   |+|||+|.+.++|+.||+.|||.+|.|+.|
T Consensus         7 p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i   76 (96)
T 2diu_A            7 GCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGNRI   76 (96)
T ss_dssp             CSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCC
T ss_pred             CcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCceE
Confidence            3445 99999999999988    55899999 599887       22   999999999999999999999999999999


Q ss_pred             EEEEcccCCC
Q 043443          134 SVVLAAESRK  143 (299)
Q Consensus       134 ~V~~a~~~~~  143 (299)
                      .|++|+....
T Consensus        77 ~v~~A~~~sd   86 (96)
T 2diu_A           77 IVSFTPKNRE   86 (96)
T ss_dssp             EEESSCCSCC
T ss_pred             EEEecCCCcc
Confidence            9999987543

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.70  E-value=6.8e-17  Score=137.05  Aligned_cols=85  Identities=22%  Similarity=0.396  Sum_probs=80.4

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      ....++|||+|||..+++++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|+.||+.|||..|+|+.|.|.+
T Consensus       111 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  190 (198)
T 2yh0_A          111 PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR  190 (198)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            35678999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             cccCC
Q 043443          138 AAESR  142 (299)
Q Consensus       138 a~~~~  142 (299)
                      +.+..
T Consensus       191 a~~~~  195 (198)
T 2yh0_A          191 ASVGA  195 (198)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            98754

>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=99.70  E-value=9.1e-17  Score=120.37  Aligned_cols=76  Identities=30%  Similarity=0.478  Sum_probs=62.9

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCce--eCCeeEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKR--FAGREISV  135 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~--l~Gr~i~V  135 (299)
                      ....++|||+|||+++|+++|+++|++||.|..|.|+.+     ++|||||+|.+.++|++    |++..  +.|+.|.|
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v   78 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVHI   78 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEEE
Confidence            456789999999999999999999999999999999874     58999999999999983    45554  56999999


Q ss_pred             EEcccCC
Q 043443          136 VLAAESR  142 (299)
Q Consensus       136 ~~a~~~~  142 (299)
                      .++.++.
T Consensus        79 ~~a~~k~   85 (89)
T 3d2w_A           79 SNAEPKH   85 (89)
T ss_dssp             EECC---
T ss_pred             EEcCCCC
Confidence            9998643

>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=99.70  E-value=4.4e-17  Score=135.16  Aligned_cols=80  Identities=24%  Similarity=0.426  Sum_probs=76.6

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      ...+|||+|||..+++++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|++||+.|||..|+|+.|.|.+|.
T Consensus        93 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~As  172 (172)
T 2g4b_A           93 GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS  172 (172)
T ss_dssp             TTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeCC
Confidence            36899999999999999999999999999999999998899999999999999999999999999999999999999973

>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=99.70  E-value=5.4e-17  Score=120.25  Aligned_cols=72  Identities=28%  Similarity=0.439  Sum_probs=66.9

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC----C-------CEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCce
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERF----G-------VVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKR  127 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~----G-------~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~  127 (299)
                      ....+|||+|||+++++++|+++|.+|    |       .|..|.+..+      +|||||+|.+.++|++|| .||+..
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~~   76 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGII   76 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCCE
Confidence            356899999999999999999999999    8       9999999865      699999999999999999 999999


Q ss_pred             eCCeeEEEEE
Q 043443          128 FAGREISVVL  137 (299)
Q Consensus       128 l~Gr~i~V~~  137 (299)
                      |+|+.|.|+.
T Consensus        77 ~~g~~l~V~r   86 (87)
T 2hzc_A           77 FQGQSLKIRR   86 (87)
T ss_dssp             ETTEECEEEC
T ss_pred             ECCeEEEEeC
Confidence            9999999973

>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=99.70  E-value=6.5e-17  Score=136.99  Aligned_cols=84  Identities=24%  Similarity=0.423  Sum_probs=77.9

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      .....++|||+|||+++|+++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|++||+. ++..|+|+.|.|.
T Consensus         9 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~   87 (196)
T 1l3k_A            9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPK   87 (196)
T ss_dssp             CCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeee
Confidence            345678999999999999999999999999999999999988999999999999999999999985 9999999999999


Q ss_pred             EcccC
Q 043443          137 LAAES  141 (299)
Q Consensus       137 ~a~~~  141 (299)
                      ++...
T Consensus        88 ~~~~~   92 (196)
T 1l3k_A           88 RAVSR   92 (196)
T ss_dssp             ECCC-
T ss_pred             cccCc
Confidence            98754

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.69  E-value=8.4e-17  Score=136.26  Aligned_cols=84  Identities=25%  Similarity=0.347  Sum_probs=75.8

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      ...++|||+|||..+++++|+++|.+||.|..|.|+.+..++.++|||||+|.+.++|++||.. ++..|+|+.|.|.++
T Consensus       102 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a  180 (196)
T 1l3k_A          102 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKA  180 (196)
T ss_dssp             -CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEEC
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEec
Confidence            3458999999999999999999999999999999999988999999999999999999999986 899999999999999


Q ss_pred             ccCCC
Q 043443          139 AESRK  143 (299)
Q Consensus       139 ~~~~~  143 (299)
                      .++..
T Consensus       181 ~~k~~  185 (196)
T 1l3k_A          181 LSKQE  185 (196)
T ss_dssp             C----
T ss_pred             CChhH
Confidence            87544

>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=99.69  E-value=9.2e-17  Score=138.69  Aligned_cols=77  Identities=22%  Similarity=0.342  Sum_probs=71.9

Q ss_pred             CCCEEEEeCCC-CCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           60 NHGSLLVRNIP-LDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        60 ~~~~l~V~nLp-~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      +.++|||+||| +.+++++|.++|.+||.|..|.|+.+.     +|||||+|.+.++|+.||+.|||..|.|+.|.|.++
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            45799999999 899999999999999999999998753     799999999999999999999999999999999999


Q ss_pred             ccC
Q 043443          139 AES  141 (299)
Q Consensus       139 ~~~  141 (299)
                      +..
T Consensus        78 ~~~   80 (205)
T 3tyt_A           78 KQP   80 (205)
T ss_dssp             SCS
T ss_pred             cCC
Confidence            754

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.69  E-value=5.8e-17  Score=140.29  Aligned_cols=81  Identities=22%  Similarity=0.364  Sum_probs=74.8

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      ...+|||+|||+.+++++|+++|.+||.|+.|.|+.+.  +.++|||||+|.+.++|++||+.|||.+|+|+.|.|.+++
T Consensus       102 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~  179 (213)
T 4f02_A          102 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK  179 (213)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             ccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC--CCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            35689999999999999999999999999999999874  4478999999999999999999999999999999999998


Q ss_pred             cCC
Q 043443          140 ESR  142 (299)
Q Consensus       140 ~~~  142 (299)
                      ++.
T Consensus       180 ~~~  182 (213)
T 4f02_A          180 SRK  182 (213)
T ss_dssp             CHH
T ss_pred             CCc
Confidence            643

>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=99.69  E-value=3.8e-17  Score=134.93  Aligned_cols=81  Identities=28%  Similarity=0.436  Sum_probs=76.9

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      ...+|||+|||..+++++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|++||+ ||+..|+|+.|.|.++.
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            35799999999999999999999999999999999998899999999999999999999998 89999999999999997


Q ss_pred             cC
Q 043443          140 ES  141 (299)
Q Consensus       140 ~~  141 (299)
                      ++
T Consensus       165 pk  166 (167)
T 2cjk_A          165 PR  166 (167)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.68  E-value=9.6e-17  Score=137.98  Aligned_cols=83  Identities=27%  Similarity=0.390  Sum_probs=75.5

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      .+.++|||+|||.++++++|+++|.+||+|..|.|+.+..++..+|||||+|.+.++|++||+.||+..|.|+.|.|.++
T Consensus        26 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~  105 (216)
T 2qfj_A           26 AIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRP  105 (216)
T ss_dssp             HHHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECC
T ss_pred             CcCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecC
Confidence            34689999999999999999999999999999999999889999999999999999999999999999999999999987


Q ss_pred             ccC
Q 043443          139 AES  141 (299)
Q Consensus       139 ~~~  141 (299)
                      ...
T Consensus       106 ~~~  108 (216)
T 2qfj_A          106 SNI  108 (216)
T ss_dssp             SCC
T ss_pred             CCc
Confidence            654

>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=99.68  E-value=1.9e-16  Score=130.61  Aligned_cols=80  Identities=33%  Similarity=0.491  Sum_probs=76.0

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCC--eeEEEE
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAG--REISVV  136 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~G--r~i~V~  136 (299)
                      ...++|||+|||..+++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|++||+.|||..|.|  ++|.|.
T Consensus        87 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~  166 (168)
T 1b7f_A           87 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR  166 (168)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEE
Confidence            456899999999999999999999999999999999998889999999999999999999999999999988  999999


Q ss_pred             Ec
Q 043443          137 LA  138 (299)
Q Consensus       137 ~a  138 (299)
                      ||
T Consensus       167 ~A  168 (168)
T 1b7f_A          167 LA  168 (168)
T ss_dssp             EC
T ss_pred             eC
Confidence            86

>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=99.67  E-value=8.6e-17  Score=119.76  Aligned_cols=77  Identities=29%  Similarity=0.403  Sum_probs=65.9

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      ...++|||+|||.++++++|+++|.+||.|..|.|+.+     ++|||||+|.+.++|++|+..  ...+.|..|.|.++
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~a   75 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEec
Confidence            34689999999999999999999999999999999864     589999999999999865332  34568999999999


Q ss_pred             ccCC
Q 043443          139 AESR  142 (299)
Q Consensus       139 ~~~~  142 (299)
                      .++.
T Consensus        76 ~~~~   79 (88)
T 1wf0_A           76 EPKH   79 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8653

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.67  E-value=4e-16  Score=120.60  Aligned_cols=82  Identities=20%  Similarity=0.212  Sum_probs=72.8

Q ss_pred             CCCCEEEEeCCCC-----CCCHHHHHHHHhcCCCEeEEEeccCCCC-CCCccEEEEEEcCHHHHHHHHHhhCCceeCCee
Q 043443           59 QNHGSLLVRNIPL-----DCRPEELRAPFERFGVVRDVYLPKDYYT-GEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGRE  132 (299)
Q Consensus        59 ~~~~~l~V~nLp~-----~~te~dL~~~F~~~G~I~~v~i~~d~~~-g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~  132 (299)
                      .+..+|+|.||..     +.++++|+++|++||+|..|.|+.++.+ +.++|||||+|.+.++|++||+.|||..|+|+.
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~   85 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRV   85 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcE
Confidence            4678999999953     2378999999999999999999987654 678999999999999999999999999999999


Q ss_pred             EEEEEccc
Q 043443          133 ISVVLAAE  140 (299)
Q Consensus       133 i~V~~a~~  140 (299)
                      |.|.++..
T Consensus        86 i~v~~a~~   93 (105)
T 2pe8_A           86 VKACFYNL   93 (105)
T ss_dssp             CEEEECCH
T ss_pred             EEEEEcCH
Confidence            99999864

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.67  E-value=2.3e-16  Score=129.58  Aligned_cols=80  Identities=21%  Similarity=0.307  Sum_probs=74.0

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcccC
Q 043443           62 GSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAES  141 (299)
Q Consensus        62 ~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~~  141 (299)
                      .+|||+|||.++++++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|+.||+.||+..|.|+.|.|.++...
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            489999999999999999999999999999999886 4678999999999999999999999999999999999999754


Q ss_pred             C
Q 043443          142 R  142 (299)
Q Consensus       142 ~  142 (299)
                      .
T Consensus        80 ~   80 (166)
T 3md3_A           80 Q   80 (166)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.66  E-value=3.1e-16  Score=128.97  Aligned_cols=80  Identities=30%  Similarity=0.476  Sum_probs=74.6

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCee--EEEE
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGRE--ISVV  136 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~--i~V~  136 (299)
                      ....+|||+|||..+++++|+++|.+||.|..|.|+.+..++.++|||||+|.+.++|++||+.|||..|.|+.  |.|.
T Consensus        86 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~  165 (167)
T 1fxl_A           86 IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVK  165 (167)
T ss_dssp             GTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEE
Confidence            34679999999999999999999999999999999998888999999999999999999999999999999965  8888


Q ss_pred             Ec
Q 043443          137 LA  138 (299)
Q Consensus       137 ~a  138 (299)
                      ||
T Consensus       166 ~A  167 (167)
T 1fxl_A          166 FA  167 (167)
T ss_dssp             EC
T ss_pred             eC
Confidence            75

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=8.4e-16  Score=119.87  Aligned_cols=81  Identities=28%  Similarity=0.495  Sum_probs=69.6

Q ss_pred             CCCCCCEEEEeCCCCCCC-----------HHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCC
Q 043443           57 KEQNHGSLLVRNIPLDCR-----------PEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNG  125 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~t-----------e~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng  125 (299)
                      ...+..+|+|.||.....           +++|+++|.+||.|..|.| .++   .++|||||+|.+.++|++||+.|||
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            445678999999944332           5899999999999999966 443   3789999999999999999999999


Q ss_pred             ceeCCeeEEEEEcccC
Q 043443          126 KRFAGREISVVLAAES  141 (299)
Q Consensus       126 ~~l~Gr~i~V~~a~~~  141 (299)
                      ..|+|+.|.|.++.+.
T Consensus        87 ~~~~gr~l~v~~a~~~  102 (112)
T 2dit_A           87 RWFGGRQITAQAWDGT  102 (112)
T ss_dssp             CEETTEECEEEECCSC
T ss_pred             CEECCcEEEEEEeCCC
Confidence            9999999999999764

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

Probab=99.65  E-value=5e-16  Score=128.81  Aligned_cols=83  Identities=23%  Similarity=0.405  Sum_probs=75.1

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCC--CCccEEEEEEcCHHHHHHHHHhhCCceeC---CeeEE
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTG--EPRGFAFVQFVDPYEAAEAQHHMNGKRFA---GREIS  134 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g--~~~g~afVeF~~~~~A~~Al~~lng~~l~---Gr~i~  134 (299)
                      +.++|||+|||+++++++|+++|.+||+|..|.|+.++.++  .++|||||+|.+.++|+.||+.||+..+.   +..|.
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            45799999999999999999999999999999999988776  88999999999999999999999998876   67888


Q ss_pred             EEEcccCC
Q 043443          135 VVLAAESR  142 (299)
Q Consensus       135 V~~a~~~~  142 (299)
                      |.++....
T Consensus        82 ~~~~~~~~   89 (175)
T 3nmr_A           82 MKPADSEK   89 (175)
T ss_dssp             EEECGGGC
T ss_pred             Eccccccc
Confidence            88877543

>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=99.64  E-value=5e-16  Score=128.86  Aligned_cols=79  Identities=24%  Similarity=0.397  Sum_probs=73.1

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeC---CeeEEEE
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFA---GREISVV  136 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~---Gr~i~V~  136 (299)
                      ...+|||+|||..+++++|+++|.+||.|..|.|+.+. ++.++|||||+|.+.++|++||+.|||..|.   ++.|.|.
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            56799999999999999999999999999999999885 5888999999999999999999999998776   4999999


Q ss_pred             Ecc
Q 043443          137 LAA  139 (299)
Q Consensus       137 ~a~  139 (299)
                      ||.
T Consensus       173 ~ad  175 (175)
T 3nmr_A          173 FAD  175 (175)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            973

>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=99.64  E-value=8.9e-16  Score=137.80  Aligned_cols=83  Identities=24%  Similarity=0.429  Sum_probs=75.8

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHH----HHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCee
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELR----APFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGRE  132 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~----~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~  132 (299)
                      +..+.++|||+|||+.+++++|+    ++|.+||.|..|.|+.   ++..+|||||+|.+.++|+.||+.|||..|.|+.
T Consensus         5 ~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   81 (282)
T 3pgw_A            5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKP   81 (282)
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcE
Confidence            45668899999999999999966    8999999999999875   6788999999999999999999999999999999


Q ss_pred             EEEEEcccCC
Q 043443          133 ISVVLAAESR  142 (299)
Q Consensus       133 i~V~~a~~~~  142 (299)
                      |.|.|++...
T Consensus        82 l~v~~a~~~~   91 (282)
T 3pgw_A           82 MRIQYAKTDS   91 (282)
T ss_pred             EEEEEeccCc
Confidence            9999997543

>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=99.64  E-value=4.4e-16  Score=128.46  Aligned_cols=79  Identities=27%  Similarity=0.460  Sum_probs=73.6

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      +.++|||+|||.++|+++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|+.||+.  +..|+|+.|.|.++.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~~   79 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRAI   79 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEccccccc
Confidence            457999999999999999999999999999999999988999999999999999999999984  678999999998876


Q ss_pred             c
Q 043443          140 E  140 (299)
Q Consensus       140 ~  140 (299)
                      .
T Consensus        80 ~   80 (167)
T 2cjk_A           80 P   80 (167)
T ss_dssp             C
T ss_pred             c
Confidence            4

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.64  E-value=5.9e-16  Score=128.96  Aligned_cols=78  Identities=24%  Similarity=0.452  Sum_probs=71.7

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      ...++|||+|||..+++++|+++|.+||.|..|     ..++.++|||||+|.+.++|++||+.|||..|+|+.|.|.|+
T Consensus        97 ~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  171 (175)
T 1fje_B           97 RAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT  171 (175)
T ss_dssp             GGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEEC
T ss_pred             ccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEec
Confidence            456899999999999999999999999998776     347788999999999999999999999999999999999999


Q ss_pred             ccC
Q 043443          139 AES  141 (299)
Q Consensus       139 ~~~  141 (299)
                      .++
T Consensus       172 ~~k  174 (175)
T 1fje_B          172 GEK  174 (175)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            764

>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=99.64  E-value=5.9e-16  Score=135.40  Aligned_cols=79  Identities=28%  Similarity=0.411  Sum_probs=73.6

Q ss_pred             CCCCCEEEEeCCCC-CCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           58 EQNHGSLLVRNIPL-DCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        58 ~~~~~~l~V~nLp~-~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      ..+.++|||+|||. .+++++|+++|++||.|..|.|+.++     +|||||+|.+.++|++||+.||+..|.|+.|.|.
T Consensus        31 ~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~  105 (229)
T 2adc_A           31 GAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRIT  105 (229)
T ss_dssp             CCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            34678999999999 99999999999999999999999874     7899999999999999999999999999999999


Q ss_pred             EcccC
Q 043443          137 LAAES  141 (299)
Q Consensus       137 ~a~~~  141 (299)
                      ++...
T Consensus       106 ~a~~~  110 (229)
T 2adc_A          106 LSKHQ  110 (229)
T ss_dssp             CCSCC
T ss_pred             EecCc
Confidence            99754

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.63  E-value=4.5e-16  Score=137.07  Aligned_cols=79  Identities=22%  Similarity=0.296  Sum_probs=71.2

Q ss_pred             CCCCCEEEEeCCCCCC---------CHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCcee
Q 043443           58 EQNHGSLLVRNIPLDC---------RPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRF  128 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~---------te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l  128 (299)
                      .....+|||+||+..+         ++++|.++|++||+|+.|.|+.+      +|||||+|.+.++|+.||+.|||..|
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            4467899999999998         79999999999999999999864      79999999999999999999999999


Q ss_pred             ------------CCeeEEEEEcccCC
Q 043443          129 ------------AGREISVVLAAESR  142 (299)
Q Consensus       129 ------------~Gr~i~V~~a~~~~  142 (299)
                                  .|+.|.|.||+...
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                        89999999998643

>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=99.63  E-value=1.1e-15  Score=130.74  Aligned_cols=78  Identities=14%  Similarity=0.298  Sum_probs=71.9

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEccc
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAE  140 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~  140 (299)
                      .++|||+|||+.+++++|+++|.+||.|..|.|+.+. ++.++|||||+|.+.++|+.||..++ ..|+|+.|.|.+++.
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~~-~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETPG-QKYKETDLLILFKDD  186 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCTT-CEETTEECEEEETTT
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhCC-CeECCEEEEEEEhHH
Confidence            5799999999999999999999999999999999875 58899999999999999999998654 599999999999864

>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=99.62  E-value=3.7e-15  Score=133.72  Aligned_cols=77  Identities=21%  Similarity=0.360  Sum_probs=71.6

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeC-CeeEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFA-GREISVV  136 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~-Gr~i~V~  136 (299)
                      ....++|||+|||..+++++|+++|.+||.|+.|.|+.+.     +|||||+|.+.++|++||+.|||..|. |+.|.|.
T Consensus       204 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~  278 (282)
T 3pgw_A          204 NPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKIS  278 (282)
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEE
Confidence            3457899999999999999999999999999999998653     589999999999999999999999999 9999999


Q ss_pred             Ecc
Q 043443          137 LAA  139 (299)
Q Consensus       137 ~a~  139 (299)
                      |++
T Consensus       279 ~ak  281 (282)
T 3pgw_A          279 FAK  281 (282)
T ss_pred             Eec
Confidence            986

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.62  E-value=1.6e-15  Score=136.81  Aligned_cols=82  Identities=28%  Similarity=0.413  Sum_probs=75.6

Q ss_pred             CCCCEEEEeCCCCC-CCHHHHHHHHhcCCCEeEEEeccCCC-CCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           59 QNHGSLLVRNIPLD-CRPEELRAPFERFGVVRDVYLPKDYY-TGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        59 ~~~~~l~V~nLp~~-~te~dL~~~F~~~G~I~~v~i~~d~~-~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      ...++|||+|||.. +++++|+++|.+||.|..|.|+.+.. |+.++|||||+|.+.++|+.|| .|||..|+|+.|.|.
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            45689999999999 99999999999999999999998876 5899999999999999999999 999999999999999


Q ss_pred             EcccC
Q 043443          137 LAAES  141 (299)
Q Consensus       137 ~a~~~  141 (299)
                      |++++
T Consensus       287 ~a~~k  291 (292)
T 2ghp_A          287 LADKK  291 (292)
T ss_dssp             ECCCC
T ss_pred             EecCC
Confidence            99864

>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=99.60  E-value=5.1e-15  Score=132.95  Aligned_cols=83  Identities=22%  Similarity=0.403  Sum_probs=78.8

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      ..++|||+|||..+++++|.++|.+||.|..|.|+.+..++.++|||||+|.+.++|+.||..||+..|+|+.|.|.++.
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            45799999999999999999999999999999999998899999999999999999999999999999999999999998


Q ss_pred             cCC
Q 043443          140 ESR  142 (299)
Q Consensus       140 ~~~  142 (299)
                      ...
T Consensus       174 ~~~  176 (284)
T 3smz_A          174 AGQ  176 (284)
T ss_dssp             GGG
T ss_pred             CCC
Confidence            654

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.59  E-value=1.9e-15  Score=128.61  Aligned_cols=77  Identities=29%  Similarity=0.426  Sum_probs=72.2

Q ss_pred             CCEEEEeCCCC-CCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           61 HGSLLVRNIPL-DCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        61 ~~~l~V~nLp~-~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      .++|||+|||. .+++++|+++|.+||.|..|.|+.++     +|||||+|.+.++|+.||+.||+..|.|+.|.|.++.
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            57999999999 99999999999999999999998864     7899999999999999999999999999999999998


Q ss_pred             cCC
Q 043443          140 ESR  142 (299)
Q Consensus       140 ~~~  142 (299)
                      ...
T Consensus        78 ~~~   80 (198)
T 1qm9_A           78 HQN   80 (198)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            643

>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=99.58  E-value=9.3e-16  Score=127.74  Aligned_cols=84  Identities=20%  Similarity=0.279  Sum_probs=72.9

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      ...+.++|||+|||..+++++|+++|..||.|.. .++.+..++.++|||||+|.+.++|++||+ ||+..|.|+.|.|.
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 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE   86 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEe
Confidence            4556889999999999999999999999998765 233444567889999999999999999995 99999999999999


Q ss_pred             EcccCC
Q 043443          137 LAAESR  142 (299)
Q Consensus       137 ~a~~~~  142 (299)
                      ++....
T Consensus        87 ~~~~~~   92 (175)
T 1fje_B           87 KPKGRD   92 (175)
T ss_dssp             CCCCSS
T ss_pred             cCCCcc
Confidence            998643

>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=99.58  E-value=5.1e-15  Score=132.94  Aligned_cols=85  Identities=20%  Similarity=0.268  Sum_probs=78.6

Q ss_pred             CCCCEEEEeCCCCCC-CHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           59 QNHGSLLVRNIPLDC-RPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~-te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      ....+|||+|||..+ ++++|+++|..||.|..|.|+.+. ++.++|||||+|.+.++|+.||..|||..|+|+.|.|.|
T Consensus       182 ~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  260 (284)
T 3smz_A          182 LHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSF  260 (284)
T ss_dssp             TSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECS-SCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECC-CCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEE
Confidence            456899999999995 999999999999999999998876 788999999999999999999999999999999999999


Q ss_pred             cccCCCC
Q 043443          138 AAESRKR  144 (299)
Q Consensus       138 a~~~~~~  144 (299)
                      +.++...
T Consensus       261 a~~~~~~  267 (284)
T 3smz_A          261 CAPGPPG  267 (284)
T ss_dssp             CCSSSCH
T ss_pred             ecCCCcc
Confidence            9876543

>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=99.57  E-value=1e-14  Score=112.67  Aligned_cols=82  Identities=21%  Similarity=0.417  Sum_probs=71.0

Q ss_pred             CCCCEEEEeCC--CCCCC--------HHHHHHHHhcCCCEeEEEeccCCCC--CCCccEEEEEEcCHHHHHHHHHhhCCc
Q 043443           59 QNHGSLLVRNI--PLDCR--------PEELRAPFERFGVVRDVYLPKDYYT--GEPRGFAFVQFVDPYEAAEAQHHMNGK  126 (299)
Q Consensus        59 ~~~~~l~V~nL--p~~~t--------e~dL~~~F~~~G~I~~v~i~~d~~~--g~~~g~afVeF~~~~~A~~Al~~lng~  126 (299)
                      .++.+|+|.||  +..+.        ++||+++|++||.|..|.|+.+..+  +.++|||||+|.+.++|++||+.|||.
T Consensus         3 ~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~   82 (105)
T 3v4m_A            3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   82 (105)
T ss_dssp             SCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            35679999998  43443        3789999999999999999987654  367899999999999999999999999


Q ss_pred             eeCCeeEEEEEccc
Q 043443          127 RFAGREISVVLAAE  140 (299)
Q Consensus       127 ~l~Gr~i~V~~a~~  140 (299)
                      .|+|+.|.|.++..
T Consensus        83 ~f~GR~i~v~~~~~   96 (105)
T 3v4m_A           83 KFANRVVVTKYCDP   96 (105)
T ss_dssp             EETTEECEEEEECH
T ss_pred             EeCCCEEEEEEeCH
Confidence            99999999999864

>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=99.57  E-value=6.2e-15  Score=131.40  Aligned_cols=77  Identities=27%  Similarity=0.544  Sum_probs=71.7

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      ....++|||+|||.++|+++|.++|.+||.|..|.|..+      +|||||+|.+.++|+.||..|||..|.|+.|.|.+
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~   92 (261)
T 3sde_A           19 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRF   92 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcEECCceeEeee
Confidence            345689999999999999999999999999999999755      69999999999999999999999999999999999


Q ss_pred             ccc
Q 043443          138 AAE  140 (299)
Q Consensus       138 a~~  140 (299)
                      +.+
T Consensus        93 a~~   95 (261)
T 3sde_A           93 ATH   95 (261)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            875

>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=99.57  E-value=8.3e-15  Score=128.06  Aligned_cols=78  Identities=22%  Similarity=0.344  Sum_probs=71.6

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCC-CEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeC-CeeEEEE
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFG-VVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFA-GREISVV  136 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G-~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~-Gr~i~V~  136 (299)
                      .+.++|||+|||..+++++|+++|.+|| .|..|.|+.+     .+|||||+|.+.++|++||+.|||..|+ |+.|.|.
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 9999999653     2689999999999999999999999999 9999999


Q ss_pred             EcccC
Q 043443          137 LAAES  141 (299)
Q Consensus       137 ~a~~~  141 (299)
                      |+++.
T Consensus       224 ~a~~~  228 (229)
T 2adc_A          224 FSKST  228 (229)
T ss_dssp             ECSSC
T ss_pred             EecCC
Confidence            99753

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.57  E-value=4.6e-15  Score=126.17  Aligned_cols=78  Identities=22%  Similarity=0.335  Sum_probs=71.9

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCC-CEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeC-CeeEEEE
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFG-VVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFA-GREISVV  136 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G-~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~-Gr~i~V~  136 (299)
                      .+.++|||+|||..+++++|+++|.+|| .|..|.|+.+.     +|||||+|.+.++|++||+.|||..|+ |+.|.|.
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            4578999999999999999999999999 99999997542     789999999999999999999999999 9999999


Q ss_pred             EcccC
Q 043443          137 LAAES  141 (299)
Q Consensus       137 ~a~~~  141 (299)
                      |+++.
T Consensus       193 ~a~~~  197 (198)
T 1qm9_A          193 FSKST  197 (198)
T ss_dssp             EECCC
T ss_pred             eeccc
Confidence            99753

>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=99.57  E-value=4.5e-15  Score=128.04  Aligned_cols=78  Identities=17%  Similarity=0.201  Sum_probs=69.3

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCE--eEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCe----e
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVV--RDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGR----E  132 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I--~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr----~  132 (299)
                      .+..+|||+|||+.++|++|+++|++||.|  +.|.|+.+.  +..+|||||+|.+.++|+.||..|||.+|.|.    +
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            356799999999999999999999999999  889888764  45569999999999999999999999999886    5


Q ss_pred             EEEEEc
Q 043443          133 ISVVLA  138 (299)
Q Consensus       133 i~V~~a  138 (299)
                      |.|.++
T Consensus       199 ~~vk~~  204 (205)
T 3tyt_A          199 YTLKLC  204 (205)
T ss_dssp             EECEEE
T ss_pred             eEEEec
Confidence            777765

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=99.56  E-value=8.8e-15  Score=115.39  Aligned_cols=81  Identities=25%  Similarity=0.352  Sum_probs=70.4

Q ss_pred             CCCEEEEeCCC--CCC---CHHHHHHHHhcCCCEeEEEeccCCC----CCCCccEEEEEEcCHHHHHHHHHhhCCceeCC
Q 043443           60 NHGSLLVRNIP--LDC---RPEELRAPFERFGVVRDVYLPKDYY----TGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAG  130 (299)
Q Consensus        60 ~~~~l~V~nLp--~~~---te~dL~~~F~~~G~I~~v~i~~d~~----~g~~~g~afVeF~~~~~A~~Al~~lng~~l~G  130 (299)
                      ++.+|+|.||-  .++   .++||+++|++||+|..|.|+.+..    ++..+||+||+|.+.++|++||+.|||..|+|
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            56899999993  222   3689999999999999999998754    34567999999999999999999999999999


Q ss_pred             eeEEEEEccc
Q 043443          131 REISVVLAAE  140 (299)
Q Consensus       131 r~i~V~~a~~  140 (299)
                      +.|.|.++..
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999999863

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3

Probab=99.54  E-value=3.1e-15  Score=115.38  Aligned_cols=72  Identities=19%  Similarity=0.363  Sum_probs=62.9

Q ss_pred             EeCCCCCCCHHHHHHHH------------hcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeE
Q 043443           66 VRNIPLDCRPEELRAPF------------ERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREI  133 (299)
Q Consensus        66 V~nLp~~~te~dL~~~F------------~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i  133 (299)
                      +.||++.+++++|+++|            ++||+|..|.|+.+. ++.++|||||+|.+.++|++|++.|||..|+|+.|
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            45666667777776666            999999999999875 47889999999999999999999999999999999


Q ss_pred             EEEEc
Q 043443          134 SVVLA  138 (299)
Q Consensus       134 ~V~~a  138 (299)
                      .|+|+
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99986

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=99.54  E-value=1.9e-14  Score=119.10  Aligned_cols=75  Identities=27%  Similarity=0.427  Sum_probs=68.0

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcC----C-------CEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCcee
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERF----G-------VVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRF  128 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~----G-------~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l  128 (299)
                      +.++|||+|||.++|+++|+++|.+|    |       .|..+.+..+      +|||||+|.+.++|++|| .||+..|
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    7       7788877654      799999999999999999 7999999


Q ss_pred             CCeeEEEEEcccC
Q 043443          129 AGREISVVLAAES  141 (299)
Q Consensus       129 ~Gr~i~V~~a~~~  141 (299)
                      .|+.|.|.++...
T Consensus        76 ~g~~i~v~~~~~~   88 (172)
T 2g4b_A           76 QGQSLKIRRPHDY   88 (172)
T ss_dssp             TTEECEEECCSSC
T ss_pred             cCceeeecCCccc
Confidence            9999999998754

>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=99.53  E-value=1.9e-14  Score=129.68  Aligned_cols=82  Identities=17%  Similarity=0.334  Sum_probs=71.0

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCC-CEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFG-VVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G-~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      ..++|||+|||..+++++|.++|.+|| .|..|.|+.+.. +.++|||||+|.+.++|+.||..|||..|.|+.|.|.++
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            468999999999999999999999999 999999998764 778999999999999999999999999999999999998


Q ss_pred             ccCC
Q 043443          139 AESR  142 (299)
Q Consensus       139 ~~~~  142 (299)
                      .+..
T Consensus       195 ~~~~  198 (292)
T 2ghp_A          195 NPLE  198 (292)
T ss_dssp             CCC-
T ss_pred             CCCc
Confidence            7644

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.53  E-value=2.9e-14  Score=120.71  Aligned_cols=75  Identities=25%  Similarity=0.390  Sum_probs=66.7

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcC----C-------CEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCcee
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERF----G-------VVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRF  128 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~----G-------~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l  128 (299)
                      ..++|||+|||+.+++++|+++|.+|    |       .|..+.+..      .+|||||+|.+.++|++|| .||+..|
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~~------~~g~afV~F~~~~~A~~Al-~l~g~~~   75 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ------DKNFAFLEFRSVDETTQAM-AFDGIIF   75 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEET------TTTEEEEEESCSHHHHHHG-GGTTEEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEecC------CCCEEEEEeCCHHHHHHHH-HhcCCEE
Confidence            45799999999999999999999999    5       677776654      4799999999999999999 7999999


Q ss_pred             CCeeEEEEEcccC
Q 043443          129 AGREISVVLAAES  141 (299)
Q Consensus       129 ~Gr~i~V~~a~~~  141 (299)
                      .|+.|.|.++...
T Consensus        76 ~g~~i~v~~~~~~   88 (198)
T 2yh0_A           76 QGQSLKIRRPHDY   88 (198)
T ss_dssp             TTEEEEEECCCCC
T ss_pred             cCceEEEeCCCCC
Confidence            9999999998754

>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=99.52  E-value=3.4e-14  Score=126.63  Aligned_cols=81  Identities=25%  Similarity=0.310  Sum_probs=73.5

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhC-CceeC---CeeEEE
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMN-GKRFA---GREISV  135 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~ln-g~~l~---Gr~i~V  135 (299)
                      +..+|||+|||..+|+++|+++|.+||.|..|.|+.+ .++.++|||||+|.+.++|..||..|| +..+.   ++.|.|
T Consensus        95 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v  173 (261)
T 3sde_A           95 HGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIV  173 (261)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE-TTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEE
T ss_pred             cCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeC-CCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEE
Confidence            3579999999999999999999999999999999988 588999999999999999999999995 55554   999999


Q ss_pred             EEcccC
Q 043443          136 VLAAES  141 (299)
Q Consensus       136 ~~a~~~  141 (299)
                      .++...
T Consensus       174 ~~~~~~  179 (261)
T 3sde_A          174 EPMEQF  179 (261)
T ss_dssp             EECCCE
T ss_pred             eecccc
Confidence            998754

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.49  E-value=2.3e-13  Score=104.03  Aligned_cols=75  Identities=16%  Similarity=0.173  Sum_probs=63.3

Q ss_pred             CCEEEEeCCC-------CCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeE
Q 043443           61 HGSLLVRNIP-------LDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREI  133 (299)
Q Consensus        61 ~~~l~V~nLp-------~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i  133 (299)
                      ..+|.|.-..       ..+++++|+++|.+||+|..|.|+.     .++|||||+|++.++|+.||+.+++  +.|+.|
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~~-----~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l   82 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLSS-----KKPGTAVVEFATVKAAELAVQNEVG--LVDNPL   82 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEES-----SSSSEEEEEESCHHHHHHHHHTCCB--CSSSBC
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEcc-----CCCCEEEEEECCHHHHHHHHHhcCC--CCCCeE
Confidence            4567776543       4589999999999999999999873     5689999999999999999997554  679999


Q ss_pred             EEEEcccCC
Q 043443          134 SVVLAAESR  142 (299)
Q Consensus       134 ~V~~a~~~~  142 (299)
                      .|.|++...
T Consensus        83 ~V~~a~~~~   91 (100)
T 2d9o_A           83 KISWLEGQP   91 (100)
T ss_dssp             EEECSSCCC
T ss_pred             EEEEccCCC
Confidence            999998654

>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=99.49  E-value=6.9e-14  Score=129.34  Aligned_cols=76  Identities=21%  Similarity=0.388  Sum_probs=66.3

Q ss_pred             CCCCCEEEEeC--CCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeC---Ce-
Q 043443           58 EQNHGSLLVRN--IPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFA---GR-  131 (299)
Q Consensus        58 ~~~~~~l~V~n--Lp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~---Gr-  131 (299)
                      ..++.+|||+|  |++.+|+++|+++|++||+|+.|.|..      .+|||||+|.+.++|++||+.|||+++.   |+ 
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            45678999999  578999999999999999999988864      3699999999999999999999999883   44 


Q ss_pred             -eEEEEEcc
Q 043443          132 -EISVVLAA  139 (299)
Q Consensus       132 -~i~V~~a~  139 (299)
                       .|.|.++.
T Consensus        89 ~~ly~~~~~   97 (345)
T 3tht_A           89 ITLYLNFVE   97 (345)
T ss_dssp             EECEEEECS
T ss_pred             eEEEEEEee
Confidence             57777774

>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=99.42  E-value=7.9e-13  Score=103.48  Aligned_cols=78  Identities=18%  Similarity=0.276  Sum_probs=66.2

Q ss_pred             CCCCEEEEeCCC--CCC--------CHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCcee
Q 043443           59 QNHGSLLVRNIP--LDC--------RPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRF  128 (299)
Q Consensus        59 ~~~~~l~V~nLp--~~~--------te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l  128 (299)
                      .++.+|.|.||=  .+.        .++||+++|++||.|..|.|..+.    .+|||||+|.+.++|++||+.|||..|
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f   80 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWF   80 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEE
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEE
Confidence            356789999982  221        136889999999999999997652    589999999999999999999999999


Q ss_pred             CCeeEEEEEccc
Q 043443          129 AGREISVVLAAE  140 (299)
Q Consensus       129 ~Gr~i~V~~a~~  140 (299)
                      +|+.|.|.++..
T Consensus        81 ~GR~i~v~~~~~   92 (114)
T 3s6e_A           81 AGKMITAAYVPL   92 (114)
T ss_dssp             TTEECEEEEECH
T ss_pred             CCEEEEEEEEcH
Confidence            999999999863

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.36  E-value=3.9e-12  Score=100.18  Aligned_cols=78  Identities=15%  Similarity=0.140  Sum_probs=69.6

Q ss_pred             CCCCCCEEEEeCCCCC-CCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcC-HHHHHHHHHhhC--CceeCCee
Q 043443           57 KEQNHGSLLVRNIPLD-CRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVD-PYEAAEAQHHMN--GKRFAGRE  132 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~-~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~-~~~A~~Al~~ln--g~~l~Gr~  132 (299)
                      .-...+.|||+||+.. +++++|+++|.+||+|.+|+|+.+.      ..|||+|.+ ..+|+.||..||  +.+|+|..
T Consensus        14 ~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~------~tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~   87 (121)
T 1owx_A           14 EEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGA------KEGIILFKEKAKEALGKAKDANNGNLQLRNKE   87 (121)
T ss_dssp             SCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTC------SEEEEEESSCHHHHHHHHHHTTTSCBCTTSSS
T ss_pred             cccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCC------CEEEEEECCChHHHHHHHHHhhcCCcEEeCcE
Confidence            4456789999999999 9999999999999999999999874      469999999 899999999994  77899999


Q ss_pred             EEEEEccc
Q 043443          133 ISVVLAAE  140 (299)
Q Consensus       133 i~V~~a~~  140 (299)
                      |+|++...
T Consensus        88 ~~~evL~G   95 (121)
T 1owx_A           88 VTWEVLEG   95 (121)
T ss_dssp             EEEEECCH
T ss_pred             EEEEECCC
Confidence            99988763

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.30  E-value=1e-11  Score=92.18  Aligned_cols=74  Identities=27%  Similarity=0.384  Sum_probs=62.9

Q ss_pred             CCEEEEeCCCC----CCCH----HHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCee
Q 043443           61 HGSLLVRNIPL----DCRP----EELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGRE  132 (299)
Q Consensus        61 ~~~l~V~nLp~----~~te----~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~  132 (299)
                      ..||+|..++.    ++..    .+|.+.|.+||+|..|.|+.+        .+||+|.+.++|.+||+ |||..|+|+.
T Consensus         7 d~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d--------~~fVtF~d~~sAlaAi~-mnG~~v~Gr~   77 (91)
T 2dnr_A            7 GGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVED--------KMWVTFLEGSSALNVLS-LNGKELLNRT   77 (91)
T ss_dssp             SCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSS--------SEEEEESSHHHHHHGGG-GTTCEETTEE
T ss_pred             CCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecC--------CEEEEECChHHHHHHHh-cCCeEeCCeE
Confidence            35888887762    2222    679999999999999999976        38999999999999998 9999999999


Q ss_pred             EEEEEcccCCC
Q 043443          133 ISVVLAAESRK  143 (299)
Q Consensus       133 i~V~~a~~~~~  143 (299)
                      |+|+++++...
T Consensus        78 LkV~lkt~dW~   88 (91)
T 2dnr_A           78 ITIALKSPSGP   88 (91)
T ss_dssp             EEEEECCCSSC
T ss_pred             EEEEeCCCCcc
Confidence            99999987543

>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=99.09  E-value=8e-11  Score=87.85  Aligned_cols=71  Identities=17%  Similarity=0.264  Sum_probs=60.7

Q ss_pred             CCCEEEEeCCCCC------CCH---HHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCC
Q 043443           60 NHGSLLVRNIPLD------CRP---EELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAG  130 (299)
Q Consensus        60 ~~~~l~V~nLp~~------~te---~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~G  130 (299)
                      +..||+|..++..      ..+   .+|.+.|.+||+|..|.|+.+        -+||+|.+.++|.+||+ |||+.|+|
T Consensus        14 pD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d--------~~fVtF~d~~sAl~AI~-ldG~~v~G   84 (95)
T 1ufw_A           14 LDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLD-VDGMKVKG   84 (95)
T ss_dssp             TTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHH-GGGSEETT
T ss_pred             CCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecC--------cEEEEEcChHHHHHHHh-cCCeeeCC
Confidence            3468999888643      232   569999999999999999987        39999999999999998 99999999


Q ss_pred             eeEEEEEcc
Q 043443          131 REISVVLAA  139 (299)
Q Consensus       131 r~i~V~~a~  139 (299)
                      +.|+|.+..
T Consensus        85 r~L~V~~k~   93 (95)
T 1ufw_A           85 RAVKISGPS   93 (95)
T ss_dssp             EEEEEECCC
T ss_pred             eEEEEeccC
Confidence            999999864

>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=99.00  E-value=1.6e-09  Score=93.76  Aligned_cols=80  Identities=25%  Similarity=0.332  Sum_probs=66.2

Q ss_pred             CCEEEEeCCC-----CCCCHHHHHHHHhcCCCEeEEEeccCC----CCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCe
Q 043443           61 HGSLLVRNIP-----LDCRPEELRAPFERFGVVRDVYLPKDY----YTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGR  131 (299)
Q Consensus        61 ~~~l~V~nLp-----~~~te~dL~~~F~~~G~I~~v~i~~d~----~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr  131 (299)
                      ...|.+.|+-     ..-.+++|.+.|.+||+|..|.|+.+.    .++..+|++||+|.+.++|++||+.|||..|+|+
T Consensus       124 s~v~~l~n~v~~~e~~~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr  203 (222)
T 3dxb_A          124 STVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGR  203 (222)
T ss_dssp             CSEEEEESSCCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSS
T ss_pred             cccchhhcCCCHHHHHHHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCe
Confidence            4456666552     223467899999999999999998543    3458899999999999999999999999999999


Q ss_pred             eEEEEEccc
Q 043443          132 EISVVLAAE  140 (299)
Q Consensus       132 ~i~V~~a~~  140 (299)
                      .|.|.++..
T Consensus       204 ~i~~~~~~~  212 (222)
T 3dxb_A          204 KVVAEVYDQ  212 (222)
T ss_dssp             BCEEEECCH
T ss_pred             EEEEEEcCH
Confidence            999999863

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.82  E-value=1.8e-08  Score=76.76  Aligned_cols=74  Identities=19%  Similarity=0.173  Sum_probs=67.9

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-----CCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeE
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERF-----GVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREI  133 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~-----G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i  133 (299)
                      +...+|-|-|||..++...|..|++.+     |.|+.|.+..|      -+-|+|+|.+...|-+|.-.|||.+|.|++|
T Consensus        19 ~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pD------H~GAivef~d~~~AgKasLaL~G~ef~gr~L   92 (117)
T 2l9w_A           19 ELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSD------FNGAIIIFRDSKFAAKMLMILNGSQFQGKVI   92 (117)
T ss_dssp             TTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETT------TTEEEEECSCHHHHHHHHHHHSSEEETTEEE
T ss_pred             cCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecC------CCceEEEEccchhhHHHHhhcCCeeecCeEE
Confidence            456789999999999999999999999     99999999988      4789999999999999999999999999999


Q ss_pred             EEEEc
Q 043443          134 SVVLA  138 (299)
Q Consensus       134 ~V~~a  138 (299)
                      .|.-.
T Consensus        93 r~gTv   97 (117)
T 2l9w_A           93 RSGTI   97 (117)
T ss_dssp             EEECH
T ss_pred             EecCH
Confidence            98644

>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=98.27  E-value=1.5e-06  Score=65.84  Aligned_cols=76  Identities=17%  Similarity=0.249  Sum_probs=64.4

Q ss_pred             CCCEEEEeCCCCCC-C----HHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEE
Q 043443           60 NHGSLLVRNIPLDC-R----PEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREIS  134 (299)
Q Consensus        60 ~~~~l~V~nLp~~~-t----e~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~  134 (299)
                      ..++|+|+||+..+ .    .+.++++|..|+++....+.+.      -.-..|.|.+.++|.+|-..||+..|.|..|+
T Consensus         4 ~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkS------FRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r   77 (104)
T 1wey_A            4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT------TTEEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCc------ceEEEEEeCChHHHHHHHHHhccceecCceeE
Confidence            35789999998865 2    2577899999999988777654      34679999999999999999999999999999


Q ss_pred             EEEcccC
Q 043443          135 VVLAAES  141 (299)
Q Consensus       135 V~~a~~~  141 (299)
                      |.++.+.
T Consensus        78 ~YFgq~~   84 (104)
T 1wey_A           78 LYFAQTL   84 (104)
T ss_dssp             EECCCCS
T ss_pred             EEecCCC
Confidence            9999843

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.01  E-value=7.7e-05  Score=56.22  Aligned_cols=71  Identities=21%  Similarity=0.189  Sum_probs=59.6

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhc-----CCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEE
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFER-----FGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV  135 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~~-----~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V  135 (299)
                      ..+|.|.|||..+.++.|+-+|++     -|+|..|....        +-|+|+|.+.+.|+..|+. ..+.|++..|.|
T Consensus         8 ~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k-~~H~L~~~~LsV   78 (104)
T 2dhx_A            8 GVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQ-ADHELHGAQLSL   78 (104)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTC-SCCBSSSSBCEE
T ss_pred             ccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcC-CcceecCeEEEE
Confidence            469999999999999999999987     26888887753        5799999999999999873 467888999998


Q ss_pred             EEccc
Q 043443          136 VLAAE  140 (299)
Q Consensus       136 ~~a~~  140 (299)
                      ....+
T Consensus        79 ~P~~~   83 (104)
T 2dhx_A           79 RPAPP   83 (104)
T ss_dssp             EECCC
T ss_pred             EcCCC
Confidence            76554

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=97.92  E-value=4.3e-05  Score=59.32  Aligned_cols=73  Identities=14%  Similarity=0.235  Sum_probs=59.7

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCC-eeEEEEE
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAG-REISVVL  137 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~G-r~i~V~~  137 (299)
                      ...+.|.|.+.|... ...|..+|.+||+|.+....      ....+..|.|.+..+|++||. .||..|+| ..|-|..
T Consensus        22 ~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~------~~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p   93 (119)
T 1wwh_A           22 LDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKP   93 (119)
T ss_dssp             GGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEE
T ss_pred             CCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC------CCCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEE
Confidence            346789999998875 67788899999999988763      235799999999999999998 59999985 6666766


Q ss_pred             cc
Q 043443          138 AA  139 (299)
Q Consensus       138 a~  139 (299)
                      ..
T Consensus        94 ~~   95 (119)
T 1wwh_A           94 CI   95 (119)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=97.79  E-value=0.00011  Score=54.51  Aligned_cols=78  Identities=13%  Similarity=0.161  Sum_probs=61.7

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCC--CCccEEEEEEcCHHHHHHHHHhhCCceeCCe-----eEE
Q 043443           62 GSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTG--EPRGFAFVQFVDPYEAAEAQHHMNGKRFAGR-----EIS  134 (299)
Q Consensus        62 ~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g--~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr-----~i~  134 (299)
                      ++|.|.+||+.+||+++.+.+..+.++....++..+.+.  ....-|||.|.+.+++....+.++|..|-+.     ...
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            589999999999999999999999888776665443322  2346799999999999999999999987432     335


Q ss_pred             EEEcc
Q 043443          135 VVLAA  139 (299)
Q Consensus       135 V~~a~  139 (299)
                      |++|.
T Consensus        82 VE~AP   86 (91)
T 1uw4_A           82 VEFAP   86 (91)
T ss_dssp             EEECS
T ss_pred             EEEcC
Confidence            66664

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=97.78  E-value=0.0001  Score=54.94  Aligned_cols=56  Identities=23%  Similarity=0.353  Sum_probs=47.1

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhC
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMN  124 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~ln  124 (299)
                      ..+.++| ++|..+...||.++|..||.| .|.++.|       .-|||.|.+.+.|..||..+.
T Consensus        15 r~HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~WidD-------TsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           15 RDHVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDD-------TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCSEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEET-------TEEEEECSCHHHHHHHHHHHH
T ss_pred             CCeEEEE-eCChhhhhHHHHHHhhccCCE-EEEEEcC-------CeEEEEecCHHHHHHHHHhcc
Confidence            3466777 999999999999999999965 4666655       489999999999999998764

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=97.52  E-value=0.0001  Score=55.02  Aligned_cols=54  Identities=24%  Similarity=0.360  Sum_probs=45.8

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhC
Q 043443           62 GSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMN  124 (299)
Q Consensus        62 ~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~ln  124 (299)
                      +.|+| ++|..+...||.++|..||.| .|.++.|       .-|||.|.+.+.|..||..+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fggv-~I~WidD-------TsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDD-------TSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSEEE-EEEEEET-------TEEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccCCE-EEEEEcC-------CeEEEEecCHHHHHHHHHhcc
Confidence            45666 999999999999999999944 5666665       489999999999999999774

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=97.41  E-value=0.00026  Score=55.68  Aligned_cols=79  Identities=19%  Similarity=0.278  Sum_probs=57.0

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeE-EEeccCC------------CCC-CCccEEEEEEcCHHHHHHHHHhhCC
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRD-VYLPKDY------------YTG-EPRGFAFVQFVDPYEAAEAQHHMNG  125 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~-v~i~~d~------------~~g-~~~g~afVeF~~~~~A~~Al~~lng  125 (299)
                      ..+.|.|.+.|..++ ..|.++|++||.|.+ +.+....            ... ...++..|+|++..+|.+||. .||
T Consensus         6 ~e~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG   83 (132)
T 3p3d_A            6 GELAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENG   83 (132)
T ss_dssp             --CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTT
T ss_pred             CceEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCC
Confidence            456788889987655 456678999999976 2222100            000 135788999999999999998 599


Q ss_pred             ceeCCeeEEEEEccc
Q 043443          126 KRFAGREISVVLAAE  140 (299)
Q Consensus       126 ~~l~Gr~i~V~~a~~  140 (299)
                      ..|+|..|-|.+..+
T Consensus        84 ~ii~G~mIGV~Py~~   98 (132)
T 3p3d_A           84 AVFNGVLLGVIPYTK   98 (132)
T ss_dssp             CEETTEECEEEECCH
T ss_pred             eEeCcEEEEEEECCH
Confidence            999999888887753

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=97.32  E-value=0.00059  Score=50.95  Aligned_cols=80  Identities=14%  Similarity=0.176  Sum_probs=57.7

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCC--CCccEEEEEEcCHHHHHHHHHhhCCceeCCe-----e
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTG--EPRGFAFVQFVDPYEAAEAQHHMNGKRFAGR-----E  132 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g--~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr-----~  132 (299)
                      -.-+|.|..||+.+||+++.+.+..+-++....++..+.+.  ..-.-|||.|.+.+++....+.++|..|-+.     +
T Consensus         8 ~~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~   87 (97)
T 2l08_A            8 HSHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYP   87 (97)
T ss_dssp             CCCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEE
T ss_pred             cceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEee
Confidence            35689999999999999998888776555433333222221  1235789999999999999999999987432     4


Q ss_pred             EEEEEcc
Q 043443          133 ISVVLAA  139 (299)
Q Consensus       133 i~V~~a~  139 (299)
                      ..|++|.
T Consensus        88 a~VE~AP   94 (97)
T 2l08_A           88 AVVEFAP   94 (97)
T ss_dssp             EEEEECC
T ss_pred             eEEEecC
Confidence            5567664

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=96.57  E-value=0.001  Score=63.40  Aligned_cols=58  Identities=17%  Similarity=0.361  Sum_probs=44.1

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHH
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQH  121 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~  121 (299)
                      ++....|||. ++..+++.+|.++|.+||.|..+.+..++     ..||+|||.+.+++..++.
T Consensus        50 ~qa~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~-----g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           50 EQAQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF-----GLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HHHHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS-----SEEEEEECC---CCHHHHS
T ss_pred             HHhcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC-----CeEEEEEeCCHHHHHHHHh
Confidence            3456799997 79999999999999999999999887653     4799999999998887765

>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=96.06  E-value=0.0021  Score=51.46  Aligned_cols=40  Identities=20%  Similarity=0.153  Sum_probs=36.6

Q ss_pred             CCCccEEEEEEcCHHHHHHHHHhh-CCceeCCeeEEEEEccc
Q 043443          100 GEPRGFAFVQFVDPYEAAEAQHHM-NGKRFAGREISVVLAAE  140 (299)
Q Consensus       100 g~~~g~afVeF~~~~~A~~Al~~l-ng~~l~Gr~i~V~~a~~  140 (299)
                      ...+|+++|+|.+.++|++||+.| |+..|+| .|.|.++..
T Consensus        10 ~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~   50 (150)
T 2i2y_A           10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATK   50 (150)
T ss_dssp             SSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTT
T ss_pred             ccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccC
Confidence            456899999999999999999999 9999999 999998764

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=95.92  E-value=0.0053  Score=49.31  Aligned_cols=34  Identities=15%  Similarity=0.036  Sum_probs=27.2

Q ss_pred             EEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCc
Q 043443           91 VYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGK  126 (299)
Q Consensus        91 v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~  126 (299)
                      +.|+.+.  ...+|||||+|.+.++|++||+.+++.
T Consensus         3 ~kl~ln~--~~~~G~~fV~f~~~~~A~~al~~~~~~   36 (158)
T 2kn4_A            3 YKLILNG--KTLKGETTTEAVDAATAEKVFKQYAND   36 (158)
T ss_dssp             EEEEEEC--SSCEEEEEEECSSHHHHHHHHHHHHHH
T ss_pred             EEEEecC--ccccchhHHHHHHHHhHHHHHHhhccc
Confidence            4455543  367899999999999999999888754

>4eyt_A Telomerase associated protein P65; RNA, LA protein, LARP7, RRM, XRRM, RNA binding protein; 2.50A {Tetrahymena thermophila} PDB: 4erd_A

Probab=93.26  E-value=0.51  Score=34.36  Aligned_cols=71  Identities=17%  Similarity=0.189  Sum_probs=55.7

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCc-------eeCCe
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGK-------RFAGR  131 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~-------~l~Gr  131 (299)
                      ...+-|-|-|||..+-..++.-.....|---+|+.+        .|.|+|.|.+.++...||++|-+.       +|.|.
T Consensus        10 kqnclikiinipqgtlkaevvlavrhlgyefycdyi--------dgqamirfqnsdeqrlaiqkllnhnnnklqieirgq   81 (129)
T 4eyt_A           10 KQNCLIKIINIPQGTLKAEVVLAVRHLGYEFYCDYI--------DGQAMIRFQNSDEQRLAIQKLLNHNNNKLQIEIRGQ   81 (129)
T ss_dssp             CCSCEEEEECCCTTCCHHHHHHHHHTTCCCEEEEEC--------SSCEEEEESSHHHHHHHHHHHEETTTTEEEEEETTE
T ss_pred             hhCcEEEEEecCCCceeeeeEEeehhcCeeEeeeee--------cCeeEEEecCChHHHHHHHHHHhcCCCEEEEEEcce
Confidence            356788899999999999988888888877788776        378999999999999999877321       35566


Q ss_pred             eEEEEE
Q 043443          132 EISVVL  137 (299)
Q Consensus       132 ~i~V~~  137 (299)
                      .+.|--
T Consensus        82 icdvis   87 (129)
T 4eyt_A           82 ICDVIS   87 (129)
T ss_dssp             EEEEEC
T ss_pred             eeeeee
Confidence            555543

>2g0c_A ATP-dependent RNA helicase DBPA; RNA recognition motif, hydrolase; 1.70A {Bacillus subtilis} PDB: 3moj_B

Probab=93.21  E-value=0.19  Score=35.16  Aligned_cols=68  Identities=10%  Similarity=0.178  Sum_probs=45.2

Q ss_pred             EEEEeCC-CCCCCHHHHHHHHhcCC-----CEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           63 SLLVRNI-PLDCRPEELRAPFERFG-----VVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        63 ~l~V~nL-p~~~te~dL~~~F~~~G-----~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      +|||..- -..+...+|..++..-+     .|-.|+|..        .|.||+... +.|+.+++.|++..++|+.|.|+
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            5666322 34567788888887654     455677753        489999976 56888999999999999999998


Q ss_pred             Ecc
Q 043443          137 LAA  139 (299)
Q Consensus       137 ~a~  139 (299)
                      .++
T Consensus        73 ~~~   75 (76)
T 2g0c_A           73 KAN   75 (76)
T ss_dssp             ECC
T ss_pred             ECC
Confidence            764

>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=92.80  E-value=0.22  Score=47.99  Aligned_cols=55  Identities=24%  Similarity=0.353  Sum_probs=45.7

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhC
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMN  124 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~ln  124 (299)
                      ...++|+ +|..+...+|.++|+.||.| .|.++.+       ..|||.|.+.+.|..++..++
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~widd-------t~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWIDD-------TSAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEECSS-------SEEEEECSCHHHHHHHHHHHT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEEcC-------CeEEEEECCHHHHHHHHHHHH
Confidence            4567776 88889999999999999965 5555544       579999999999999999885

>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=90.91  E-value=1.9  Score=40.57  Aligned_cols=24  Identities=13%  Similarity=0.313  Sum_probs=15.5

Q ss_pred             EEcCHHHHHHHHHhhCCceeCCeeEE
Q 043443          109 QFVDPYEAAEAQHHMNGKRFAGREIS  134 (299)
Q Consensus       109 eF~~~~~A~~Al~~lng~~l~Gr~i~  134 (299)
                      .|.+.++.+.|..+|.  .|+|..|.
T Consensus       147 aFV~F~~~e~A~~Ai~--~lng~~i~  170 (437)
T 3pgw_S          147 AFIEYEHERDMHSAYK--HADGKKID  170 (437)
T ss_pred             EEEeeccHHHHHHHHH--HcCCCEEC
Confidence            5566677777777664  35676654

---

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	299
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	3e-18
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	4e-17
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	8e-16
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	1e-15
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	6e-15
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	2e-14
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	2e-14
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-14
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-14
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	1e-13
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	2e-13
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	2e-13
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-13
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	5e-13
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	6e-13
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	7e-13
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	2e-12
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	2e-12
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	2e-12
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	2e-12
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	6e-12
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	6e-12
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	7e-12
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	8e-12
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	9e-12
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	9e-12
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	1e-11
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	1e-11
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	2e-11
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	2e-11
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	2e-11
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	3e-11
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-11
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	3e-11
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	4e-11
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	5e-11
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	5e-11
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	7e-11
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	9e-11
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	1e-10
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	1e-10
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 1e-10
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	1e-10
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-10
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	3e-10
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	4e-10
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	4e-10
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	9e-10
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-07
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	1e-09
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	1e-09
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	1e-09
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	1e-09
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-09
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	2e-09
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	6e-09
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	9e-09
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	2e-08
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	2e-08
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	3e-08
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	3e-08
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	9e-08
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	1e-07
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	3e-07
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	3e-07
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	9e-07
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	9e-07
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	1e-06
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	3e-06
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	8e-06
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	1e-05
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	1e-05
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	1e-05
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	2e-05
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	5e-05
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	5e-05
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	9e-05
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	1e-04
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-04
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-04
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	3e-04

>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 = 75.3 bits (185), Expect = 3e-18
 Identities = 19/76 (25%), Positives = 33/76 (43%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           SL V ++  D     L   F   G +  + + +D  T    G+A+V F  P +A  A   
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 123 MNGKRFAGREISVVLA 138
           MN     G+ + ++ +
Sbjct: 62  MNFDVIKGKPVRIMWS 77

>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 = 73.0 bits (179), Expect = 4e-17
 Identities = 31/92 (33%), Positives = 46/92 (50%), Gaps = 3/92 (3%)

Query: 57  KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDY-YTGEPRGFAFVQFVDPYE 115
           K+Q    +LVRNIP      E+R  F  FG ++ V LPK    TG  RGF FV F+   +
Sbjct: 4   KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQD 63

Query: 116 AAEAQHHM-NGKRFAGREISVVLAAESRKRPE 146
           A +A + + +     GR + +   A+S    +
Sbjct: 64  AKKAFNALCHSTHLYGRRLVLEW-ADSEVTVQ 94

>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 = 68.8 bits (168), Expect = 8e-16
 Identities = 20/77 (25%), Positives = 33/77 (42%), Gaps = 1/77 (1%)

Query: 62  GSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQH 121
           G LLV N+       +++  F  FG ++   +     +G   G A V F    +A +A  
Sbjct: 1   GKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHY-DRSGRSLGTADVHFERKADALKAMK 59

Query: 122 HMNGKRFAGREISVVLA 138
             NG    GR +++ L 
Sbjct: 60  QYNGVPLDGRPMNIQLV 76

>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 = 68.8 bits (168), Expect = 1e-15
 Identities = 26/78 (33%), Positives = 40/78 (51%), Gaps = 2/78 (2%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           +L V N+P     ++L   F ++G +    + +D  TG PRG AFV++    EA EA   
Sbjct: 8   NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 67

Query: 123 MNGKRFAG--REISVVLA 138
           +N     G  + +SV LA
Sbjct: 68  LNNVIPEGGSQPLSVRLA 85

>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 = 67.3 bits (164), Expect = 6e-15
 Identities = 23/90 (25%), Positives = 43/90 (47%), Gaps = 3/90 (3%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L +RN+P     EE+   F ++G +R + +     T E RG A+V + D ++A  A  H+
Sbjct: 10  LYIRNLPYKITAEEMYDIFGKYGPIRQIRVG---NTPETRGTAYVVYEDIFDAKNACDHL 66

Query: 124 NGKRFAGREISVVLAAESRKRPEEMRQRHR 153
           +G     R + V+    +R   +   ++  
Sbjct: 67  SGFNVCNRYLVVLYYNANRAFQKMDTKKKE 96

>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 = 65.0 bits (158), Expect = 2e-14
 Identities = 18/75 (24%), Positives = 31/75 (41%), Gaps = 1/75 (1%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           + +  +      E LR  F +FG V++  + +D  T   RGF FV F+D     +     
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ-AGVDKVLAQ 61

Query: 124 NGKRFAGREISVVLA 138
           +      + I   +A
Sbjct: 62  SRHELDSKTIDPKVA 76

>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 = 65.0 bits (158), Expect = 2e-14
 Identities = 23/76 (30%), Positives = 35/76 (46%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           +L+V  +P D    EL A F   G +    + +DY TG   G+AFV F    ++  A   
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 123 MNGKRFAGREISVVLA 138
           +NG     + + V  A
Sbjct: 64  LNGITVRNKRLKVSYA 79

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 65.1 bits (158), Expect = 2e-14
 Identities = 18/85 (21%), Positives = 35/85 (41%), Gaps = 4/85 (4%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRD---VYLPKDYYTGEPRGFAFVQFVDPYEAAEAQ 120
           L ++N+      E L+  F + G ++                 GF FV++  P +A +A 
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 121 HHMNGKRFAGREISVVLAAESRKRP 145
             + G    G ++ V + +E   +P
Sbjct: 61  KQLQGHTVDGHKLEVRI-SERATKP 84

>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 = 65.1 bits (158), Expect = 2e-14
 Identities = 31/82 (37%), Positives = 42/82 (51%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
            L V  +  +   + L A F  FG + D+ +P DY T + RGFAFV+F    +AA A  +
Sbjct: 7   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66

Query: 123 MNGKRFAGREISVVLAAESRKR 144
           MN     GR I V LA   R +
Sbjct: 67  MNESELFGRTIRVNLAKPMRIK 88

>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 = 63.4 bits (154), Expect = 1e-13
 Identities = 19/89 (21%), Positives = 37/89 (41%)

Query: 56  RKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYE 115
           +  +   +L V N+      E++   F + G ++ + +  D       GF FV++    +
Sbjct: 2   KLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRAD 61

Query: 116 AAEAQHHMNGKRFAGREISVVLAAESRKR 144
           A  A  ++NG R   R I     A  ++ 
Sbjct: 62  AENAMRYINGTRLDDRIIRTDWDAGFKEG 90

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.2 bits (153), Expect = 2e-13
 Identities = 20/92 (21%), Positives = 33/92 (35%), Gaps = 5/92 (5%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRD--VYLPKDYYTGEPRGFAFVQFVDPYEAAEAQH 121
           L +  IP   + EE+     +        +         + RGFAFV++     AA A+ 
Sbjct: 4   LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 63

Query: 122 HMNGKRF--AGREISVVLAAESRKR-PEEMRQ 150
            +   R    G +I+V  A        + M  
Sbjct: 64  KLMPGRIQLWGHQIAVDWAEPEIDVDEDVMET 95

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.1 bits (153), Expect = 2e-13
 Identities = 21/88 (23%), Positives = 40/88 (45%), Gaps = 1/88 (1%)

Query: 57  KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEA 116
           +E++  ++    +    RP +L   F   G VRDV +  D  +   +G A+V+F +  ++
Sbjct: 14  EERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEI-QS 72

Query: 117 AEAQHHMNGKRFAGREISVVLAAESRKR 144
                 + G+R  G  I V  +   + R
Sbjct: 73  VPLAIGLTGQRLLGVPIIVQASQAEKNR 100

>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 = 62.3 bits (151), Expect = 3e-13
 Identities = 20/80 (25%), Positives = 39/80 (48%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L +  +P     ++++     FG ++   L KD  TG  +G+AF ++VD     +A   +
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 124 NGKRFAGREISVVLAAESRK 143
           NG +   +++ V  A+   K
Sbjct: 64  NGMQLGDKKLLVQRASVGAK 83

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.3 bits (148), Expect = 5e-13
 Identities = 25/76 (32%), Positives = 41/76 (53%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           +L+V  +P +   EE R+ F   G +    L +D  TG+  G+ FV ++DP +A +A + 
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 123 MNGKRFAGREISVVLA 138
           +NG R   + I V  A
Sbjct: 64  LNGLRLQTKTIKVSYA 79

>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 = 61.6 bits (149), Expect = 6e-13
 Identities = 25/91 (27%), Positives = 43/91 (47%), Gaps = 1/91 (1%)

Query: 54  GRRKEQNHG-SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVD 112
           G   E+N   ++ V  +        L   F + G V + ++PKD  TG+ +G+ FV+F+ 
Sbjct: 1   GPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLS 60

Query: 113 PYEAAEAQHHMNGKRFAGREISVVLAAESRK 143
             +A  A   M+  +  G+ I V  A+   K
Sbjct: 61  EEDADYAIKIMDMIKLYGKPIRVNKASAHNK 91

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.1 bits (148), Expect = 7e-13
 Identities = 24/92 (26%), Positives = 39/92 (42%), Gaps = 3/92 (3%)

Query: 55  RRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPY 114
           +R  Q    L+V  +P     ++L+  F  FG V  V + KD  TG  +GF FV+F +  
Sbjct: 2   KRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYE 61

Query: 115 EAAEAQHHMNGKRFAGREISVVLAAESRKRPE 146
              +     +     GR     L   S++  +
Sbjct: 62  TQVKVMSQRHM--IDGRWCDCKL-PNSKQSQD 90

>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 = 60.1 bits (145), Expect = 2e-12
 Identities = 26/73 (35%), Positives = 36/73 (49%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
            L V  + L     +LR  F ++G + DV +  D  +   RGFAFV F +  +A EA+  
Sbjct: 11  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 70

Query: 123 MNGKRFAGREISV 135
            NG    GR I V
Sbjct: 71  ANGMELDGRRIRV 83

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 60.1 bits (145), Expect = 2e-12
 Identities = 20/75 (26%), Positives = 32/75 (42%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           + V+N+P     +E+   F  + V+      K    G P G A V F    EA  A   +
Sbjct: 12  IKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDL 71

Query: 124 NGKRFAGREISVVLA 138
           N +    R++ +VL 
Sbjct: 72  NDRPIGSRKVKLVLG 86

>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 = 60.0 bits (145), Expect = 2e-12
 Identities = 22/85 (25%), Positives = 38/85 (44%), Gaps = 6/85 (7%)

Query: 54  GRRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDP 113
           G +       L V N+P D   EE+R  FE++G   +V++ KD        F F++    
Sbjct: 1   GEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG------FGFIRLETR 54

Query: 114 YEAAEAQHHMNGKRFAGREISVVLA 138
             A  A+  ++     G+++ V  A
Sbjct: 55  TLAEIAKVELDNMPLRGKQLRVRFA 79

>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 = 60.1 bits (145), Expect = 2e-12
 Identities = 24/77 (31%), Positives = 37/77 (48%), Gaps = 2/77 (2%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L V  +P     +EL   F ++G +    +  D  TG  RG  F++F    EA EA   +
Sbjct: 9   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 68

Query: 124 NGKRFAGRE--ISVVLA 138
           NG++ +G    I+V  A
Sbjct: 69  NGQKPSGATEPITVKFA 85

>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 = 6e-12
 Identities = 20/84 (23%), Positives = 35/84 (41%), Gaps = 1/84 (1%)

Query: 55  RRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPY 114
           +R+++    L +  +  +   E LR  +E++G + D  + +D  +   RGF FV F    
Sbjct: 14  KREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMA 73

Query: 115 EAAEAQHHMNGKRFAGREISVVLA 138
           E   A          GR +    A
Sbjct: 74  EVDAAM-AARPHSIDGRVVEPKRA 96

>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 = 58.2 bits (140), Expect = 6e-12
 Identities = 19/75 (25%), Positives = 32/75 (42%), Gaps = 1/75 (1%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           + V  + ++   E+++  FE+FG V D  L  D  T   RGF FV F    +  E    +
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESE-DIVEKVCEI 60

Query: 124 NGKRFAGREISVVLA 138
           +      + +    A
Sbjct: 61  HFHEINNKMVECKKA 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 = 58.5 bits (141), Expect = 7e-12
 Identities = 26/83 (31%), Positives = 45/83 (54%)

Query: 56  RKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYE 115
           R+  ++ ++ V N+  D R  +L+  F  FG +  +YL KD  TG+ +GFAF+ F    +
Sbjct: 3   RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRED 62

Query: 116 AAEAQHHMNGKRFAGREISVVLA 138
           AA A   ++G  +    ++V  A
Sbjct: 63  AARAIAGVSGFGYDHLILNVEWA 85

>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 = 58.1 bits (140), Expect = 8e-12
 Identities = 20/75 (26%), Positives = 34/75 (45%), Gaps = 1/75 (1%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L +  +  +   E LR+ FE++G + D  + +D  T   RGF FV +    E  +A  + 
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATV-EEVDAAMNA 67

Query: 124 NGKRFAGREISVVLA 138
              +  GR +    A
Sbjct: 68  RPHKVDGRVVEPKRA 82

>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 = 57.7 bits (139), Expect = 9e-12
 Identities = 21/75 (28%), Positives = 33/75 (44%), Gaps = 1/75 (1%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           + +  +  D   ++L+  F +FG V D  L  D  TG  RGF FV F +  E+ +     
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKES-ESVDKVMDQ 60

Query: 124 NGKRFAGREISVVLA 138
              +  G+ I    A
Sbjct: 61  KEHKLNGKVIDPKRA 75

>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 = 58.4 bits (141), Expect = 9e-12
 Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 4/63 (6%)

Query: 76  EELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV 135
           E+LR    +FG +R + L   +      G A V F DP EA      ++G+ F GR+I+ 
Sbjct: 34  EDLRVECSKFGQIRKLLLFDRHP----DGVASVSFRDPEEADYCIQTLDGRWFGGRQITA 89

Query: 136 VLA 138
              
Sbjct: 90  QAW 92

>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 = 58.1 bits (140), Expect = 1e-11
 Identities = 16/88 (18%), Positives = 32/88 (36%), Gaps = 6/88 (6%)

Query: 55  RRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPY 114
            +    + ++    I      + +R  F  FG + ++ +  +        ++FV+F    
Sbjct: 12  NQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG------YSFVRFSTHE 65

Query: 115 EAAEAQHHMNGKRFAGREISVVLAAESR 142
            AA A   +NG    G  +      ES 
Sbjct: 66  SAAHAIVSVNGTTIEGHVVKCYWGKESP 93

>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 = 57.7 bits (139), Expect = 1e-11
 Identities = 18/90 (20%), Positives = 37/90 (41%), Gaps = 5/90 (5%)

Query: 56  RKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYE 115
           +K +   +LL +N+  +   +EL+  FE       + +      G+ +G A+++F    +
Sbjct: 11  KKVRAARTLLAKNLSFNITEDELKEVFEDA-----LEIRLVSQDGKSKGIAYIEFKSEAD 65

Query: 116 AAEAQHHMNGKRFAGREISVVLAAESRKRP 145
           A +      G    GR +S+    E     
Sbjct: 66  AEKNLEEKQGAEIDGRSVSLYYTGEKGGTR 95

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.9 bits (137), Expect = 2e-11
 Identities = 19/75 (25%), Positives = 31/75 (41%), Gaps = 1/75 (1%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           + V  +  D   E++R  F  FG V  + LP D  T + RGF F+ F +  E  +     
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEE-EPVKKIMEK 60

Query: 124 NGKRFAGREISVVLA 138
                   +  + +A
Sbjct: 61  KYHNVGLSKCEIKVA 75

>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 = 57.1 bits (137), Expect = 2e-11
 Identities = 13/75 (17%), Positives = 24/75 (32%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L + N P       +R   +   VV              R FA++      +A      +
Sbjct: 4   LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 63

Query: 124 NGKRFAGREISVVLA 138
           NG +  G  +   ++
Sbjct: 64  NGLKIEGYTLVTKVS 78

>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 = 57.1 bits (137), Expect = 2e-11
 Identities = 21/82 (25%), Positives = 37/82 (45%), Gaps = 1/82 (1%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVY-LPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           + + N+  +   + L   F  FGV+     + +D  TG  +G+AF+ F     +  A   
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 123 MNGKRFAGREISVVLAAESRKR 144
           MNG+    R I+V  A +   +
Sbjct: 61  MNGQYLCNRPITVSYAFKKDSK 82

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.1 bits (137), Expect = 3e-11
 Identities = 29/83 (34%), Positives = 41/83 (49%)

Query: 62  GSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQH 121
           G L V  +  D   + L   F ++G + +V + KD  T   RGF FV F +  +A +A  
Sbjct: 6   GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 65

Query: 122 HMNGKRFAGREISVVLAAESRKR 144
            MNGK   GR+I V  A +S   
Sbjct: 66  AMNGKSVDGRQIRVDQAGKSSDN 88

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.3 bits (138), Expect = 3e-11
 Identities = 16/80 (20%), Positives = 36/80 (45%), Gaps = 2/80 (2%)

Query: 65  LVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEP--RGFAFVQFVDPYEAAEAQHH 122
           L+ +   +   E++R    ++G+V+ + +P+     E    G  FV+F   ++  +A   
Sbjct: 18  LLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQG 77

Query: 123 MNGKRFAGREISVVLAAESR 142
           + G++FA R +         
Sbjct: 78  LTGRKFANRVVVTKYCDPDS 97

>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 = 3e-11
 Identities = 19/87 (21%), Positives = 37/87 (42%), Gaps = 2/87 (2%)

Query: 58  EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAA 117
           +    +L V N+  D     +   F + G  +   +  ++       + FV+F +  +AA
Sbjct: 5   DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH--TSNDPYCFVEFYEHRDAA 62

Query: 118 EAQHHMNGKRFAGREISVVLAAESRKR 144
            A   MNG++  G+E+ V  A     +
Sbjct: 63  AALAAMNGRKILGKEVKVNWATTPSSQ 89

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.6 bits (136), Expect = 4e-11
 Identities = 27/96 (28%), Positives = 43/96 (44%), Gaps = 3/96 (3%)

Query: 49  GGGGYGRRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFV 108
           GGG        N   + V N+P D R +++   F ++G +RD+ L           FAFV
Sbjct: 2   GGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRG---GPPFAFV 58

Query: 109 QFVDPYEAAEAQHHMNGKRFAGREISVVLAAESRKR 144
           +F DP +A +A +  +G  + G  + V      R  
Sbjct: 59  EFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGT 94

>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 = 56.6 bits (136), Expect = 5e-11
 Identities = 25/97 (25%), Positives = 40/97 (41%), Gaps = 1/97 (1%)

Query: 49  GGGGYGRRKEQNHGS-LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAF 107
             G  G +KE   G+ L + ++P +   ++L   F  FG V    +  D  T   + F F
Sbjct: 5   SIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGF 64

Query: 108 VQFVDPYEAAEAQHHMNGKRFAGREISVVLAAESRKR 144
           V + +P  A  A   MNG +   + + V L       
Sbjct: 65  VSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDS 101

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.7 bits (136), Expect = 5e-11
 Identities = 31/95 (32%), Positives = 50/95 (52%), Gaps = 1/95 (1%)

Query: 57  KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEA 116
            +++  S+ V NIP +   E+L+  F   G V    L  D  TG+P+G+ F ++ D   A
Sbjct: 4   VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETA 63

Query: 117 AEAQHHMNGKRFAGREISVVLAAESRKRPEEMRQR 151
             A  ++NG+ F+GR + V   A S K  EE++  
Sbjct: 64  LSAMRNLNGREFSGRALRVDN-AASEKNKEELKSL 97

>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 = 55.1 bits (132), Expect = 7e-11
 Identities = 21/75 (28%), Positives = 32/75 (42%), Gaps = 1/75 (1%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           + V  I  D     LR  FE++G +  + +  D  +G+ RGFAFV F D  ++ +     
Sbjct: 5   IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH-DSVDKIVIQ 63

Query: 124 NGKRFAGREISVVLA 138
                 G    V  A
Sbjct: 64  KYHTVNGHNCEVRKA 78

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.4 bits (133), Expect = 9e-11
 Identities = 19/85 (22%), Positives = 33/85 (38%), Gaps = 2/85 (2%)

Query: 60  NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEA 119
             G++ ++N+      + L   F  FG +    +  D      +G+ FV F     A  A
Sbjct: 7   GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERA 64

Query: 120 QHHMNGKRFAGREISVVLAAESRKR 144
              MNG     R++ V      ++R
Sbjct: 65  IEKMNGMLLNDRKVFVGRFKSRKER 89

>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 = 55.4 bits (133), Expect = 1e-10
 Identities = 17/87 (19%), Positives = 33/87 (37%), Gaps = 1/87 (1%)

Query: 63  SLLVRNIPLDCRPEELR-APFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQH 121
           ++ + N+    + +EL+ +    F     +       + + RG AFV F +   A  A  
Sbjct: 5   TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALR 64

Query: 122 HMNGKRFAGREISVVLAAESRKRPEEM 148
            M G  F  + + +  A        +M
Sbjct: 65  SMQGFPFYDKPMRIQYAKTDSDIIAKM 91

>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 = 55.0 bits (132), Expect = 1e-10
 Identities = 24/81 (29%), Positives = 31/81 (38%), Gaps = 6/81 (7%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L VRN+ L    E +   F                  + R +AFV F +  +A EA   +
Sbjct: 11  LYVRNLMLSTSEEMIEKEFNNIKPG------AVERVKKIRDYAFVHFSNREDAVEAMKAL 64

Query: 124 NGKRFAGREISVVLAAESRKR 144
           NGK   G  I V LA    K 
Sbjct: 65  NGKVLDGSPIEVTLAKPVDKD 85

>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 = 55.4 bits (133), Expect = 1e-10
 Identities = 13/70 (18%), Positives = 29/70 (41%), Gaps = 1/70 (1%)

Query: 66  VRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNG 125
           ++    +   E      E++G V ++ +  +       G  +V+F    +A +A   +N 
Sbjct: 32  MQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNN 90

Query: 126 KRFAGREISV 135
           + F G+ I  
Sbjct: 91  RWFNGQPIHA 100

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.4 bits (130), Expect = 1e-10
 Identities = 13/70 (18%), Positives = 26/70 (37%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L +R +      ++L    + +G +       D  T + +G+ FV F  P  A +A   +
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 124 NGKRFAGREI 133
                  +  
Sbjct: 61  KASGVQAQMA 70

>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 = 54.9 bits (132), Expect = 2e-10
 Identities = 24/99 (24%), Positives = 46/99 (46%), Gaps = 10/99 (10%)

Query: 48  GGGGGYGRRKEQNHGS-LLVRNIPLD-CRPEELRAPFERFGVVRDVYLPKDYYTGEPRGF 105
           G  G  G+   ++  S + + N+     +  ++ A F ++G +    +         +GF
Sbjct: 1   GSSGSSGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH--------KGF 52

Query: 106 AFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAESRKR 144
           AFVQ+V+   A  A    +G+  AG+ + + LAAE +  
Sbjct: 53  AFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPKVN 91

>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 = 54.0 bits (129), Expect = 3e-10
 Identities = 27/97 (27%), Positives = 47/97 (48%), Gaps = 11/97 (11%)

Query: 57  KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLP--------KDYYTGEPRGFAFV 108
           ++ ++ ++ V+ +      ++L   F++ GVV+              D  TG+P+G A V
Sbjct: 4   EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATV 63

Query: 109 QFVDPYEAAEAQHHMNGKRFAGREISVVLAAESRKRP 145
            + DP  A  A    +GK F G ++ V LA   RK+P
Sbjct: 64  SYEDPPTAKAAVEWFDGKDFQGSKLKVSLA---RKKP 97

>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 = 53.2 bits (127), Expect = 4e-10
 Identities = 17/82 (20%), Positives = 30/82 (36%), Gaps = 7/82 (8%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L + N+      ++LR  F    +                G+AFV + D   A  A   +
Sbjct: 4   LYIGNLSPAVTADDLRQLFGDRKLPLA------GQVLLKSGYAFVDYPDQNWAIRAIETL 57

Query: 124 NGK-RFAGREISVVLAAESRKR 144
           +GK    G+ + V  +   + R
Sbjct: 58  SGKVELHGKIMEVDYSVSKKLR 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 = 53.6 bits (128), Expect = 4e-10
 Identities = 28/93 (30%), Positives = 48/93 (51%)

Query: 54  GRRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDP 113
           G       G L VRN+      E+L   F  +G + +++ P D  T +P+GFAFV F+ P
Sbjct: 1   GSSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFP 60

Query: 114 YEAAEAQHHMNGKRFAGREISVVLAAESRKRPE 146
             A +A   ++G+ F GR + V+ +   ++  +
Sbjct: 61  EHAVKAYAEVDGQVFQGRMLHVLPSTIKKEASQ 93

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.6 bits (130), Expect = 9e-10
 Identities = 23/97 (23%), Positives = 35/97 (36%), Gaps = 5/97 (5%)

Query: 53  YGRRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVD 112
                      + V  I  D     LR  FE++G +  + +  D  +G+ RGFAFV F D
Sbjct: 89  QRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 148

Query: 113 PYEAAEAQHHMNGKRFAGREISVVLAAESRKRPEEMR 149
             ++ +           G    V  A       +EM 
Sbjct: 149 H-DSVDKIVIQKYHTVNGHNCEVRKA----LSKQEMA 180

>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 = 48.5 bits (114), Expect = 1e-07
 Identities = 18/65 (27%), Positives = 29/65 (44%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L +  +  +   E LR+ FE++G + D  + +D  T   RGF FV +    E   A +  
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 68

Query: 124 NGKRF 128
             K  
Sbjct: 69  PHKVD 73

>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 = 52.4 bits (125), Expect = 1e-09
 Identities = 20/76 (26%), Positives = 40/76 (52%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
            L V +I  + + +E++  F  +G +++++L  D  TG  +G+A V++    +A  A+  
Sbjct: 9   ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 68

Query: 123 MNGKRFAGREISVVLA 138
           +NG    G+ I V   
Sbjct: 69  LNGAEIMGQTIQVDWC 84

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.5 bits (125), Expect = 1e-09
 Identities = 21/100 (21%), Positives = 38/100 (38%), Gaps = 6/100 (6%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
              + NIP      ++    E   V  +         G+  G A VQF +  +A +++  
Sbjct: 10  CAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER- 68

Query: 123 MNGKRFAGREISVVLAAESRKRPEEMRQRHRFRGGSSYGG 162
           ++ K+  GRE  V +        E+MR+  +        G
Sbjct: 69  LHRKKLNGREAFVHVV-----TLEDMREIEKNPPAQGKSG 103

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.4 bits (125), Expect = 1e-09
 Identities = 27/89 (30%), Positives = 40/89 (44%), Gaps = 5/89 (5%)

Query: 57  KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEA 116
            +     L V NIP   R  +LR  F +FG + DV +  +      +GF FV F +  +A
Sbjct: 7   SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADA 64

Query: 117 AEAQHHMNGKRFAGREISVVLAAESRKRP 145
             A+  ++G    GR+I V  A     R 
Sbjct: 65  DRAREKLHGTVVEGRKIEVNNA---TARV 90

>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 = 51.7 bits (123), Expect = 1e-09
 Identities = 13/85 (15%), Positives = 36/85 (42%), Gaps = 2/85 (2%)

Query: 56  RKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYE 115
           + +  + S+ ++  P D   ++++   E  G V +    +       +G  FV F    E
Sbjct: 1   KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLN-IQMRRTLHKAFKGSIFVVFDSI-E 58

Query: 116 AAEAQHHMNGKRFAGREISVVLAAE 140
           +A+      G+++   ++ ++   +
Sbjct: 59  SAKKFVETPGQKYKETDLLILFKDD 83

>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 = 51.7 bits (123), Expect = 2e-09
 Identities = 17/87 (19%), Positives = 31/87 (35%), Gaps = 6/87 (6%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPK-----DYYTGEPRGFAFVQFVDPYEAAE 118
           L V NIP     E +   F     +  +              + + FAF++F    E  +
Sbjct: 4   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 63

Query: 119 AQHHMNGKRFAGREISVVLAAESRKRP 145
           A    +G  F G+ + +    + +  P
Sbjct: 64  AM-AFDGIIFQGQSLKIRRPHDYQPLP 89

>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 = 51.7 bits (123), Expect = 2e-09
 Identities = 27/97 (27%), Positives = 41/97 (42%), Gaps = 2/97 (2%)

Query: 54  GRRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDP 113
           G +K+     + V  +P       LR  FE FG + +  +  D  TG+ RG+ FV   D 
Sbjct: 3   GSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADR 62

Query: 114 YEAAEAQHHMNGKRFAGREISVVLAAESRKRPEEMRQ 150
             A  A    N     GR+ +V L A    +P  ++ 
Sbjct: 63  AAAERACKDPNPI-IDGRKANVNL-AYLGAKPRSLQT 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 = 51.4 bits (122), Expect = 6e-09
 Identities = 30/98 (30%), Positives = 45/98 (45%), Gaps = 3/98 (3%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           +L+V  IP      +LR  FER+G +  V +  D  T + RG+ FV+F     A +A   
Sbjct: 44  NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103

Query: 123 MNGKRFAGREISVVLAAESRKRPEEMRQRHRFRGGSSY 160
           +NG     + + V LAA   +RP           G+ Y
Sbjct: 104 LNGFNILNKRLKVALAASGHQRPGIAGAV---GDGNGY 138

>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 = 50.2 bits (119), Expect = 9e-09
 Identities = 29/113 (25%), Positives = 41/113 (36%), Gaps = 10/113 (8%)

Query: 47  GGGGGGYGRRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFA 106
           G  G         N G + +R +P  C  EE+   F    +V +       + G   G A
Sbjct: 1   GSSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEA 60

Query: 107 FVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAESRKRPEEMRQRHRFRGGSS 159
           FVQF    E AE     + +R   R I +  +        E+R      G SS
Sbjct: 61  FVQFASQ-EIAEKALKKHKERIGHRYIEIFKS-----SRAEVRT----SGPSS 103

>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 = 49.0 bits (116), Expect = 2e-08
 Identities = 20/81 (24%), Positives = 37/81 (45%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           L ++N+       +L + F RF   +   +     TG  RG AF+ F +   A +A H +
Sbjct: 21  LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 80

Query: 124 NGKRFAGREISVVLAAESRKR 144
           NG +  G+ + +      ++R
Sbjct: 81  NGYKLYGKILVIEFGKNKKQR 101

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.7 bits (115), Expect = 2e-08
 Identities = 22/88 (25%), Positives = 39/88 (44%), Gaps = 7/88 (7%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           ++ +RN+  D   E L    ++FG ++ V +     T   +G AF QF+    A +    
Sbjct: 10  TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA 69

Query: 123 MN------GKRFAGREISVVLAAESRKR 144
            +      G +  GR++ V L A +R  
Sbjct: 70  ASLEAEGGGLKLDGRQLKVDL-AVTRDE 96

>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 = 48.6 bits (115), Expect = 3e-08
 Identities = 16/99 (16%), Positives = 38/99 (38%), Gaps = 1/99 (1%)

Query: 47  GGGGGGYGRRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFA 106
           G  G    R  +    +  + N+P D   E ++  F    +       +       +GF 
Sbjct: 1   GSSGSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFG 60

Query: 107 FVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAESRKRP 145
           + +F D  ++  +   +N +    + I V +A +++ + 
Sbjct: 61  YAEFEDL-DSLLSALSLNEESLGNKRIRVDVADQAQDKD 98

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.2 bits (114), Expect = 3e-08
 Identities = 16/84 (19%), Positives = 28/84 (33%), Gaps = 1/84 (1%)

Query: 55  RRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPY 114
           +++EQ+  +L + N+PL    +EL     +              +G  RG  F +     
Sbjct: 12  KQQEQDPTNLYISNLPLSMDEQELEN-MLKPFGQVISTRILRDSSGTSRGVGFARMESTE 70

Query: 115 EAAEAQHHMNGKRFAGREISVVLA 138
           +      H NGK            
Sbjct: 71  KCEAVIGHFNGKFIKTPPGVSAPT 94

>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 = 46.5 bits (109), Expect = 9e-08
 Identities = 19/75 (25%), Positives = 33/75 (44%), Gaps = 7/75 (9%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           +L+R +P D   +E+             Y  K  +  + +G AFV  ++  +A  A +  
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSD-------YELKYCFVDKYKGTAFVTLLNGEQAEAAINTF 53

Query: 124 NGKRFAGREISVVLA 138
           +  R   RE+SV L 
Sbjct: 54  HQSRLRERELSVQLQ 68

>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 = 46.7 bits (110), Expect = 1e-07
 Identities = 14/76 (18%), Positives = 25/76 (32%), Gaps = 6/76 (7%)

Query: 66  VRNIPLDCRPEELRAPFE---RFGVVRDVYLPKDYYTGE---PRGFAFVQFVDPYEAAEA 119
           V  +       E+    E   +FG +  V +           P   A+V ++   +A  A
Sbjct: 13  VVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRA 72

Query: 120 QHHMNGKRFAGREISV 135
              +N     GR +  
Sbjct: 73  IQCVNNVVVDGRTLKA 88

>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 = 46.2 bits (109), Expect = 3e-07
 Identities = 15/92 (16%), Positives = 32/92 (34%), Gaps = 4/92 (4%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM 123
           ++V N+      + L   F +FG V  +           +  A +Q+ DP  A  A+  +
Sbjct: 10  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSL 65

Query: 124 NGKRFAGREISVVLAAESRKRPEEMRQRHRFR 155
           +G+       ++ +               + R
Sbjct: 66  DGQNIYNACCTLRIDFSKLTSLNVKYNNDKSR 97

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.0 bits (106), Expect = 3e-07
 Identities = 22/83 (26%), Positives = 34/83 (40%), Gaps = 11/83 (13%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           +L V     D  P  LR  F  FG + D+ +            AFV +     A +A   
Sbjct: 7   TLYVYG--EDMTPTLLRGAFSPFGNIIDLSMDPPR------NCAFVTYEKMESADQAVAE 58

Query: 123 MNGKRFAGREISVVLAAESRKRP 145
           +NG +    ++ V +A   RK+P
Sbjct: 59  LNGTQVESVQLKVNIA---RKQP 78

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.9 bits (103), Expect = 9e-07
 Identities = 21/83 (25%), Positives = 30/83 (36%), Gaps = 7/83 (8%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
            + V     D   +ELR  F ++G V DV++PK +       FAFV F D   A      
Sbjct: 7   GVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFR-----AFAFVTFADDQIAQSL--C 59

Query: 123 MNGKRFAGREISVVLAAESRKRP 145
                  G  + +  A       
Sbjct: 60  GEDLIIKGISVHISNAEPKHNSN 82

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.0 bits (103), Expect = 9e-07
 Identities = 17/76 (22%), Positives = 32/76 (42%), Gaps = 7/76 (9%)

Query: 63  SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
            +LV+N+P D   +E+    + +         K  Y    +  AFV  ++  +A  A   
Sbjct: 7   GILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNAIQM 59

Query: 123 MNGKRFAGREISVVLA 138
            +   F G+++ V L 
Sbjct: 60  FHQYSFRGKDLIVQLQ 75

>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 = 43.6 bits (102), Expect = 1e-06
 Identities = 26/87 (29%), Positives = 39/87 (44%), Gaps = 6/87 (6%)

Query: 61  HGSLLVRNIPLDCRPEE-LRAPFERFGVVRDVYLPKDY-YTGEPRGFAFVQFVDPYEAAE 118
              +++RN+  +   E  LR  FE FG +  + +P            AF+ F +  ++AE
Sbjct: 4   GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENK-DSAE 62

Query: 119 AQHHMNGKRFAGREISVVLAAESRKRP 145
               MN      REISV LA    K+P
Sbjct: 63  RALQMNRSLLGNREISVSLA---DKKP 86

>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 = 42.8 bits (100), Expect = 3e-06
 Identities = 12/71 (16%), Positives = 26/71 (36%), Gaps = 7/71 (9%)

Query: 68  NIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKR 127
            +       +L    E+ G+V  + +P +        ++F ++    E+  A   +NGK 
Sbjct: 27  GLGNGVSRNQLLPVLEKCGLVDALLMPPNKP------YSFARYRTTEESKRAYVTLNGKE 80

Query: 128 -FAGREISVVL 137
                   + L
Sbjct: 81  VVDDLGQKITL 91

>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 = 41.6 bits (97), Expect = 8e-06
 Identities = 24/101 (23%), Positives = 36/101 (35%), Gaps = 7/101 (6%)

Query: 45  GYGGGGGGYGRRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRG 104
           G  G  G  G  K      L V  +  +     L   F+RFG +R +   K         
Sbjct: 1   GSSGSSGKIGYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS------ 54

Query: 105 FAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA-AESRKR 144
           FA++Q+     A  A   M G    G +  + +  A+S   
Sbjct: 55  FAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGPS 95

>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 = 41.3 bits (96), Expect = 1e-05
 Identities = 29/120 (24%), Positives = 45/120 (37%), Gaps = 18/120 (15%)

Query: 64  LLVRNI-PLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHH 122
           LLV N+ P    P+ L   F  +G V+ V +  +         A VQ  D  +A  A  H
Sbjct: 5   LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE-----NALVQMADGNQAQLAMSH 59

Query: 123 MNGKRFAGREISVVLAAESRKRPEEMRQRHRFRGGSSYGGPRSSYYGRYRSRSLSRSRSP 182
           +NG +  G+ I + L+            +H+       G         Y +  L R + P
Sbjct: 60  LNGHKLHGKPIRITLS------------KHQNVQLPREGQEDQGLTKDYGNSPLHRFKKP 107

>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 = 40.9 bits (95), Expect = 1e-05
 Identities = 14/99 (14%), Positives = 30/99 (30%), Gaps = 7/99 (7%)

Query: 47  GGGGGGYGRRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFA 106
           G  G   G    ++   +LV  +P     ++L+                 Y   +  G  
Sbjct: 1   GSSGSSGGPPTRRSDFRVLVSGLPPSGSWQDLKDHMRE-------AGDVCYADVQKDGMG 53

Query: 107 FVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAESRKRP 145
            V+++   +   A   ++  +F   E          +R 
Sbjct: 54  MVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYPERS 92

>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 = 40.9 bits (95), Expect = 1e-05
 Identities = 16/104 (15%), Positives = 32/104 (30%), Gaps = 11/104 (10%)

Query: 63  SLLVRNIPLD-----CRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAA 117
            L+      D         +  + F  +         K            + F +P  AA
Sbjct: 7   GLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK------SFKRVRINFSNPLSAA 60

Query: 118 EAQHHMNGKRFAGREISVVLAAESRKRPEEMRQRHRFRGGSSYG 161
           +A+  ++   F G+E+ +  A         +   +  + G S G
Sbjct: 61  DARLRLHKTEFLGKEMKLYFAQTLHIGSSHLAPPNPDKSGPSSG 104

>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 = 40.7 bits (94), Expect = 2e-05
 Identities = 16/82 (19%), Positives = 30/82 (36%), Gaps = 2/82 (2%)

Query: 57  KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEA 116
           +     +L + N+  +    EL+          D+ +     TG  R F +V F    + 
Sbjct: 9   ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAEDL 67

Query: 117 AEAQHHMNGKRFAGREISVVLA 138
            +A   + G +  G EI +   
Sbjct: 68  EKALE-LTGLKVFGNEIKLEKP 88

>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 = 39.9 bits (92), Expect = 5e-05
 Identities = 16/101 (15%), Positives = 36/101 (35%), Gaps = 1/101 (0%)

Query: 55  RRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPY 114
           R   +    + ++ +P +   + +   F++  +V D         G+  G  FV+F +  
Sbjct: 12  RSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNE- 70

Query: 115 EAAEAQHHMNGKRFAGREISVVLAAESRKRPEEMRQRHRFR 155
              +A    + +    R I V    +     +    R R +
Sbjct: 71  ADYKAALCRHKQYMGNRFIQVHPITKKGMLEKIDMIRKRLQ 111

>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 = 38.9 bits (90), Expect = 5e-05
 Identities = 13/94 (13%), Positives = 32/94 (34%), Gaps = 11/94 (11%)

Query: 56  RKEQNHGS--LLVRNIPLD-CRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVD 112
           +K +      + + +         +L    E FGV+ +  +            AF++   
Sbjct: 1   QKGRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKIN------EAFIEMAT 54

Query: 113 PY--EAAEAQHHMNGKRFAGREISVVLAAESRKR 144
               +AA   +        G+ + V L+ + ++ 
Sbjct: 55  TEDAQAAVDYYTTTPALVFGKPVRVHLSQKYKRI 88

>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 = 39.0 bits (90), Expect = 9e-05
 Identities = 10/91 (10%), Positives = 24/91 (26%), Gaps = 7/91 (7%)

Query: 64  LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAE-AQHH 122
               ++      E+L   F   G ++ +   +            + F +  + A      
Sbjct: 14  KFSGDLDDQTCREDLHILFSNHGEIKWIDFVR------GAKEGIILFKEKAKEALGKAKD 67

Query: 123 MNGKRFAGREISVVLAAESRKRPEEMRQRHR 153
            N      R   V       +  +E  ++  
Sbjct: 68  ANNGNLQLRNKEVTWEVLEGEVEKEALKKII 98

>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 = 37.6 bits (87), Expect = 1e-04
 Identities = 10/71 (14%), Positives = 23/71 (32%), Gaps = 8/71 (11%)

Query: 66  VRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNG 125
           V   P       L   F ++G +    +           +  +++    +A +A    +G
Sbjct: 9   VFGFPQASASYILLQ-FAQYGNILKHVMSNT------GNWMHIRYQSKLQARKAL-SKDG 60

Query: 126 KRFAGREISVV 136
           + F    +  V
Sbjct: 61  RIFGESIMIGV 71

>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 = 37.8 bits (87), Expect = 2e-04
 Identities = 16/92 (17%), Positives = 27/92 (29%), Gaps = 3/92 (3%)

Query: 47  GGGGGGYGRRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFA 106
           G  G      +      + +R +P      ++   F     +R          G   G A
Sbjct: 1   GSSGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIE--IGPDGRVTGEA 58

Query: 107 FVQFVDPYEAAEAQHHMNGKRFAGREISVVLA 138
            V+F    E A A    +      R + + L 
Sbjct: 59  DVEFATH-EDAVAAMAKDKANMQHRYVELFLN 89

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.9 bits (87), Expect = 2e-04
 Identities = 18/110 (16%), Positives = 27/110 (24%), Gaps = 6/110 (5%)

Query: 47  GGGGGGYGRRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFA 106
           G  G      K      + VR +       +L    E+FG +  V +            A
Sbjct: 1   GSSGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR------QA 54

Query: 107 FVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAESRKRPEEMRQRHRFRG 156
            V+F +   A E                      + KR           G
Sbjct: 55  LVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITRPGNSGPSSG 104

>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 = 3e-04
 Identities = 28/117 (23%), Positives = 47/117 (40%), Gaps = 9/117 (7%)

Query: 51  GGYGRRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQF 110
           G  G         +L +N+P      E++  F RFG +  V LP+          A V+F
Sbjct: 1   GSSGSSGRSKT-VILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGG------ITAIVEF 53

Query: 111 VDPYEAAEAQHHMNGKRFAGREISVVLAAES--RKRPEEMRQRHRFRGGSSYGGPRS 165
           ++P EA +A  H+   +F    + +  A        P++   +H      +  GP S
Sbjct: 54  LEPLEARKAFRHLAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEKAESGPSS 110

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	299
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.88
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.88
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.88
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.88
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.87
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.87
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.87
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.87
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.86
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.86
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.86
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.86
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.86
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.86
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.85
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.85
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.85
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.85
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.85
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.85
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.85
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.85
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.84
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.84
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.84
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.84
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.84
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.84
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.83
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.83
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.83
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.83
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.83
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.83
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.83
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.82
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.82
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.82
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.82
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.82
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.82
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.82
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.81
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.81
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.81
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.81
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.8
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.8
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.8
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.8
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.79
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.79
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.79
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.79
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.79
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.79
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.79
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.78
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.78
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.78
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.78
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.78
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.78
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.78
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.78
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.77
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.77
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.76
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.76
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.76
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.75
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.75
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.75
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.74
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.72
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.71
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.71
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.7
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.67
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.65
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	99.61
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.6
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.6
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.54
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.51
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.5
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.45
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	98.06
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.84
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.81
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	96.81

>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=99.88  E-value=8.5e-23  Score=149.29  Aligned_cols=80  Identities=29%  Similarity=0.487  Sum_probs=77.3

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEccc
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAE  140 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~  140 (299)
                      .++|||+|||.++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|+.||+.|||..|+|+.|.|+||++
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            47899999999999999999999999999999999988999999999999999999999999999999999999999975

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.88  E-value=2.3e-22  Score=152.37  Aligned_cols=84  Identities=32%  Similarity=0.596  Sum_probs=79.5

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      ...++|||+|||+++++++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|+.||+.||++.|+|+.|+|.++
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            34678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCC
Q 043443          139 AESR  142 (299)
Q Consensus       139 ~~~~  142 (299)
                      +.+.
T Consensus        86 ~~~~   89 (99)
T d1whwa_          86 TIKK   89 (99)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            8653

>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=99.88  E-value=1.5e-22  Score=150.09  Aligned_cols=84  Identities=24%  Similarity=0.394  Sum_probs=79.2

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      ..+.++|||+|||..+++++|.++|.+||+|..|.|+.++.++.++|||||+|.+.++|+.||+.|||..|+|+.|.|+|
T Consensus         4 s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~   83 (88)
T d1rk8a_           4 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW   83 (88)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            44568999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccC
Q 043443          138 AAES  141 (299)
Q Consensus       138 a~~~  141 (299)
                      |..+
T Consensus        84 a~~k   87 (88)
T d1rk8a_          84 CFVK   87 (88)
T ss_dssp             SEEC
T ss_pred             ecCC
Confidence            9864

>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=99.88  E-value=2.2e-22  Score=150.77  Aligned_cols=85  Identities=25%  Similarity=0.358  Sum_probs=80.4

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      .+..++|||+|||..+|+++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|+.||+.||+..|+|+.|+|.+
T Consensus         6 ~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   85 (93)
T d1x5ua1           6 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNK   85 (93)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34468999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCC
Q 043443          138 AAESR  142 (299)
Q Consensus       138 a~~~~  142 (299)
                      |.++.
T Consensus        86 A~~~~   90 (93)
T d1x5ua1          86 ASAHN   90 (93)
T ss_dssp             TTTTS
T ss_pred             cCCCC
Confidence            98754

>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=99.87  E-value=2.9e-22  Score=146.37  Aligned_cols=80  Identities=31%  Similarity=0.574  Sum_probs=76.9

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEccc
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAE  140 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~  140 (299)
                      .++|||+|||.++++++|+++|++||+|..|.|+.+..++..+|||||+|.+.++|+.||+.|||..|+|+.|.|+||++
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            36899999999999999999999999999999999988999999999999999999999999999999999999999975

>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=99.87  E-value=1.8e-22  Score=150.00  Aligned_cols=83  Identities=37%  Similarity=0.527  Sum_probs=79.2

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      ...+|||+|||+++++++|+++|++||+|..|.|+.++.++.++|||||+|.+.++|+.||+.||+..|+|+.|.|++|+
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~   83 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   83 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            45799999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cCC
Q 043443          140 ESR  142 (299)
Q Consensus       140 ~~~  142 (299)
                      ++.
T Consensus        84 p~~   86 (89)
T d2cqba1          84 PMR   86 (89)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.87  E-value=4.1e-22  Score=149.27  Aligned_cols=82  Identities=23%  Similarity=0.373  Sum_probs=78.7

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      ...++|||+|||+++|+++|+++|++||+|..|.|+.++.++.++|||||+|.+.++|+.||+.|||..|+|+.|.|+|+
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            45789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cc
Q 043443          139 AE  140 (299)
Q Consensus       139 ~~  140 (299)
                      ..
T Consensus        85 ~~   86 (93)
T d1h2vz_          85 AG   86 (93)
T ss_dssp             SC
T ss_pred             CC
Confidence            64

>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=99.87  E-value=2.4e-22  Score=149.57  Aligned_cols=84  Identities=31%  Similarity=0.510  Sum_probs=79.7

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      ..+.++|||+|||..+++++|.++|++||+|..|.|+.++.++.++|||||+|.+.++|+.||+.|||..|+|+.|.|+|
T Consensus         5 ~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~   84 (90)
T d2cq0a1           5 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   84 (90)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            44568999999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             cccC
Q 043443          138 AAES  141 (299)
Q Consensus       138 a~~~  141 (299)
                      |++.
T Consensus        85 akp~   88 (90)
T d2cq0a1          85 AKPS   88 (90)
T ss_dssp             SSCC
T ss_pred             eeCC
Confidence            9864

>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=99.86  E-value=5.2e-22  Score=151.25  Aligned_cols=84  Identities=24%  Similarity=0.363  Sum_probs=79.4

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      +.++|||+|||+++++++|+++|.+||.|..|.++.+..++.++|||||+|.+.++|+.||+.|||..|.|+.|.|+|+.
T Consensus        17 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a~   96 (102)
T d2cpza1          17 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKR   96 (102)
T ss_dssp             TTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEeC
Confidence            45689999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cCCC
Q 043443          140 ESRK  143 (299)
Q Consensus       140 ~~~~  143 (299)
                      ++..
T Consensus        97 ~k~~  100 (102)
T d2cpza1          97 SKND  100 (102)
T ss_dssp             CSCC
T ss_pred             CCCC
Confidence            7543

>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=99.86  E-value=5.6e-22  Score=144.34  Aligned_cols=78  Identities=24%  Similarity=0.390  Sum_probs=75.6

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEccc
Q 043443           63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAE  140 (299)
Q Consensus        63 ~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~  140 (299)
                      .|||+|||+.+|+++|.++|.+||+|..|.|+.++.++.++|||||+|.+.++|+.||+.|||..|+|+.|+|.|++.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~~   79 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR   79 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECCC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            699999999999999999999999999999999999999999999999999999999999999999999999999863

>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=99.86  E-value=3.5e-22  Score=147.15  Aligned_cols=81  Identities=23%  Similarity=0.414  Sum_probs=77.8

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcccC
Q 043443           62 GSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAES  141 (299)
Q Consensus        62 ~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~~  141 (299)
                      ++|||+|||+.+|+++|+++|++||+|+.|.|+.|+.+|.++|||||+|.+.++|+.||+.||+..|.|+.|.|++|...
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            47999999999999999999999999999999999999999999999999999999999999999999999999999864


Q ss_pred             C
Q 043443          142 R  142 (299)
Q Consensus       142 ~  142 (299)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=9.9e-22  Score=143.94  Aligned_cols=77  Identities=34%  Similarity=0.509  Sum_probs=73.8

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEE
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV  135 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V  135 (299)
                      .+.++|||+|||..+|+++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|+.||+.||+..|+|+.|+|
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            44679999999999999999999999999999999999989999999999999999999999999999999999987

>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=99.86  E-value=1.9e-21  Score=148.28  Aligned_cols=85  Identities=29%  Similarity=0.448  Sum_probs=78.6

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEE
Q 043443           56 RKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV  135 (299)
Q Consensus        56 ~~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V  135 (299)
                      ..+.+.++|||+|||+.+++++|+++|++||+|..|.|+.++.++.++|||||+|.+.++|+.||+.||+ +|+|+.|.|
T Consensus         5 ~~d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V   83 (103)
T d2cqda1           5 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANV   83 (103)
T ss_dssp             CCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEE
T ss_pred             CCCCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEE
Confidence            4455668899999999999999999999999999999999999999999999999999999999998876 799999999


Q ss_pred             EEcccC
Q 043443          136 VLAAES  141 (299)
Q Consensus       136 ~~a~~~  141 (299)
                      .++...
T Consensus        84 ~~a~~~   89 (103)
T d2cqda1          84 NLAYLG   89 (103)
T ss_dssp             EESTTT
T ss_pred             EEcCCC
Confidence            999754

>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=99.86  E-value=1.2e-21  Score=157.23  Aligned_cols=87  Identities=31%  Similarity=0.473  Sum_probs=80.8

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      ....++|||+|||+++|+++|+++|++||+|+.|.|+.++.++.++|||||+|.+.++|+.||+.|||.+|+|+.|.|.+
T Consensus        39 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~  118 (139)
T d1u6fa1          39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34457899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCC
Q 043443          138 AAESRKR  144 (299)
Q Consensus       138 a~~~~~~  144 (299)
                      +.....+
T Consensus       119 a~~~~~~  125 (139)
T d1u6fa1         119 AASGHQR  125 (139)
T ss_dssp             SSCCCCC
T ss_pred             cCCCCCC
Confidence            9865443

>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=99.85  E-value=1.8e-21  Score=146.02  Aligned_cols=86  Identities=35%  Similarity=0.608  Sum_probs=78.7

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCC-CCCCCccEEEEEEcCHHHHHHHHHhh-CCceeCCeeEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDY-YTGEPRGFAFVQFVDPYEAAEAQHHM-NGKRFAGREIS  134 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~-~~g~~~g~afVeF~~~~~A~~Al~~l-ng~~l~Gr~i~  134 (299)
                      .....++|||+|||..+++++|+++|.+||.|..|.|+.+. .+|.++|||||+|.+.++|+.||+.| |+..|+|+.|.
T Consensus         4 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~   83 (94)
T d2cpha1           4 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV   83 (94)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEE
Confidence            34567899999999999999999999999999999998875 47899999999999999999999998 89999999999


Q ss_pred             EEEcccCC
Q 043443          135 VVLAAESR  142 (299)
Q Consensus       135 V~~a~~~~  142 (299)
                      |+||..+.
T Consensus        84 V~~A~~~~   91 (94)
T d2cpha1          84 LEWADSEV   91 (94)
T ss_dssp             EEECCCCC
T ss_pred             EEEcCCCC
Confidence            99998653

>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=99.85  E-value=1.4e-21  Score=143.82  Aligned_cols=80  Identities=33%  Similarity=0.491  Sum_probs=75.7

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCC--eeEEEE
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAG--REISVV  136 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~G--r~i~V~  136 (299)
                      ...++|||+|||..+++++|+++|++||+|..|.|+.++.++.++|||||+|.+.++|+.||+.||+..|.|  ++|.|.
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~   83 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR   83 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEE
Confidence            346789999999999999999999999999999999999999999999999999999999999999999987  889999


Q ss_pred             Ec
Q 043443          137 LA  138 (299)
Q Consensus       137 ~a  138 (299)
                      ||
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            86

>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=99.85  E-value=1.1e-21  Score=145.89  Aligned_cols=83  Identities=35%  Similarity=0.572  Sum_probs=78.7

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      +..+|||+|||+++++++|+++|.+||.|..|.++.+..++.++|||||+|.+.++|+.||+.|||..|+|+.|.|++|.
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            45789999999999999999999999999999999988899999999999999999999999999999999999999997


Q ss_pred             cCC
Q 043443          140 ESR  142 (299)
Q Consensus       140 ~~~  142 (299)
                      ++.
T Consensus        84 ~~~   86 (90)
T d1x5sa1          84 KSS   86 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>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=99.85  E-value=1.5e-21  Score=143.64  Aligned_cols=78  Identities=31%  Similarity=0.498  Sum_probs=74.1

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCC--eeEEEEEc
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAG--REISVVLA  138 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~G--r~i~V~~a  138 (299)
                      .++|||+|||..+|+++|+++|++||+|..|.|+.++.++.++|||||+|.+.++|+.||+.|||..|.|  .+|.|.||
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            5789999999999999999999999999999999998899999999999999999999999999999998  55999886

>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=99.85  E-value=1.1e-21  Score=142.89  Aligned_cols=80  Identities=16%  Similarity=0.255  Sum_probs=70.0

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEccc
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAE  140 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~  140 (299)
                      .++|||+|||+++|+++|.++|++||.|..+.++.+..++.++|||||+|.+.++|+.||+.|||+.|+|++|.|+++++
T Consensus         1 d~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           1 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CcEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            37999999999999999999999999999888888888899999999999999999999999999999999999999975

>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=99.85  E-value=4.9e-21  Score=142.39  Aligned_cols=84  Identities=23%  Similarity=0.379  Sum_probs=76.5

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      ++.+..+|||+|||.++++++|+++|++||.|..|.|+.+..++  ++||||+|.+.++|+.||+.|||..|.|+.|+|.
T Consensus         4 d~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~   81 (90)
T d2cqia1           4 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVN   81 (90)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999886544  7899999999999999999999999999999999


Q ss_pred             EcccCC
Q 043443          137 LAAESR  142 (299)
Q Consensus       137 ~a~~~~  142 (299)
                      ||++..
T Consensus        82 ~a~~~~   87 (90)
T d2cqia1          82 WATTPS   87 (90)
T ss_dssp             ECCCTT
T ss_pred             EcCCCC
Confidence            998643

>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=99.85  E-value=2.8e-21  Score=139.92  Aligned_cols=76  Identities=26%  Similarity=0.449  Sum_probs=73.2

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        63 ~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      +|||+|||+++++++|+++|.+||.|..|.|+.++ +++++|||||+|.+.++|+.||+.|||..|+|++|.|+++.
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            69999999999999999999999999999999885 88999999999999999999999999999999999999985

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=6.4e-21  Score=143.18  Aligned_cols=81  Identities=28%  Similarity=0.516  Sum_probs=73.7

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      ..+.++|||+|||+++++++|+++|.+||.|..|.+..+   ...++||||+|++.++|+.||+.||+++|+|++|+|+|
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            345679999999999999999999999999999988654   45689999999999999999999999999999999999


Q ss_pred             cccC
Q 043443          138 AAES  141 (299)
Q Consensus       138 a~~~  141 (299)
                      ++..
T Consensus        88 a~~~   91 (95)
T d1x4aa1          88 PRSG   91 (95)
T ss_dssp             CCCC
T ss_pred             ccCC
Confidence            8753

>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=99.84  E-value=1.1e-20  Score=141.43  Aligned_cols=85  Identities=31%  Similarity=0.480  Sum_probs=77.3

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEE
Q 043443           56 RKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV  135 (299)
Q Consensus        56 ~~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V  135 (299)
                      ......++|||+|||+.+++++|+++|.+||+|..|.|+.+.  +.++|||||+|.+.++|+.||+.||+.+|+|+.|.|
T Consensus         6 ~~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~--~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V   83 (93)
T d2cq3a1           6 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV   83 (93)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc--cCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            345567899999999999999999999999999999999875  346899999999999999999999999999999999


Q ss_pred             EEcccCC
Q 043443          136 VLAAESR  142 (299)
Q Consensus       136 ~~a~~~~  142 (299)
                      ++|+++.
T Consensus        84 ~~A~~r~   90 (93)
T d2cq3a1          84 NNATARV   90 (93)
T ss_dssp             EECCSSC
T ss_pred             EecCcCC
Confidence            9998753

>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=99.84  E-value=4.9e-21  Score=142.44  Aligned_cols=83  Identities=27%  Similarity=0.426  Sum_probs=76.3

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      .+..++|||+|||+++|+++|+++|++||.|..|.|+.|+.++.++|||||+|.+.++|++||+.  ...|+|+.|.|.+
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            34567899999999999999999999999999999999999999999999999999999999985  4589999999999


Q ss_pred             cccCC
Q 043443          138 AAESR  142 (299)
Q Consensus       138 a~~~~  142 (299)
                      +.++.
T Consensus        83 a~~k~   87 (90)
T d2cqga1          83 PNSKQ   87 (90)
T ss_dssp             CCTTC
T ss_pred             CCCCC
Confidence            98643

>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=99.84  E-value=2.8e-21  Score=141.46  Aligned_cols=79  Identities=27%  Similarity=0.454  Sum_probs=74.1

Q ss_pred             EEEeCCCCCCCHHHHHHHHhcCCCEeEE-EeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcccCC
Q 043443           64 LLVRNIPLDCRPEELRAPFERFGVVRDV-YLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAESR  142 (299)
Q Consensus        64 l~V~nLp~~~te~dL~~~F~~~G~I~~v-~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~~~  142 (299)
                      |||+|||+++++++|+++|.+||.|..+ .|+.+..+++++|||||+|.+.++|+.||+.|||..|+|+.|.|+||.++.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            8999999999999999999999999764 788888899999999999999999999999999999999999999998643

>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=99.84  E-value=3.9e-21  Score=142.66  Aligned_cols=80  Identities=23%  Similarity=0.367  Sum_probs=74.0

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEccc
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAE  140 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~  140 (299)
                      ..+|||+|||+++++++|+++|.+||.|..|.|+.+.  +.++|||||+|.+.++|+.||+.|||+.|+|+.|.|.++++
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~   85 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   85 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            4589999999999999999999999999999999875  34679999999999999999999999999999999999986


Q ss_pred             CC
Q 043443          141 SR  142 (299)
Q Consensus       141 ~~  142 (299)
                      +.
T Consensus        86 ~~   87 (89)
T d1cvja2          86 RK   87 (89)
T ss_dssp             TT
T ss_pred             CC
Confidence            54

>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=99.84  E-value=5.3e-21  Score=140.44  Aligned_cols=79  Identities=25%  Similarity=0.439  Sum_probs=74.8

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      ...+|||+|||+++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+ ++++.|+|+.|.|..|.
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            34689999999999999999999999999999999999999999999999999999999997 69999999999998874

>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=99.84  E-value=1.1e-21  Score=141.83  Aligned_cols=76  Identities=24%  Similarity=0.432  Sum_probs=73.4

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           62 GSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        62 ~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      |+|||+|||+++|+++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+ +|++.|+|+.|.|.+|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            689999999999999999999999999999999999999999999999999999999997 7999999999999986

>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=99.83  E-value=6.6e-21  Score=145.28  Aligned_cols=81  Identities=23%  Similarity=0.387  Sum_probs=76.8

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEccc
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAE  140 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~  140 (299)
                      ..+|||+|||+++++++|+++|.+||+|..|.|+.++.++.++|||||+|.+.++|++||+ |+++.|+|+.|.|.+|.+
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            4799999999999999999999999999999999999999999999999999999999996 799999999999999986


Q ss_pred             CC
Q 043443          141 SR  142 (299)
Q Consensus       141 ~~  142 (299)
                      +.
T Consensus        99 ke  100 (103)
T d1x4ba1          99 RE  100 (103)
T ss_dssp             CC
T ss_pred             cC
Confidence            54

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.83  E-value=4.9e-21  Score=140.74  Aligned_cols=77  Identities=22%  Similarity=0.515  Sum_probs=72.0

Q ss_pred             EEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCC---CCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEccc
Q 043443           64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTG---EPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAE  140 (299)
Q Consensus        64 l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g---~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~  140 (299)
                      |||+|||+++|+++|+++|++||.|..|.|+.++.++   .++|||||+|.+.++|+.||+.|||..|+|+.|.|+|+..
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            8999999999999999999999999999998877665   3589999999999999999999999999999999999864

>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=99.83  E-value=2.7e-21  Score=147.61  Aligned_cols=83  Identities=34%  Similarity=0.569  Sum_probs=78.3

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      ...+|||+|||+++++++|+++|++||+|..|.|+.++.++.++|||||+|.+.++|+.||+.||+..|.|+.|.|+++.
T Consensus         7 ~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~   86 (104)
T d1p1ta_           7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            34689999999999999999999999999999999999899999999999999999999999999999999999999987


Q ss_pred             cCC
Q 043443          140 ESR  142 (299)
Q Consensus       140 ~~~  142 (299)
                      ...
T Consensus        87 ~~~   89 (104)
T d1p1ta_          87 SEK   89 (104)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            643

>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=99.83  E-value=1e-20  Score=143.41  Aligned_cols=86  Identities=28%  Similarity=0.461  Sum_probs=78.1

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEe--------EEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCcee
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVR--------DVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRF  128 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~--------~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l  128 (299)
                      ++...++|||+|||..+|+++|+++|.+||.|.        .+.+..+..++..++||||+|.+.++|+.||+.|||.+|
T Consensus         4 ~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~   83 (101)
T d2cpea1           4 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   83 (101)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEE
Confidence            455678999999999999999999999999884        466777788899999999999999999999999999999


Q ss_pred             CCeeEEEEEcccCC
Q 043443          129 AGREISVVLAAESR  142 (299)
Q Consensus       129 ~Gr~i~V~~a~~~~  142 (299)
                      +|+.|.|.+++.+.
T Consensus        84 ~gr~i~V~~a~~~~   97 (101)
T d2cpea1          84 QGSKLKVSLARKKP   97 (101)
T ss_dssp             TTEECEEECSSCCC
T ss_pred             CCEEEEEEEcCCCC
Confidence            99999999998643

>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=99.83  E-value=6.2e-21  Score=144.92  Aligned_cols=80  Identities=25%  Similarity=0.418  Sum_probs=76.3

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      +..+|||+|||+++++++|+++|..||+|..|.|+.+..++.++|||||+|.+.++|++||+ |||..|+|+.|.|.+++
T Consensus        17 ~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~   95 (101)
T d2cq4a1          17 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQ   95 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECC
Confidence            45799999999999999999999999999999999999999999999999999999999995 99999999999999986


Q ss_pred             c
Q 043443          140 E  140 (299)
Q Consensus       140 ~  140 (299)
                      +
T Consensus        96 ~   96 (101)
T d2cq4a1          96 A   96 (101)
T ss_dssp             H
T ss_pred             C
Confidence            4

>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=99.83  E-value=5.9e-21  Score=137.17  Aligned_cols=75  Identities=27%  Similarity=0.468  Sum_probs=71.2

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        63 ~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      +|||+|||+++++++|.++|++||+|..|.|+.++.+++++|||||+|.+.++|++||+ +++..|+|+.|.|..|
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            49999999999999999999999999999999999999999999999999999999997 7999999999998643

>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=99.83  E-value=2e-20  Score=140.90  Aligned_cols=86  Identities=24%  Similarity=0.393  Sum_probs=78.8

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhC------CceeCC
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMN------GKRFAG  130 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~ln------g~~l~G  130 (299)
                      +..+.++|||+|||+++|+++|+++|.+||.|..+.++.+..++.++|||||+|.+.++|+.||+.||      |..|+|
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            34557899999999999999999999999999999999998899999999999999999999999886      677899


Q ss_pred             eeEEEEEcccCC
Q 043443          131 REISVVLAAESR  142 (299)
Q Consensus       131 r~i~V~~a~~~~  142 (299)
                      +.|.|+++.++.
T Consensus        84 r~l~v~~a~~k~   95 (98)
T d1x4ha1          84 RQLKVDLAVTRD   95 (98)
T ss_dssp             CEEEEECCCCCC
T ss_pred             EEEEEEECCCCC
Confidence            999999998643

>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=99.82  E-value=3.1e-20  Score=134.45  Aligned_cols=77  Identities=27%  Similarity=0.366  Sum_probs=73.3

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      ..+|||+|||+++|+++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++|++ ||+++|+|+.|.|..|
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            4689999999999999999999999999999999999999999999999999999999996 8999999999999876

>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=99.82  E-value=1e-20  Score=135.56  Aligned_cols=75  Identities=24%  Similarity=0.373  Sum_probs=72.2

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        63 ~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      +|||+|||+++|+++|+++|++||.|..|.++.++.++.+++||||+|.+.++|++||+ ||++.|+|+.|.|++|
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            49999999999999999999999999999999999999999999999999999999997 9999999999999876

>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=99.82  E-value=1.6e-20  Score=138.33  Aligned_cols=81  Identities=28%  Similarity=0.413  Sum_probs=70.8

Q ss_pred             CCCEEEEeCCCCCCC-HHHHHHHHhcCCCEeEEEeccC-CCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           60 NHGSLLVRNIPLDCR-PEELRAPFERFGVVRDVYLPKD-YYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        60 ~~~~l~V~nLp~~~t-e~dL~~~F~~~G~I~~v~i~~d-~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      +..+|||+|||++++ +++|+++|++||.|..|.|+.+ ..++.++|||||+|.+.++|++||+ ||++.|+|+.|.|.+
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            467999999999876 5669999999999999998764 5688999999999999999999996 999999999999999


Q ss_pred             cccC
Q 043443          138 AAES  141 (299)
Q Consensus       138 a~~~  141 (299)
                      ++++
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9864

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=8e-21  Score=136.47  Aligned_cols=75  Identities=24%  Similarity=0.391  Sum_probs=71.2

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           63 SLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        63 ~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      +|||+|||+++|+++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+ +++.+|+|+.|.|..|
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            59999999999999999999999999999999999999999999999999999999997 4778999999999865

>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=99.82  E-value=3.6e-20  Score=139.88  Aligned_cols=80  Identities=15%  Similarity=0.206  Sum_probs=72.7

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEE
Q 043443           56 RKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV  135 (299)
Q Consensus        56 ~~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V  135 (299)
                      .......+|||+|||+.+++++|+++|.+||+|+.|.|..       +|||||+|.+.++|++||+.|||.+|.|+.|.|
T Consensus        10 ~~~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v   82 (98)
T d1wg4a_          10 PTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGET   82 (98)
T ss_dssp             CCCSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEE
Confidence            3445677999999999999999999999999999999875       489999999999999999999999999999999


Q ss_pred             EEcccCC
Q 043443          136 VLAAESR  142 (299)
Q Consensus       136 ~~a~~~~  142 (299)
                      .+++...
T Consensus        83 ~~~~~~~   89 (98)
T d1wg4a_          83 SYIRVYP   89 (98)
T ss_dssp             EEEEEEC
T ss_pred             EEEecCC
Confidence            9987543

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=5.4e-20  Score=140.21  Aligned_cols=83  Identities=20%  Similarity=0.392  Sum_probs=72.8

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCC-CCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDY-YTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~-~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      ..+.++|||+|||+++++++|+++|++|| |+.|.++.+. .++.++|||||+|.+.++|++|++ ||+++|+|+.|.|.
T Consensus        12 ~~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~-~~~~~~~gr~l~V~   89 (104)
T d1wi8a_          12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRVD   89 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHG-GGTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHH-cCCCEECCEEEEEE
Confidence            34568999999999999999999999999 7777776654 478899999999999999987775 99999999999999


Q ss_pred             EcccCC
Q 043443          137 LAAESR  142 (299)
Q Consensus       137 ~a~~~~  142 (299)
                      ++..+.
T Consensus        90 ~a~~~~   95 (104)
T d1wi8a_          90 VADQAQ   95 (104)
T ss_dssp             ECCCCC
T ss_pred             ECCCCC
Confidence            998643

>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=99.82  E-value=5.5e-20  Score=142.43  Aligned_cols=79  Identities=27%  Similarity=0.492  Sum_probs=73.2

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      ..+.+|||+|||..+++++|.++|++||.|..|.|..+   +..+|||||+|.+.++|+.||+.|||+.|+|+.|.|.++
T Consensus         5 ~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a   81 (114)
T d2f9da1           5 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYY   81 (114)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            34679999999999999999999999999999999764   467899999999999999999999999999999999998


Q ss_pred             cc
Q 043443          139 AE  140 (299)
Q Consensus       139 ~~  140 (299)
                      ..
T Consensus        82 ~~   83 (114)
T d2f9da1          82 NA   83 (114)
T ss_dssp             CH
T ss_pred             CC
Confidence            64

>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=99.81  E-value=5.1e-20  Score=138.48  Aligned_cols=76  Identities=22%  Similarity=0.403  Sum_probs=71.7

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      ..++|||+|||..+++++|+++|++||+|..|.|+.+      +|||||+|.+.++|+.||..|||++|+|+.|+|.|++
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak   90 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGK   90 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            4578999999999999999999999999999999976      6999999999999999999999999999999999997


Q ss_pred             cC
Q 043443          140 ES  141 (299)
Q Consensus       140 ~~  141 (299)
                      ..
T Consensus        91 ~~   92 (96)
T d1x4ga1          91 ES   92 (96)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.81  E-value=5.4e-21  Score=145.25  Aligned_cols=85  Identities=22%  Similarity=0.358  Sum_probs=78.9

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      .+.++|||+|||.++++++|+++|.+||.|..|.++.+..++.+++||||+|.+.++|+.||+.|||..|.|+.|.|+|+
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            35689999999999999999999999999999888887778999999999999999999999999999999999999999


Q ss_pred             ccCCC
Q 043443          139 AESRK  143 (299)
Q Consensus       139 ~~~~~  143 (299)
                      +++..
T Consensus        96 k~k~~  100 (102)
T d2cpxa1          96 KNKKQ  100 (102)
T ss_dssp             CCCSC
T ss_pred             CCccc
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=99.81  E-value=6.6e-20  Score=138.38  Aligned_cols=76  Identities=28%  Similarity=0.507  Sum_probs=69.2

Q ss_pred             CCCCCEEEEeCCC-CCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           58 EQNHGSLLVRNIP-LDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        58 ~~~~~~l~V~nLp-~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      ....++|||+||+ ..+++++|+++|.+||.|+.|.|.        +|||||+|++.++|++||+.|||++|+|+.|.|+
T Consensus        12 ~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~--------rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~   83 (98)
T d1wf2a_          12 RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH--------KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDIN   83 (98)
T ss_dssp             SSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE--------TEEEEEEESSHHHHHHHHHTTTTCEETTEECEEE
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe--------CCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3456789999996 578899999999999999999984        5899999999999999999999999999999999


Q ss_pred             EcccC
Q 043443          137 LAAES  141 (299)
Q Consensus       137 ~a~~~  141 (299)
                      |++..
T Consensus        84 ~a~~~   88 (98)
T d1wf2a_          84 LAAEP   88 (98)
T ss_dssp             ETTSC
T ss_pred             ECCCC
Confidence            99753

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.81  E-value=4.7e-20  Score=135.86  Aligned_cols=76  Identities=30%  Similarity=0.579  Sum_probs=71.5

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      ..++|||+|||.++++++|+++|++||+|..|.|..+      ++||||+|++.++|+.||+.|||..|+|+.|.|+||.
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            4578999999999999999999999999999999876      5899999999999999999999999999999999997


Q ss_pred             cC
Q 043443          140 ES  141 (299)
Q Consensus       140 ~~  141 (299)
                      ..
T Consensus        81 ~~   82 (86)
T d2cpja1          81 HS   82 (86)
T ss_dssp             CC
T ss_pred             Cc
Confidence            64

>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=99.80  E-value=1.1e-19  Score=132.83  Aligned_cols=78  Identities=19%  Similarity=0.374  Sum_probs=70.9

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCcee-CCeeEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRF-AGREISV  135 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l-~Gr~i~V  135 (299)
                      +.++.++|||+|||..+++++|.++|.+||.|..|.|+.+.     +|||||+|.+.++|+.|++.|||..| +|+.|.|
T Consensus         4 ~~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v   78 (83)
T d2b0ga1           4 EQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFTTELQSNAAKEALQGFKITPTHAMKI   78 (83)
T ss_dssp             CCSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT-----CSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc-----ceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEE
Confidence            34557899999999999999999999999999999998653     68999999999999999999999988 4689999


Q ss_pred             EEcc
Q 043443          136 VLAA  139 (299)
Q Consensus       136 ~~a~  139 (299)
                      .||+
T Consensus        79 ~~ak   82 (83)
T d2b0ga1          79 TFAK   82 (83)
T ss_dssp             EECC
T ss_pred             EEec
Confidence            9986

>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=99.80  E-value=3.4e-20  Score=140.72  Aligned_cols=86  Identities=23%  Similarity=0.377  Sum_probs=77.5

Q ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeE
Q 043443           54 GRRKEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREI  133 (299)
Q Consensus        54 ~~~~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i  133 (299)
                      ....+.+.++|||+|||.++++++|+++|++||.|..+.++.+ .++.++|||||+|.+.++|++||+.|||.+|.|++|
T Consensus        11 ~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~-~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~   89 (101)
T d1x5oa1          11 AKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPG   89 (101)
T ss_dssp             CSCCCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTT
T ss_pred             hccccCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecc-cccccccceeEEeCCHHHHHHHHHHhCCCEECCcCC
Confidence            3345566789999999999999999999999999999988877 478899999999999999999999999999999999


Q ss_pred             EEEEccc
Q 043443          134 SVVLAAE  140 (299)
Q Consensus       134 ~V~~a~~  140 (299)
                      .|.++++
T Consensus        90 ~v~~~~P   96 (101)
T d1x5oa1          90 VSAPTEP   96 (101)
T ss_dssp             SCCCSSC
T ss_pred             ccCCCCC
Confidence            8877654

>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=99.80  E-value=2.1e-19  Score=137.01  Aligned_cols=85  Identities=25%  Similarity=0.383  Sum_probs=76.2

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      ...+..+|||+|||+++||+||++||..||.|..+.++.+..++.++|||||+|.+.++|++||+ ||+..|.|+.|.|.
T Consensus        11 ~~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~   89 (104)
T d1wg5a_          11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIF   89 (104)
T ss_dssp             SCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEE
Confidence            34456689999999999999999999999999887777777789999999999999999999996 89999999999999


Q ss_pred             EcccCC
Q 043443          137 LAAESR  142 (299)
Q Consensus       137 ~a~~~~  142 (299)
                      ++....
T Consensus        90 ~~~~~~   95 (104)
T d1wg5a_          90 KSSRAE   95 (104)
T ss_dssp             EECTTT
T ss_pred             ECCHHH
Confidence            998643

>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=99.80  E-value=4.2e-20  Score=142.27  Aligned_cols=76  Identities=28%  Similarity=0.466  Sum_probs=70.6

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      ..++|||+|||+.+++++|+++|.+||+|..|.|...      ++||||+|.+.++|+.||+.|||..|.|+.|.|+|+.
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~~------kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~   82 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG------GITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCSS------SSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeecc------CceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECC
Confidence            4579999999999999999999999999999988643      6999999999999999999999999999999999987


Q ss_pred             cC
Q 043443          140 ES  141 (299)
Q Consensus       140 ~~  141 (299)
                      ..
T Consensus        83 ~~   84 (111)
T d1whxa_          83 IG   84 (111)
T ss_dssp             TT
T ss_pred             CC
Confidence            54

>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=99.79  E-value=4.2e-20  Score=134.25  Aligned_cols=76  Identities=21%  Similarity=0.316  Sum_probs=68.9

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCc-eeCCeeEEEEEccc
Q 043443           62 GSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGK-RFAGREISVVLAAE  140 (299)
Q Consensus        62 ~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~-~l~Gr~i~V~~a~~  140 (299)
                      ++|||+|||.++|+++|+++|.+||.|..+.+...      +|||||+|.+.++|+.||+.|||. .|+|+.|.|+|+.+
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~------rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~   75 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK------SGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE------TTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc------cceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            57999999999999999999999999987766654      699999999999999999999996 69999999999987


Q ss_pred             CCC
Q 043443          141 SRK  143 (299)
Q Consensus       141 ~~~  143 (299)
                      +..
T Consensus        76 k~~   78 (80)
T d2cqha1          76 KKL   78 (80)
T ss_dssp             CCC
T ss_pred             cCc
Confidence            544

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.79  E-value=3.7e-19  Score=133.94  Aligned_cols=78  Identities=26%  Similarity=0.383  Sum_probs=71.3

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCC--eeEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAG--REISV  135 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~G--r~i~V  135 (299)
                      ..+.++|||+|||.++++++|+++|++||+|..|.|..+      ++||||+|.+.++|+.||+.||+.+|.|  .+|+|
T Consensus        14 ~~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v   87 (97)
T d1whya_          14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRV   87 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEE
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEE
Confidence            345789999999999999999999999999999999865      5899999999999999999999999986  58999


Q ss_pred             EEcccC
Q 043443          136 VLAAES  141 (299)
Q Consensus       136 ~~a~~~  141 (299)
                      +|++..
T Consensus        88 ~~ak~~   93 (97)
T d1whya_          88 DFAKSG   93 (97)
T ss_dssp             EECCCC
T ss_pred             EeCCCC
Confidence            999864

>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=99.79  E-value=7.8e-20  Score=134.50  Aligned_cols=79  Identities=25%  Similarity=0.340  Sum_probs=70.5

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      ..++|||+|||++++++||+++|..||.|..+.++.+..++.++|||||+|.+.++|++||+.||++.|.|++|+|.++
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            4578999999999999999999999999876433334458899999999999999999999999999999999999885

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=2.8e-20  Score=137.35  Aligned_cols=73  Identities=18%  Similarity=0.252  Sum_probs=68.1

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcccC
Q 043443           62 GSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAES  141 (299)
Q Consensus        62 ~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~~  141 (299)
                      ++|||+|||+.+++++|+++|++||+|..|.|+.+       |||||+|.+.++|++||..|||.+|.|+.|.|.++..+
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~   73 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            36999999999999999999999999999998764       89999999999999999999999999999999887653

>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=99.79  E-value=1.6e-19  Score=138.57  Aligned_cols=76  Identities=29%  Similarity=0.428  Sum_probs=70.2

Q ss_pred             CCEEEEeCCC-CCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           61 HGSLLVRNIP-LDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        61 ~~~l~V~nLp-~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      .++|||+||+ ..+|+++|.++|++||+|+.|.|+.++     +|||||+|++.++|++||+.|||..|+|+.|.|+|++
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            4799999995 469999999999999999999998764     7899999999999999999999999999999999987


Q ss_pred             cC
Q 043443          140 ES  141 (299)
Q Consensus       140 ~~  141 (299)
                      ..
T Consensus        77 ~~   78 (109)
T d2adca1          77 HQ   78 (109)
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=99.79  E-value=2.2e-20  Score=139.16  Aligned_cols=81  Identities=20%  Similarity=0.287  Sum_probs=73.9

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      .....+|||+|||+.+++++|+++|.+||.|..|.|+. ..++.++|||||+|.+.++|+.||+ ||+.+|+|+.|.|.+
T Consensus        10 ~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~-~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~   87 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVD-VRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   87 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCE-EEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEEC
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeee-cCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEe
Confidence            34567999999999999999999999999999888764 4588999999999999999999996 999999999999999


Q ss_pred             ccc
Q 043443          138 AAE  140 (299)
Q Consensus       138 a~~  140 (299)
                      |+.
T Consensus        88 ak~   90 (91)
T d1fjeb1          88 PKG   90 (91)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            875

>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=99.79  E-value=3.6e-19  Score=130.89  Aligned_cols=76  Identities=32%  Similarity=0.384  Sum_probs=69.8

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEccc
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAE  140 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~  140 (299)
                      ..+|||+|||.++++++|+++|++||.|..+.+...      +|||||+|.+.++|+.||..|||..|+|+.|.|.|+++
T Consensus         8 ~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~~------rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP   81 (86)
T d2cpda1           8 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKP   81 (86)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEccc------cEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccC
Confidence            468999999999999999999999999888877543      68999999999999999999999999999999999986


Q ss_pred             CC
Q 043443          141 SR  142 (299)
Q Consensus       141 ~~  142 (299)
                      ..
T Consensus        82 ~~   83 (86)
T d2cpda1          82 VD   83 (86)
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=99.78  E-value=2.1e-19  Score=130.19  Aligned_cols=74  Identities=26%  Similarity=0.389  Sum_probs=68.6

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      ..++|||+||+  +|+++|+++|++||+|..|.+..+      ++||||+|.+.++|+.||+.|||..|+|+.|+|.|++
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            45799999996  899999999999999999999865      5899999999999999999999999999999999997


Q ss_pred             cC
Q 043443          140 ES  141 (299)
Q Consensus       140 ~~  141 (299)
                      ++
T Consensus        76 ~~   77 (79)
T d2bz2a1          76 KQ   77 (79)
T ss_dssp             SS
T ss_pred             CC
Confidence            54

>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=99.78  E-value=1.2e-19  Score=134.44  Aligned_cols=77  Identities=17%  Similarity=0.276  Sum_probs=70.1

Q ss_pred             CCCEEEEeCCCCCCCHHHH---HHHHhcCCCEeEEEeccCCCCCCC---ccEEEEEEcCHHHHHHHHHhhCCceeCCeeE
Q 043443           60 NHGSLLVRNIPLDCRPEEL---RAPFERFGVVRDVYLPKDYYTGEP---RGFAFVQFVDPYEAAEAQHHMNGKRFAGREI  133 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL---~~~F~~~G~I~~v~i~~d~~~g~~---~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i  133 (299)
                      ..++|||+|||+.+++++|   .++|.+||+|..|.|+.++.++..   .|||||+|.+.++|+.||+.|||..|+|+.|
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~l   86 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   86 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEE
Confidence            4568999999999999999   778999999999999988766554   4899999999999999999999999999999


Q ss_pred             EEE
Q 043443          134 SVV  136 (299)
Q Consensus       134 ~V~  136 (299)
                      +|.
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            984

>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=99.78  E-value=4.2e-19  Score=130.39  Aligned_cols=78  Identities=15%  Similarity=0.321  Sum_probs=72.6

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      ...+|||+|||.++|+++|.++|+.||.|..|.|..+. ++.++|||||+|.+.++|++||+ +++..|.|+.|.|.|+.
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            35799999999999999999999999999999998764 78899999999999999999996 79999999999999875

>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=99.78  E-value=2.8e-19  Score=134.28  Aligned_cols=83  Identities=25%  Similarity=0.294  Sum_probs=73.9

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCC-EeEEEeccCC-CCCCCccEEEEEEcCHHHHHHHHHhhCC--ceeCCeeEEEE
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFERFGV-VRDVYLPKDY-YTGEPRGFAFVQFVDPYEAAEAQHHMNG--KRFAGREISVV  136 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~~~G~-I~~v~i~~d~-~~g~~~g~afVeF~~~~~A~~Al~~lng--~~l~Gr~i~V~  136 (299)
                      +|+|||+|||..+++++|+++|.+||+ |..|.|+.+. .++.++|||||+|.+.++|..||+.|++  ..++|+.|.|+
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~   80 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVD   80 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEE
Confidence            468999999999999999999999996 8999998875 4688999999999999999999999964  45679999999


Q ss_pred             EcccCCC
Q 043443          137 LAAESRK  143 (299)
Q Consensus       137 ~a~~~~~  143 (299)
                      ||+++..
T Consensus        81 ~A~p~~~   87 (96)
T d2disa1          81 WAEPEID   87 (96)
T ss_dssp             ESCSSCS
T ss_pred             EcCCCCC
Confidence            9987544

>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=99.78  E-value=4.4e-19  Score=131.02  Aligned_cols=78  Identities=21%  Similarity=0.274  Sum_probs=70.1

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCcee-CCeeEEEEE
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRF-AGREISVVL  137 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l-~Gr~i~V~~  137 (299)
                      .+..+|||+|||.++++++|+++|.+||.|..+.+...    +.++||||+|++.++|..||..|||..| +|+.|.|.|
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~----~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~   83 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF   83 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee----cccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEe
Confidence            34679999999999999999999999999988877643    4578999999999999999999999988 589999999


Q ss_pred             ccc
Q 043443          138 AAE  140 (299)
Q Consensus       138 a~~  140 (299)
                      ++.
T Consensus        84 sk~   86 (88)
T d2adca2          84 SKS   86 (88)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            975

>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=99.78  E-value=2.2e-19  Score=136.45  Aligned_cols=82  Identities=16%  Similarity=0.214  Sum_probs=72.3

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      ......+|||.|||+++|++||+++|..||. +.|.++.+. ++..+|||||+|.+.++|++||+ ||++.|+|+.|.|.
T Consensus        11 ~~~~~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~   87 (102)
T d1weza_          11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELF   87 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEec-CCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEE
Confidence            4455679999999999999999999999974 567776664 67889999999999999999997 89999999999999


Q ss_pred             EcccC
Q 043443          137 LAAES  141 (299)
Q Consensus       137 ~a~~~  141 (299)
                      ++...
T Consensus        88 ~s~~~   92 (102)
T d1weza_          88 LNSTA   92 (102)
T ss_dssp             EECCC
T ss_pred             EcCCC
Confidence            98754

>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=99.78  E-value=2.8e-19  Score=132.19  Aligned_cols=74  Identities=22%  Similarity=0.433  Sum_probs=65.1

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEccc
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAE  140 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~  140 (299)
                      ..+|||+|||++++++||+++|.+|| |..+.+.      ..++||||+|.+.++|++||+.||+++|+|+.|.|+|++.
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~~------~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~   77 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPT   77 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcC-ceeeeee------ccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            46899999999999999999999999 3334443      2379999999999999999999999999999999999975


Q ss_pred             C
Q 043443          141 S  141 (299)
Q Consensus       141 ~  141 (299)
                      +
T Consensus        78 ~   78 (88)
T d1wg1a_          78 D   78 (88)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.78  E-value=2.4e-19  Score=134.70  Aligned_cols=80  Identities=24%  Similarity=0.429  Sum_probs=72.0

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      ..+..+|||+|||.++++++|+++|.+||.|..|..     ++.+++||||+|.+.++|+.||+.||+..|+|+.|.|.|
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~-----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~   87 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY   87 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE-----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee-----cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            345689999999999999999999999998876643     457799999999999999999999999999999999999


Q ss_pred             cccCC
Q 043443          138 AAESR  142 (299)
Q Consensus       138 a~~~~  142 (299)
                      +.++.
T Consensus        88 a~~k~   92 (96)
T d1fjca_          88 TGEKG   92 (96)
T ss_dssp             CSSSC
T ss_pred             eCCCC
Confidence            98754

>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=99.77  E-value=8.7e-20  Score=129.75  Aligned_cols=71  Identities=18%  Similarity=0.294  Sum_probs=68.4

Q ss_pred             EEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEE
Q 043443           64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREIS  134 (299)
Q Consensus        64 l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~  134 (299)
                      |||+|||.++|+++|.++|.+||.|..+.++.++.++.++|||||+|.+.++|+.||+.|||..|+|+.|+
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            89999999999999999999999999999999999999999999999999999999999999999998764

>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=99.77  E-value=5.9e-19  Score=126.53  Aligned_cols=74  Identities=22%  Similarity=0.232  Sum_probs=68.0

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           62 GSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        62 ~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      ++|||+|||+.+++++|+++|..||.|..|.|+.++.  ...+||||+|.+.++|++||. ||++.|+|+.|.|..+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~--~~~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT--SSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecc--ccceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            5899999999999999999999999999999988764  345799999999999999996 8999999999999875

>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=99.76  E-value=4.1e-19  Score=132.08  Aligned_cols=80  Identities=25%  Similarity=0.436  Sum_probs=71.5

Q ss_pred             CCCEEEEeCCCCCCCHHHHHH----HHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEE
Q 043443           60 NHGSLLVRNIPLDCRPEELRA----PFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISV  135 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~----~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V  135 (299)
                      +.++|||+|||..++++||++    +|++||+|..|.+..   ++.++|||||+|.+.++|+.||+.|||..|+|+.|.|
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            468999999999999998864    689999999998864   3567899999999999999999999999999999999


Q ss_pred             EEcccCC
Q 043443          136 VLAAESR  142 (299)
Q Consensus       136 ~~a~~~~  142 (299)
                      .||+.+.
T Consensus        79 ~~ak~~~   85 (91)
T d1nu4a_          79 QYAKTDS   85 (91)
T ss_dssp             EECSSCC
T ss_pred             EEeCCCc
Confidence            9998643

>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=99.76  E-value=4.2e-19  Score=131.23  Aligned_cols=76  Identities=29%  Similarity=0.409  Sum_probs=68.5

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAA  139 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~  139 (299)
                      ..++|||+|||+.+|+++|+++|++||+|..|.+..+     .++||||+|.+.++|+.||.  ++++|+|+.|.|.+++
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            4679999999999999999999999999999987643     47999999999999999985  7889999999999997


Q ss_pred             cCC
Q 043443          140 ESR  142 (299)
Q Consensus       140 ~~~  142 (299)
                      ++.
T Consensus        77 ~k~   79 (88)
T d1wf0a_          77 PKH   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            643

>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=99.76  E-value=4e-19  Score=135.12  Aligned_cols=81  Identities=21%  Similarity=0.242  Sum_probs=72.3

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      ....+|||+|||+++|+++|.++|..||.|..+.++....+|.++|||||+|.+.++|+.||+ ||+..|+|+.|.|.++
T Consensus         6 ~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~   84 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVV   84 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEEC
Confidence            345789999999999999999999999999875455555689999999999999999999996 8999999999999998


Q ss_pred             cc
Q 043443          139 AE  140 (299)
Q Consensus       139 ~~  140 (299)
                      ..
T Consensus        85 ~~   86 (103)
T d2cpya1          85 TL   86 (103)
T ss_dssp             CH
T ss_pred             CH
Confidence            64

>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=99.75  E-value=3.4e-18  Score=126.20  Aligned_cols=80  Identities=16%  Similarity=0.205  Sum_probs=72.0

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhh--CCceeCCeeEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM--NGKRFAGREIS  134 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~l--ng~~l~Gr~i~  134 (299)
                      +..+..+|||+|||..+++++|+++|++||.|..|.+..+      ++||||+|.+.++|+.||+.|  ++..|+|+.|.
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            3467889999999999999999999999999999999865      589999999999999999865  57789999999


Q ss_pred             EEEcccCC
Q 043443          135 VVLAAESR  142 (299)
Q Consensus       135 V~~a~~~~  142 (299)
                      |.|++.+.
T Consensus        78 v~~sk~~~   85 (88)
T d2cq1a1          78 IQYSNHKE   85 (88)
T ss_dssp             EEECSCSS
T ss_pred             EEECCCCC
Confidence            99997543

>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=99.75  E-value=2.4e-18  Score=123.31  Aligned_cols=71  Identities=24%  Similarity=0.451  Sum_probs=64.5

Q ss_pred             EEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEcccC
Q 043443           64 LLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAES  141 (299)
Q Consensus        64 l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~~  141 (299)
                      |||+|||.++++++|+++|.+|| |..+.+.      ..+|||||+|.+.++|++||+.|||..|+|+.|.|+|++..
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~~------~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVD------KYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEE------TTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeec------ccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999999 5555554      34799999999999999999999999999999999999753

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.75  E-value=7.6e-18  Score=128.22  Aligned_cols=80  Identities=20%  Similarity=0.187  Sum_probs=71.4

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhh--CCceeCCeeEE
Q 043443           57 KEQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM--NGKRFAGREIS  134 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~l--ng~~l~Gr~i~  134 (299)
                      ...+..+|||+|||..+++++|.++|.+||.|+.|.|..+      +++|||+|++.++|+.||+.|  ++..|.|++|.
T Consensus        11 ~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~   84 (104)
T d1wexa_          11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAF   84 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEE
Confidence            3456789999999999999999999999999999999865      689999999999999999987  55678999999


Q ss_pred             EEEcccCC
Q 043443          135 VVLAAESR  142 (299)
Q Consensus       135 V~~a~~~~  142 (299)
                      |+|++.+.
T Consensus        85 v~~s~~~~   92 (104)
T d1wexa_          85 FNYSTSKR   92 (104)
T ss_dssp             EEECSSSS
T ss_pred             EEEcCCCc
Confidence            99997643

>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=99.74  E-value=1.6e-18  Score=132.84  Aligned_cols=80  Identities=19%  Similarity=0.283  Sum_probs=71.5

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCcee--CCeeEEEE
Q 043443           59 QNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRF--AGREISVV  136 (299)
Q Consensus        59 ~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l--~Gr~i~V~  136 (299)
                      .+..+|||+|||+.+|+++|+++|++||.|..|.|+.+    +.+|||||+|.+.++|+.||+.|||..|  .+..|.|.
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 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID   80 (108)
T ss_dssp             CCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEE----TTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEE
T ss_pred             CCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEee----CCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEE
Confidence            34568999999999999999999999999999998865    3579999999999999999999999998  57899999


Q ss_pred             EcccCC
Q 043443          137 LAAESR  142 (299)
Q Consensus       137 ~a~~~~  142 (299)
                      +++.+.
T Consensus        81 ~s~~~~   86 (108)
T d2adba1          81 FSKLTS   86 (108)
T ss_dssp             ECSSCS
T ss_pred             ecCCcc
Confidence            987643

>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=99.72  E-value=2.3e-18  Score=132.91  Aligned_cols=82  Identities=16%  Similarity=0.235  Sum_probs=73.4

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      ....++|||+|||+++|++||.+||..||.|..+.++.+..+|.++|||||+|.+.++|++||+ ||+..|+|+.|.|.+
T Consensus        15 ~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~   93 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP   93 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEE
Confidence            3456799999999999999999999999999776566666789999999999999999999996 899999999999998


Q ss_pred             ccc
Q 043443          138 AAE  140 (299)
Q Consensus       138 a~~  140 (299)
                      +..
T Consensus        94 ~~~   96 (112)
T d1wela1          94 ITK   96 (112)
T ss_dssp             ECH
T ss_pred             cCh
Confidence            864

>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=99.71  E-value=1.2e-17  Score=126.09  Aligned_cols=80  Identities=18%  Similarity=0.263  Sum_probs=71.0

Q ss_pred             CCCCCCEEEEeCCCCC-CCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHH--hhCCceeCCeeE
Q 043443           57 KEQNHGSLLVRNIPLD-CRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQH--HMNGKRFAGREI  133 (299)
Q Consensus        57 ~~~~~~~l~V~nLp~~-~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~--~lng~~l~Gr~i  133 (299)
                      ......+|||+|||.+ +|+++|.++|++||.|..|.|+.+      ++||||+|.+.++|+.||+  .+++..|+|+.|
T Consensus        14 ~~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l   87 (99)
T d1x4fa1          14 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCV   87 (99)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCC
T ss_pred             CCCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEE
Confidence            3455689999999985 899999999999999999999865      5899999999999999997  468889999999


Q ss_pred             EEEEcccCC
Q 043443          134 SVVLAAESR  142 (299)
Q Consensus       134 ~V~~a~~~~  142 (299)
                      .|.|++...
T Consensus        88 ~V~~s~~~~   96 (99)
T d1x4fa1          88 KVDLSEKYK   96 (99)
T ss_dssp             EEEEECSCS
T ss_pred             EEEEcCCcc
Confidence            999997543

>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=99.71  E-value=1.9e-17  Score=122.46  Aligned_cols=78  Identities=15%  Similarity=0.181  Sum_probs=69.9

Q ss_pred             CCCCCEEEEeCCCCC-CCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhh--CCceeCCeeEE
Q 043443           58 EQNHGSLLVRNIPLD-CRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHM--NGKRFAGREIS  134 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~-~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~l--ng~~l~Gr~i~  134 (299)
                      .+...+|||+|||.. +|++||.++|++||+|..|.|+.+      +++|||+|++.++|+.||+.|  ++..|.|++|.
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~------k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~   78 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   78 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc------ceEEEEEEcchhhHHHHHHHHhhCCCccCCceEE
Confidence            355679999999986 789999999999999999999876      579999999999999999966  67889999999


Q ss_pred             EEEcccC
Q 043443          135 VVLAAES  141 (299)
Q Consensus       135 V~~a~~~  141 (299)
                      |.|++..
T Consensus        79 V~~s~~~   85 (89)
T d1x4da1          79 VHLSQKY   85 (89)
T ss_dssp             EEEECCC
T ss_pred             EEECCCc
Confidence            9999753

>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=99.70  E-value=1.1e-17  Score=127.34  Aligned_cols=78  Identities=17%  Similarity=0.238  Sum_probs=69.2

Q ss_pred             CCCEEEEeCCCCCC-CH----HHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEE
Q 043443           60 NHGSLLVRNIPLDC-RP----EELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREIS  134 (299)
Q Consensus        60 ~~~~l~V~nLp~~~-te----~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~  134 (299)
                      ..++|||+||+..+ ++    ++|+++|.+||.|+.|.+++.      ++||||+|.+.++|++||+.|||+.|+|+.|+
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~   77 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT------TTEEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecC------CCEEEEEECCHHHHHHHHHHhcccccCCCEeE
Confidence            45789999999876 33    569999999999999999854      68999999999999999999999999999999


Q ss_pred             EEEcccCCC
Q 043443          135 VVLAAESRK  143 (299)
Q Consensus       135 V~~a~~~~~  143 (299)
                      |.|++....
T Consensus        78 v~~a~~~~~   86 (104)
T d1weya_          78 LYFAQTLHI   86 (104)
T ss_dssp             EECCCCSSC
T ss_pred             EeecccCCC
Confidence            999976543

>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=99.67  E-value=1.6e-16  Score=131.92  Aligned_cols=83  Identities=25%  Similarity=0.333  Sum_probs=77.3

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEE
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVL  137 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~  137 (299)
                      .....+|||+|||..+|+++|.++|..||.|..|.|+.+..++.++|||||+|.+.++|++||+ +++..|+|+.|.|.+
T Consensus        94 ~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~  172 (183)
T d1u1qa_          94 HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRK  172 (183)
T ss_dssp             TCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEE
T ss_pred             ccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEe
Confidence            3456799999999999999999999999999999999998899999999999999999999997 799999999999999


Q ss_pred             cccC
Q 043443          138 AAES  141 (299)
Q Consensus       138 a~~~  141 (299)
                      |.++
T Consensus       173 A~~k  176 (183)
T d1u1qa_         173 ALSK  176 (183)
T ss_dssp             CCCH
T ss_pred             cCCc
Confidence            8754

>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=99.65  E-value=1.5e-18  Score=128.67  Aligned_cols=77  Identities=21%  Similarity=0.301  Sum_probs=67.0

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEec-----cCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEE
Q 043443           62 GSLLVRNIPLDCRPEELRAPFERFGVVRDVYLP-----KDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVV  136 (299)
Q Consensus        62 ~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~-----~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~  136 (299)
                      .+|||+|||+++|+++|+++|++||.|..+.+.     .+..++.++|||||+|.+.++|+.||+ |||+.|.|+.|+|.
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEEC
Confidence            579999999999999999999999988765543     234567789999999999999999985 99999999999997


Q ss_pred             Ecc
Q 043443          137 LAA  139 (299)
Q Consensus       137 ~a~  139 (299)
                      .++
T Consensus        81 r~k   83 (90)
T d1u2fa_          81 RPH   83 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            554

>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=99.61  E-value=5.6e-17  Score=123.36  Aligned_cols=76  Identities=18%  Similarity=0.262  Sum_probs=70.4

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEc
Q 043443           62 GSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLA  138 (299)
Q Consensus        62 ~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a  138 (299)
                      +.|+|.+++..++|++|+++|++||+|+.|.|+.+ .++.++|||||+|.+.++|++||+.|||..|+|+.|.|+|+
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~-~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCS-SSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecC-CCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            35778888888999999999999999999999866 58899999999999999999999999999999999999986

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=9.7e-16  Score=118.10  Aligned_cols=73  Identities=14%  Similarity=0.110  Sum_probs=64.2

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCH-HHHHHHHHhhCCceeCCeeEEEEEccc
Q 043443           62 GSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDP-YEAAEAQHHMNGKRFAGREISVVLAAE  140 (299)
Q Consensus        62 ~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~-~~A~~Al~~lng~~l~Gr~i~V~~a~~  140 (299)
                      ..+||+|||..+|+++|+++|.+||+|..|.|+.+      ++||||+|.+. ++|..|+..||+..|.+..+.|.|+..
T Consensus        12 ~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~   85 (113)
T d1owxa_          12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVL   85 (113)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEEC
T ss_pred             eEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeec
Confidence            35599999999999999999999999999999865      69999999985 789999999999998877777766653

>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=99.60  E-value=9.6e-16  Score=115.79  Aligned_cols=65  Identities=23%  Similarity=0.414  Sum_probs=59.3

Q ss_pred             CCCCCEEEEeC--CCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCcee
Q 043443           58 EQNHGSLLVRN--IPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRF  128 (299)
Q Consensus        58 ~~~~~~l~V~n--Lp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l  128 (299)
                      ..++.+|||.|  ||..+|+++|+++|++||.|+.|.++.+      ++||||+|.+.++|+.|++.|||+.|
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            45567899955  9999999999999999999999998876      58999999999999999999999987

>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=99.54  E-value=1.2e-14  Score=109.18  Aligned_cols=82  Identities=29%  Similarity=0.554  Sum_probs=69.6

Q ss_pred             CCCCCCCEEEEeCC--CCCC---------CHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhC
Q 043443           56 RKEQNHGSLLVRNI--PLDC---------RPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMN  124 (299)
Q Consensus        56 ~~~~~~~~l~V~nL--p~~~---------te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~ln  124 (299)
                      .......+|+|.||  |.++         .++||.+.|++||.|..|.+..+    ..+|||||+|.+.++|+.||..||
T Consensus         3 ~~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~ln   78 (99)
T d2dita1           3 SRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLD   78 (99)
T ss_dssp             CCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHST
T ss_pred             CCCCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhC
Confidence            34456789999999  5432         13678899999999999988765    467999999999999999999999


Q ss_pred             CceeCCeeEEEEEcccC
Q 043443          125 GKRFAGREISVVLAAES  141 (299)
Q Consensus       125 g~~l~Gr~i~V~~a~~~  141 (299)
                      |..|+|++|.|+++.++
T Consensus        79 g~~~~gr~i~v~~~~g~   95 (99)
T d2dita1          79 GRWFGGRQITAQAWDGT   95 (99)
T ss_dssp             TCEETTEECEEEECCSC
T ss_pred             CcEECCEEEEEEEeCCc
Confidence            99999999999998754

>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=99.51  E-value=1.4e-14  Score=104.73  Aligned_cols=73  Identities=15%  Similarity=0.261  Sum_probs=62.2

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCee-EEEEEc
Q 043443           60 NHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGRE-ISVVLA  138 (299)
Q Consensus        60 ~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~-i~V~~a  138 (299)
                      +.+.|+|++||++++++.| ++|++||+|.++.+..+      ++||||+|.+.++|++||+ |||+.|+|+. |.|..+
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~~------~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~   74 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNT------GNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   74 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECSS------SSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEecCC------CCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeC
Confidence            3568999999999887655 57999999999988644      6999999999999999996 8999999975 568776


Q ss_pred             cc
Q 043443          139 AE  140 (299)
Q Consensus       139 ~~  140 (299)
                      .+
T Consensus        75 ~~   76 (81)
T d1wwha1          75 ID   76 (81)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.50  E-value=4.3e-14  Score=116.94  Aligned_cols=79  Identities=25%  Similarity=0.437  Sum_probs=71.9

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEccc
Q 043443           61 HGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAE  140 (299)
Q Consensus        61 ~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~  140 (299)
                      ..+|||+|||+.+|+++|.++|.+||.|..|.|+.+..++.++|||||+|.+.++|++|+. +++..+.+..|.+.....
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~~~~~~   84 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAVS   84 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcccccchhhhhhhh
Confidence            3699999999999999999999999999999999998899999999999999999999998 567778888888877654

>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=99.45  E-value=6.8e-14  Score=105.94  Aligned_cols=82  Identities=21%  Similarity=0.417  Sum_probs=69.1

Q ss_pred             CCCCEEEEeCC--CCCCC--------HHHHHHHHhcCCCEeEEEeccCCCC--CCCccEEEEEEcCHHHHHHHHHhhCCc
Q 043443           59 QNHGSLLVRNI--PLDCR--------PEELRAPFERFGVVRDVYLPKDYYT--GEPRGFAFVQFVDPYEAAEAQHHMNGK  126 (299)
Q Consensus        59 ~~~~~l~V~nL--p~~~t--------e~dL~~~F~~~G~I~~v~i~~d~~~--g~~~g~afVeF~~~~~A~~Al~~lng~  126 (299)
                      +++.+|+|.||  +..+.        .+||++.|.+||.|+.|.|+.+..+  ....|++||+|.+.++|++|++.|||.
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr   81 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   81 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSC
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCC
Confidence            35678999999  44432        3578999999999999999876544  334689999999999999999999999


Q ss_pred             eeCCeeEEEEEccc
Q 043443          127 RFAGREISVVLAAE  140 (299)
Q Consensus       127 ~l~Gr~i~V~~a~~  140 (299)
                      .|+|+.|.|.++..
T Consensus        82 ~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          82 KFANRVVVTKYCDP   95 (104)
T ss_dssp             CSSSSCCEEEEECH
T ss_pred             EECCeEEEEEEcCH
Confidence            99999999999863

>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=98.06  E-value=4.5e-06  Score=59.36  Aligned_cols=70  Identities=17%  Similarity=0.259  Sum_probs=56.1

Q ss_pred             CCCEEEEeCCCCCC------CH---HHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCC
Q 043443           60 NHGSLLVRNIPLDC------RP---EELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAG  130 (299)
Q Consensus        60 ~~~~l~V~nLp~~~------te---~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~G  130 (299)
                      +..||.|.=+....      ++   .+|.+.|..||+|.-|.++.+        ..+|+|.+-+.|.+|++ |+++++.|
T Consensus        14 pDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~-l~g~~v~G   84 (95)
T d1ufwa_          14 LDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLD-VDGMKVKG   84 (95)
T ss_dssp             TTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHH-GGGSEETT
T ss_pred             CCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhc-cCCeEEcc
Confidence            34577775443322      22   468888999999999999865        69999999999999998 89999999


Q ss_pred             eeEEEEEc
Q 043443          131 REISVVLA  138 (299)
Q Consensus       131 r~i~V~~a  138 (299)
                      +.|+|...
T Consensus        85 ~~l~It~~   92 (95)
T d1ufwa_          85 RAVKISGP   92 (95)
T ss_dssp             EEEEEECC
T ss_pred             eEEEEecC
Confidence            99999754

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.84  E-value=5.3e-05  Score=51.12  Aligned_cols=62  Identities=26%  Similarity=0.303  Sum_probs=52.5

Q ss_pred             HHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhCCceeCCeeEEEEEccc
Q 043443           76 EELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMNGKRFAGREISVVLAAE  140 (299)
Q Consensus        76 ~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~lng~~l~Gr~i~V~~a~~  140 (299)
                      +.|.++|.+++.|..+.|....   ...-.|-|...+.++|..||..|+...|+++.|.|.+++.
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~---dg~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~~   72 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHT---DYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATG   72 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCC---STTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             HHHHHHHHhheeEEEEEEEecc---CCcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEecC
Confidence            4466778999999999886542   2245799999999999999999999999999999999863

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.81  E-value=3.8e-05  Score=55.07  Aligned_cols=79  Identities=13%  Similarity=0.130  Sum_probs=63.6

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCC--CccEEEEEEcCHHHHHHHHHhhCCceeCCe-----eEE
Q 043443           62 GSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGE--PRGFAFVQFVDPYEAAEAQHHMNGKRFAGR-----EIS  134 (299)
Q Consensus        62 ~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~--~~g~afVeF~~~~~A~~Al~~lng~~l~Gr-----~i~  134 (299)
                      ++|.|.+||+.+||+++.+.+...|++..+..+..+.+.+  ...-|||.|.+.+++....+.++|..|.+.     +-.
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            6899999999999999999999999998877765544332  346799999999999999999999987432     345


Q ss_pred             EEEccc
Q 043443          135 VVLAAE  140 (299)
Q Consensus       135 V~~a~~  140 (299)
                      |++|.-
T Consensus        82 VE~AP~   87 (91)
T d1uw4a_          82 VEFAPF   87 (91)
T ss_dssp             EEECSS
T ss_pred             EEEcCc
Confidence            666643

>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=96.81  E-value=0.0029  Score=45.25  Aligned_cols=59  Identities=20%  Similarity=0.366  Sum_probs=47.6

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCEeEEEeccCCCCCCCccEEEEEEcCHHHHHHHHHhhC
Q 043443           58 EQNHGSLLVRNIPLDCRPEELRAPFERFGVVRDVYLPKDYYTGEPRGFAFVQFVDPYEAAEAQHHMN  124 (299)
Q Consensus        58 ~~~~~~l~V~nLp~~~te~dL~~~F~~~G~I~~v~i~~d~~~g~~~g~afVeF~~~~~A~~Al~~ln  124 (299)
                      ......||.-.+|......||.++|..||.|.-.+| .+       .-|||...+.++|+.++..++
T Consensus        12 ~p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswI-dd-------TSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          12 QPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWI-DD-------TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEE-ET-------TEEEEECSCHHHHHHHHHHHH
T ss_pred             CCCcceeEEEeCCcccchhHHHHHhcCCCceEEEEe-cC-------ceEEEEecCHHHHHHHHHHhc
Confidence            334556888889999999999999999999864444 33       379999999999999887654