Psyllid ID: psy8615

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------13
Protein Sequence
MQNLVTLAAMTGAGTMSPTALSGLASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDYLGQSFLKPSFNTYVLMNVI
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccEEEEEcccccccHHHHHHHHcccccEEEEEEEEEccccccccEEEEEEccHHHHHHHHHHHcccccccEEEEEEEEEEEEEccc
Secondary Structure Prediction (SSPRO)
cccHccccccccccccccccccHHHcccccccccccccccccccEEEEEEccccccHHHHHHHHcccccEEEEEEEEEcccccccccEEEEccccccEEEEEEccHHHHHHHHcccccccEEEEEEcc
Coil and Loop (DISEMBL)
MQNLVTLAAMtgagtmsptalsglassnaavgssgkqltgpeganlfiyhlppefsdadlasmfgpfgtVLSAKVFidkqnnrskcfGTIIFMRKFFILTIRFdtandylgqsflkpsfntyvLMNVI
Flexible Loop (DISEMBL)
MQNLVTLAAMTGAGTMSPTALSGLASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDYLGqsflkpsfntyvLMNVI
Low Complexity Region (SEG)
MQNLVTLAAMTGAGTMSPTALSGLASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDYLGQSFLKPSFNTYVLMNVI
Disordered region (IsUnstruct)
*******************************************ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDYLGQSFLKPSFNTYVLMN**
Disordered Region (DISOPRED)
********************************************NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDYLGQSFLKPSFNTYVLMNV*
Disordered Region (DISEMBL)
MQNLVTLAAMTGAGTMSPTALSGL************QLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDYLGQSFLKPSFNTYVLMNVI
Disordered Region (DISPRO)
**********TGA*TMSPTALSGLAS*************GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDYLGQSFLKPSFNTYVLMNVI
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MQNLVTLAAMTGAGTMSPTALSGLASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDYLGQSFLKPSFNTYVLMNVI
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	128	2.2.26 [Sep-21-2011]
Q9IBD0	501	CUGBP Elav-like family me	yes	N/A	0.687	0.175	0.554	5e-20
Q6PF35	489	CUGBP Elav-like family me	N/A	N/A	0.515	0.134	0.651	1e-19
Q5F3T7	489	CUGBP Elav-like family me	yes	N/A	0.515	0.134	0.636	1e-19
Q5R995	513	CUGBP Elav-like family me	yes	N/A	0.515	0.128	0.636	1e-19
Q28HE9	490	CUGBP Elav-like family me	yes	N/A	0.515	0.134	0.651	1e-19
Q4QQT3	487	CUGBP Elav-like family me	yes	N/A	0.515	0.135	0.636	1e-19
P28659	486	CUGBP Elav-like family me	yes	N/A	0.515	0.135	0.636	1e-19
Q92879	486	CUGBP Elav-like family me	yes	N/A	0.515	0.135	0.636	1e-19
O57406	489	CUGBP Elav-like family me	N/A	N/A	0.515	0.134	0.636	3e-19
A4IIM2	513	CUGBP Elav-like family me	no	N/A	0.429	0.107	0.666	2e-18

>sp|Q9IBD0|CELF1_DANRE CUGBP Elav-like family member 1 OS=Danio rerio GN=celf1 PE=1 SV=1

 Score = 96.3 bits (238), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 51/92 (55%), Positives = 59/92 (64%), Gaps = 4/92 (4%)

Query: 5   VTLAAMTGAGTMSPTALSGLAS----SNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADL 60
           +T AA +G    +  AL  L S    S   V ++G Q  GPEGANLFIYHLP EF D DL
Sbjct: 373 LTQAAYSGIQQYAAAALPSLYSQSLLSQQNVSAAGSQKEGPEGANLFIYHLPQEFGDQDL 432

Query: 61  ASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
             MF PFG V+SAKVFIDKQ N SKCFG + +
Sbjct: 433 LQMFMPFGNVISAKVFIDKQTNLSKCFGFVSY 464

RNA-binding protein implicated in the regulation of several post-transcriptional events. May be involved in mRNA translation activation and stability (By similarity). Involved in the regulation of muscle-specific splicing of alpha actinin pre-mRNAs via the binding to the UR-repeat element (URE) at the branch point of the non-muscle (NM) exon.
Danio rerio (taxid: 7955)

>sp|Q6PF35|CEL1B_XENLA CUGBP Elav-like family member 1-B OS=Xenopus laevis GN=cugbp1-b PE=2 SV=1

 Score = 95.5 bits (236), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 43/66 (65%), Positives = 49/66 (74%)

Query: 27  SNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKC 86
           S   +G++G Q  GPEGANLFIYHLP EF D DL  MF PFG ++SAKVFIDKQ N SKC
Sbjct: 387 SQQGLGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNIVSAKVFIDKQTNLSKC 446

Query: 87  FGTIIF 92
           FG I +
Sbjct: 447 FGFISY 452

RNA-binding protein implicated in the regulation of several post-transcriptional events. May be involved in pre-mRNA alternative splicing, mRNA translation activation and stability (By similarity). Mediates the rapid and sequence-specific cytoplasmic deadenylation of EDEN-containing maternal mRNAs following fertilization. Binds to AU-rich sequences (AREs) of jun mRNA. Binds to the embryonic deadenylation element (EDEN) motif localized in the 3'-UTR of maternal mRNAs. Binds to RNA containing several repeats of the consensus sequence 5'-UGU-3'. EDEN-dependent deadenylation is enhanced by the presence of an additional cis element composed of three AUU repeats.

Xenopus laevis (taxid: 8355)

>sp|Q5F3T7|CELF1_CHICK CUGBP Elav-like family member 1 OS=Gallus gallus GN=CELF1 PE=1 SV=2

 Score = 95.1 bits (235), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 42/66 (63%), Positives = 50/66 (75%)

Query: 27  SNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKC 86
           +  ++G++G Q  GPEGANLFIYHLP EF D DL  MF PFG V+SAKVFIDKQ N SKC
Sbjct: 387 TQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKC 446

Query: 87  FGTIIF 92
           FG + +
Sbjct: 447 FGFVSY 452

RNA-binding protein that may be involved in pre-mRNA alternative splicing, mRNA translation activation and stability.

Gallus gallus (taxid: 9031)

>sp|Q5R995|CELF1_PONAB CUGBP Elav-like family member 1 OS=Pongo abelii GN=CELF1 PE=2 SV=1

 Score = 95.1 bits (235), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 42/66 (63%), Positives = 50/66 (75%)

Query: 27  SNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKC 86
           +  ++G++G Q  GPEGANLFIYHLP EF D DL  MF PFG V+SAKVFIDKQ N SKC
Sbjct: 411 TQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKC 470

Query: 87  FGTIIF 92
           FG + +
Sbjct: 471 FGFVSY 476

RNA-binding protein implicated in the regulation of several post-transcriptional events. Involved in pre-mRNA alternative splicing, mRNA translation and stability. Mediates exon inclusion and/or exclusion in pre-mRNA that are subject to tissue-specific and developmentally regulated alternative splicing. Specifically activates exon 5 inclusion of cardiac isoforms of TNNT2 during heart remodeling at the juvenile to adult transition. Acts as both an activator and repressor of a pair of coregulated exons: promotes inclusion of the smooth muscle (SM) exon but exclusion of the non-muscle (NM) exon in actinin pre-mRNAs. Activates SM exon 5 inclusion by antagonizing the repressive effect of PTB. Promotes exclusion of exon 11 of the INSR pre-mRNA. Inhibits, together with HNRNPH1, insulin receptor (IR) pre-mRNA exon 11 inclusion in myoblast. Increases translation and controls the choice of translation initiation codon of CEBPB mRNA. Increases mRNA translation of CEBPB in aging liver. Increases translation of CDKN1A mRNA by antagonizing the repressive effect of CALR3. Mediates rapid cytoplasmic mRNA deadenylation. Recruits the deadenylase PARN to the poly(A) tail of EDEN-containing mRNAs to promote their deadenylation. Required for completion of spermatogenesis. Binds to (CUG)n triplet repeats in the 3'-UTR of transcripts such as DMPK and to Bruno response elements (BREs). Binds to muscle-specific splicing enhancer (MSE) intronic sites flanking the alternative exon 5 of TNNT2 pre-mRNA. Binds to AU-rich sequences (AREs or EDEN-like) localized in the 3'-UTR of JUN and FOS mRNAs. Binds to the IR RNA. Binds to the 5'-region of CDKN1A and CEBPB mRNAs. Binds with the 5'-region of CEBPB mRNA in aging liver.

Pongo abelii (taxid: 9601)

>sp|Q28HE9|CELF1_XENTR CUGBP Elav-like family member 1 OS=Xenopus tropicalis GN=celf1 PE=2 SV=1

 Score = 95.1 bits (235), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 43/66 (65%), Positives = 49/66 (74%)

Query: 27  SNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKC 86
           S   +G++G Q  GPEGANLFIYHLP EF D DL  MF PFG V+SAKVFIDKQ N SKC
Sbjct: 388 SQQGLGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKC 447

Query: 87  FGTIIF 92
           FG + +
Sbjct: 448 FGFVSY 453

RNA-binding protein implicated in the regulation of several post-transcriptional events. May be involved in pre-mRNA alternative splicing, mRNA translation activation and stability (By similarity). Mediates the rapid and sequence-specific cytoplasmic deadenylation of EDEN-containing maternal mRNAs following fertilization. Binds to AU-rich sequences (AREs) of jun mRNA. Binds to the embryonic deadenylation element (EDEN) motif localized in the 3'-UTR of maternal mRNAs. Binds to RNA containing several repeats of the consensus sequence 5'-UGU-3'. EDEN-dependent deadenylation is enhanced by the presence of an additional cis element composed of three AUU repeats.

Xenopus tropicalis (taxid: 8364)

>sp|Q4QQT3|CELF1_RAT CUGBP Elav-like family member 1 OS=Rattus norvegicus GN=Celf1 PE=2 SV=1

 Score = 95.1 bits (235), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 42/66 (63%), Positives = 50/66 (75%)

Query: 27  SNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKC 86
           +  ++G++G Q  GPEGANLFIYHLP EF D DL  MF PFG V+SAKVFIDKQ N SKC
Sbjct: 385 TQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKC 444

Query: 87  FGTIIF 92
           FG + +
Sbjct: 445 FGFVSY 450

RNA-binding protein implicated in the regulation of several post-transcriptional events. Involved in pre-mRNA alternative splicing, mRNA translation and stability. Mediates exon inclusion and/or exclusion in pre-mRNA that are subject to tissue-specific and developmentally regulated alternative splicing. Specifically activates exon 5 inclusion of cardiac isoforms of TNNT2 during heart remodeling at the juvenile to adult transition. Acts as both an activator and repressor of a pair of coregulated exons: promotes inclusion of the smooth muscle (SM) exon but exclusion of the non-muscle (NM) exon in actinin pre-mRNAs. Activates SM exon 5 inclusion by antagonizing the repressive effect of PTB. Promotes exclusion of exon 11 of the INSR pre-mRNA. Inhibits, together with HNRNPH1, insulin receptor (IR) pre-mRNA exon 11 inclusion in myoblast. Increases translation and controls the choice of translation initiation codon of CEBPB mRNA. Increases mRNA translation of CEBPB in aging liver. Increases translation of CDKN1A mRNA by antagonizing the repressive effect of CALR3. Mediates rapid cytoplasmic mRNA deadenylation. Recruits the deadenylase PARN to the poly(A) tail of EDEN-containing mRNAs to promote their deadenylation. Required for completion of spermatogenesis. Binds to (CUG)n triplet repeats in the 3'-UTR of transcripts such as DMPK and to Bruno response elements (BREs). Binds to muscle-specific splicing enhancer (MSE) intronic sites flanking the alternative exon 5 of TNNT2 pre-mRNA. Binds to AU-rich sequences (AREs or EDEN-like) localized in the 3'-UTR of JUN and FOS mRNAs. Binds to the IR RNA. Binds to the 5'-region of CDKN1A and CEBPB mRNAs. Binds with the 5'-region of CEBPB mRNA in aging liver.

Rattus norvegicus (taxid: 10116)

>sp|P28659|CELF1_MOUSE CUGBP Elav-like family member 1 OS=Mus musculus GN=Celf1 PE=1 SV=2

 Score = 95.1 bits (235), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 42/66 (63%), Positives = 50/66 (75%)

Query: 27  SNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKC 86
           +  ++G++G Q  GPEGANLFIYHLP EF D DL  MF PFG V+SAKVFIDKQ N SKC
Sbjct: 384 TQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKC 443

Query: 87  FGTIIF 92
           FG + +
Sbjct: 444 FGFVSY 449

RNA-binding protein implicated in the regulation of several post-transcriptional events. Involved in pre-mRNA alternative splicing, mRNA translation and stability. Mediates exon inclusion and/or exclusion in pre-mRNA that are subject to tissue-specific and developmentally regulated alternative splicing (By similarity). Specifically activates exon 5 inclusion of cardiac isoforms of TNNT2 during heart remodeling at the juvenile to adult transition (By similarity). Acts as both an activator and repressor of a pair of coregulated exons: promotes inclusion of the smooth muscle (SM) exon but exclusion of the non-muscle (NM) exon in actinin pre-mRNAs (By similarity). Activates SM exon 5 inclusion by antagonizing the repressive effect of PTB (By similarity). Promotes exclusion of exon 11 of the INSR pre-mRNA (By similarity). Inhibits, together with HNRNPH1, insulin receptor (IR) pre-mRNA exon 11 inclusion in myoblast (By similarity). Increases translation and controls the choice of translation initiation codon of CEBPB mRNA (By similarity). Increases mRNA translation of CEBPB in aging liver. Increases translation of CDKN1A mRNA by antagonizing the repressive effect of CALR3 (By similarity). Mediates rapid cytoplasmic mRNA deadenylation (By similarity). Recruits the deadenylase PARN to the poly(A) tail of EDEN-containing mRNAs to promote their deadenylation (By similarity). Required for completion of spermatogenesis. Binds to (CUG)n triplet repeats in the 3'-UTR of transcripts such as DMPK and to Bruno response elements (BREs) (By similarity). Binds to muscle-specific splicing enhancer (MSE) intronic sites flanking the alternative exon 5 of TNNT2 pre-mRNA (By similarity). Binds to AU-rich sequences (AREs or EDEN-like) localized in the 3'-UTR of JUN and FOS mRNAs. Binds to the IR RNA (By similarity). Binds to the 5'-region of CDKN1A and CEBPB mRNAs (By similarity). Binds with the 5'-region of CEBPB mRNA in aging liver.

Mus musculus (taxid: 10090)

>sp|Q92879|CELF1_HUMAN CUGBP Elav-like family member 1 OS=Homo sapiens GN=CELF1 PE=1 SV=2

 Score = 95.1 bits (235), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 42/66 (63%), Positives = 50/66 (75%)

Query: 27  SNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKC 86
           +  ++G++G Q  GPEGANLFIYHLP EF D DL  MF PFG V+SAKVFIDKQ N SKC
Sbjct: 384 TQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKC 443

Query: 87  FGTIIF 92
           FG + +
Sbjct: 444 FGFVSY 449

RNA-binding protein implicated in the regulation of several post-transcriptional events. Involved in pre-mRNA alternative splicing, mRNA translation and stability. Mediates exon inclusion and/or exclusion in pre-mRNA that are subject to tissue-specific and developmentally regulated alternative splicing. Specifically activates exon 5 inclusion of cardiac isoforms of TNNT2 during heart remodeling at the juvenile to adult transition. Acts as both an activator and repressor of a pair of coregulated exons: promotes inclusion of the smooth muscle (SM) exon but exclusion of the non-muscle (NM) exon in actinin pre-mRNAs. Activates SM exon 5 inclusion by antagonizing the repressive effect of PTB. Promotes exclusion of exon 11 of the INSR pre-mRNA. Inhibits, together with HNRNPH1, insulin receptor (IR) pre-mRNA exon 11 inclusion in myoblast. Increases translation and controls the choice of translation initiation codon of CEBPB mRNA. Increases mRNA translation of CEBPB in aging liver (By similarity). Increases translation of CDKN1A mRNA by antagonizing the repressive effect of CALR3. Mediates rapid cytoplasmic mRNA deadenylation. Recruits the deadenylase PARN to the poly(A) tail of EDEN-containing mRNAs to promote their deadenylation. Required for completion of spermatogenesis (By similarity). Binds to (CUG)n triplet repeats in the 3'-UTR of transcripts such as DMPK and to Bruno response elements (BREs). Binds to muscle-specific splicing enhancer (MSE) intronic sites flanking the alternative exon 5 of TNNT2 pre-mRNA. Binds to AU-rich sequences (AREs or EDEN-like) localized in the 3'-UTR of JUN and FOS mRNAs. Binds to the IR RNA. Binds to the 5'-region of CDKN1A and CEBPB mRNAs. Binds with the 5'-region of CEBPB mRNA in aging liver.

Homo sapiens (taxid: 9606)

>sp|O57406|CEL1A_XENLA CUGBP Elav-like family member 1-A OS=Xenopus laevis GN=cugbp1-a PE=1 SV=1

 Score = 94.0 bits (232), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 42/66 (63%), Positives = 49/66 (74%)

Query: 27  SNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKC 86
           S   +G++G Q  GPEGANLFIYHLP EF D DL  MF PFG V+S+KVFIDKQ N SKC
Sbjct: 387 SQQGLGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSSKVFIDKQTNLSKC 446

Query: 87  FGTIIF 92
           FG + +
Sbjct: 447 FGFVSY 452

RNA-binding protein implicated in the regulation of several post-transcriptional events. May be involved in pre-mRNA alternative splicing, mRNA translation activation and stability (By similarity). Mediates the rapid and sequence-specific cytoplasmic deadenylation of EDEN-containing maternal mRNAs following fertilization. Binds to AU-rich sequences (AREs) of jun mRNA. Binds to the embryonic deadenylation element (EDEN) motif localized in the 3'-UTR of maternal mRNAs. Binds to RNA containing several repeats of the consensus sequence 5'-UGU-3'. EDEN-dependent deadenylation is enhanced by the presence of an additional cis element composed of three AUU repeats.

Xenopus laevis (taxid: 8355)

>sp|A4IIM2|CELF2_XENTR CUGBP Elav-like family member 2 OS=Xenopus tropicalis GN=celf2 PE=2 SV=1

 Score = 90.9 bits (224), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 40/60 (66%), Positives = 46/60 (76%)

Query: 33  SSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
           ++G Q  GPEGANLFIYHLP EF D D+  MF PFG V+SAKVFIDKQ N SKCFG + +
Sbjct: 417 AAGSQKEGPEGANLFIYHLPQEFGDQDILQMFMPFGNVISAKVFIDKQTNLSKCFGFVSY 476

RNA-binding protein implicated in the regulation of several post-transcriptional events. May be involved in pre-mRNA alternative splicing, mRNA translation repression and stability.

Xenopus tropicalis (taxid: 8364)

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	128
28574145	737	bruno-2, isoform D [Drosophila melanogas	0.664	0.115	0.590	1e-18
116007320	893	bruno-2, isoform E [Drosophila melanogas	0.664	0.095	0.590	1e-18
386769533	350	bruno-2, isoform I [Drosophila melanogas	0.5	0.182	0.703	1e-18
221307768	350	MIP02242p [Drosophila melanogaster]	0.5	0.182	0.703	1e-18
386769529	651	bruno-2, isoform H [Drosophila melanogas	0.5	0.098	0.703	2e-18
270013480	469	hypothetical protein TcasGA2_TC012080 [T	0.718	0.196	0.464	2e-18
91090137	494	PREDICTED: similar to arrest CG31762-PC	0.718	0.186	0.464	3e-18
29436780	534	Cugbp1 protein [Danio rerio]	0.687	0.164	0.554	3e-18
18858491	501	CUGBP Elav-like family member 1 [Danio r	0.687	0.175	0.554	4e-18
350580113	337	PREDICTED: CUGBP, Elav-like family membe	0.492	0.186	0.666	5e-18

>gi|28574145|ref|NP_788039.1| bruno-2, isoform D [Drosophila melanogaster] gi|442627591|ref|NP_001260410.1| bruno-2, isoform K [Drosophila melanogaster] gi|28380348|gb|AAO41184.1| bruno-2, isoform D [Drosophila melanogaster] gi|440213740|gb|AGB92945.1| bruno-2, isoform K [Drosophila melanogaster]

 Score = 97.8 bits (242), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 52/88 (59%), Positives = 61/88 (69%), Gaps = 3/88 (3%)

Query: 5   VTLAAMTGAGTMSPTALSGLASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMF 64
           +T  A  GA +  P   S L +  AA G +GKQ+ GP+G+NLFIYHLP EF D DLAS F
Sbjct: 616 LTNGAAYGAASQ-PVTTSALQA--AAAGVTGKQIEGPDGSNLFIYHLPQEFIDTDLASTF 672

Query: 65  GPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
            PFG VLSAKVFIDKQ N SKCFG + +
Sbjct: 673 LPFGNVLSAKVFIDKQTNLSKCFGFVSY 700

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|116007320|ref|NP_001036356.1| bruno-2, isoform E [Drosophila melanogaster] gi|442627593|ref|NP_001260411.1| bruno-2, isoform L [Drosophila melanogaster] gi|113194979|gb|ABI31310.1| bruno-2, isoform E [Drosophila melanogaster] gi|440213741|gb|AGB92946.1| bruno-2, isoform L [Drosophila melanogaster]

 Score = 97.8 bits (242), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 52/88 (59%), Positives = 61/88 (69%), Gaps = 3/88 (3%)

Query: 5   VTLAAMTGAGTMSPTALSGLASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMF 64
           +T  A  GA +  P   S L +  AA G +GKQ+ GP+G+NLFIYHLP EF D DLAS F
Sbjct: 772 LTNGAAYGAASQ-PVTTSALQA--AAAGVTGKQIEGPDGSNLFIYHLPQEFIDTDLASTF 828

Query: 65  GPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
            PFG VLSAKVFIDKQ N SKCFG + +
Sbjct: 829 LPFGNVLSAKVFIDKQTNLSKCFGFVSY 856

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|386769533|ref|NP_001246001.1| bruno-2, isoform I [Drosophila melanogaster] gi|383291459|gb|AFH03675.1| bruno-2, isoform I [Drosophila melanogaster]

 Score = 97.4 bits (241), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 45/64 (70%), Positives = 51/64 (79%)

Query: 29  AAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
           AA G +GKQ+ GP+G+NLFIYHLP EF D DLAS F PFG VLSAKVFIDKQ N SKCFG
Sbjct: 250 AAAGVTGKQIEGPDGSNLFIYHLPQEFIDTDLASTFLPFGNVLSAKVFIDKQTNLSKCFG 309

Query: 89  TIIF 92
            + +
Sbjct: 310 FVSY 313

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|221307768|gb|ACM16743.1| MIP02242p [Drosophila melanogaster]

 Score = 97.4 bits (241), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 45/64 (70%), Positives = 51/64 (79%)

Query: 29  AAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
           AA G +GKQ+ GP+G+NLFIYHLP EF D DLAS F PFG VLSAKVFIDKQ N SKCFG
Sbjct: 250 AAAGVTGKQIEGPDGSNLFIYHLPQEFIDTDLASTFLPFGNVLSAKVFIDKQTNLSKCFG 309

Query: 89  TIIF 92
            + +
Sbjct: 310 FVSY 313

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|386769529|ref|NP_001245999.1| bruno-2, isoform H [Drosophila melanogaster] gi|386769535|ref|NP_001246002.1| bruno-2, isoform J [Drosophila melanogaster] gi|226371828|gb|ACO51539.1| MIP06224p [Drosophila melanogaster] gi|383291457|gb|AFH03673.1| bruno-2, isoform H [Drosophila melanogaster] gi|383291460|gb|AFH03676.1| bruno-2, isoform J [Drosophila melanogaster]

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 45/64 (70%), Positives = 51/64 (79%)

Query: 29  AAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
           AA G +GKQ+ GP+G+NLFIYHLP EF D DLAS F PFG VLSAKVFIDKQ N SKCFG
Sbjct: 551 AAAGVTGKQIEGPDGSNLFIYHLPQEFIDTDLASTFLPFGNVLSAKVFIDKQTNLSKCFG 610

Query: 89  TIIF 92
            + +
Sbjct: 611 FVSY 614

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270013480|gb|EFA09928.1| hypothetical protein TcasGA2_TC012080 [Tribolium castaneum]

 Score = 97.1 bits (240), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 58/125 (46%), Positives = 73/125 (58%), Gaps = 33/125 (26%)

Query: 1   MQNLVTLAAMT---------------GAG---TMSPTALSGLASSNAAVGSS-------- 34
           +QNLVTLAAM+               GAG   T++    +G+++S+ +   S        
Sbjct: 308 VQNLVTLAAMSQPTAAPLCVANLLGKGAGVERTLTTGLQTGMSTSDLSTYGSLITNATLN 367

Query: 35  -------GKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCF 87
                  GKQ+ GP+G NLFIYHLP EF+D DLAS F PFG V+SAKVFIDKQ N SKCF
Sbjct: 368 AAAIAAAGKQIEGPDGCNLFIYHLPQEFTDTDLASTFLPFGPVISAKVFIDKQTNLSKCF 427

Query: 88  GTIIF 92
           G + F
Sbjct: 428 GFVSF 432

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91090137|ref|XP_976135.1| PREDICTED: similar to arrest CG31762-PC isoform 4 [Tribolium castaneum]

 Score = 96.7 bits (239), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 58/125 (46%), Positives = 73/125 (58%), Gaps = 33/125 (26%)

Query: 1   MQNLVTLAAMT---------------GAG---TMSPTALSGLASSNAAVGSS-------- 34
           +QNLVTLAAM+               GAG   T++    +G+++S+ +   S        
Sbjct: 333 VQNLVTLAAMSQPTAAPLCVANLLGKGAGVERTLTTGLQTGMSTSDLSTYGSLITNATLN 392

Query: 35  -------GKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCF 87
                  GKQ+ GP+G NLFIYHLP EF+D DLAS F PFG V+SAKVFIDKQ N SKCF
Sbjct: 393 AAAIAAAGKQIEGPDGCNLFIYHLPQEFTDTDLASTFLPFGPVISAKVFIDKQTNLSKCF 452

Query: 88  GTIIF 92
           G + F
Sbjct: 453 GFVSF 457

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|29436780|gb|AAH49453.1| Cugbp1 protein [Danio rerio]

 Score = 96.3 bits (238), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 51/92 (55%), Positives = 59/92 (64%), Gaps = 4/92 (4%)

Query: 5   VTLAAMTGAGTMSPTALSGLAS----SNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADL 60
           +T AA +G    +  AL  L S    S   V ++G Q  GPEGANLFIYHLP EF D DL
Sbjct: 406 LTQAAYSGIQQYAAAALPSLYSQSLLSQQNVSAAGSQKEGPEGANLFIYHLPQEFGDQDL 465

Query: 61  ASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
             MF PFG V+SAKVFIDKQ N SKCFG + +
Sbjct: 466 LQMFMPFGNVISAKVFIDKQTNLSKCFGFVSY 497

Source: Danio rerio

Species: Danio rerio

Genus: Danio

Family: Cyprinidae

Order: Cypriniformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|18858491|ref|NP_571688.1| CUGBP Elav-like family member 1 [Danio rerio] gi|82247731|sp|Q9IBD0.1|CELF1_DANRE RecName: Full=CUGBP Elav-like family member 1; Short=CELF-1; AltName: Full=Bruno-like protein 2; AltName: Full=CUG triplet repeat RNA-binding protein 1; Short=CUG-BP1; AltName: Full=CUG-BP- and ETR-3-like factor 1; AltName: Full=EDEN-BP/Bruno-like protein; AltName: Full=RNA-binding protein BRUNOL-2 gi|7670538|dbj|BAA95119.1| brul [Danio rerio]

 Score = 96.3 bits (238), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 51/92 (55%), Positives = 59/92 (64%), Gaps = 4/92 (4%)

Query: 5   VTLAAMTGAGTMSPTALSGLAS----SNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADL 60
           +T AA +G    +  AL  L S    S   V ++G Q  GPEGANLFIYHLP EF D DL
Sbjct: 373 LTQAAYSGIQQYAAAALPSLYSQSLLSQQNVSAAGSQKEGPEGANLFIYHLPQEFGDQDL 432

Query: 61  ASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
             MF PFG V+SAKVFIDKQ N SKCFG + +
Sbjct: 433 LQMFMPFGNVISAKVFIDKQTNLSKCFGFVSY 464

Source: Danio rerio

Species: Danio rerio

Genus: Danio

Family: Cyprinidae

Order: Cypriniformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|350580113|ref|XP_003122868.3| PREDICTED: CUGBP, Elav-like family member 1, partial [Sus scrofa]

 Score = 95.9 bits (237), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 42/63 (66%), Positives = 49/63 (77%)

Query: 30  AVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGT 89
           ++G++G Q  GPEGANLFIYHLP EF D DL  MF PFG V+SAKVFIDKQ N SKCFG 
Sbjct: 238 SIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGF 297

Query: 90  IIF 92
           + +
Sbjct: 298 VSY 300

Source: Sus scrofa

Species: Sus scrofa

Genus: Sus

Family: Suidae

Class: Mammalia

Phylum: Chordata

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	128
FB|FBgn0000114	810	aret "arrest" [Drosophila mela	0.718	0.113	0.554	7.6e-21
FB|FBgn0262475	893	bru-2 "bruno-2" [Drosophila me	0.664	0.095	0.590	1.1e-19
UNIPROTKB|F1SID9	344	CELF1 "Uncharacterized protein	0.593	0.220	0.592	2.5e-19
ZFIN|ZDB-GENE-000501-1	535	celf1 "cugbp, Elav-like family	0.687	0.164	0.554	4.7e-19
UNIPROTKB|F1ND14	485	CELF1 "CUGBP Elav-like family	0.625	0.164	0.562	5.9e-19
UNIPROTKB|Q5F3T7	489	CELF1 "CUGBP Elav-like family	0.625	0.163	0.562	6e-19
UNIPROTKB|A7MB95	486	CUGBP1 "Uncharacterized protei	0.625	0.164	0.562	7.7e-19
UNIPROTKB|Q92879	486	CELF1 "CUGBP Elav-like family	0.625	0.164	0.562	7.7e-19
MGI|MGI:1342295	486	Celf1 "CUGBP, Elav-like family	0.625	0.164	0.562	7.7e-19
RGD|1307721	487	Celf1 "CUGBP, Elav-like family	0.625	0.164	0.562	7.7e-19

FB|FBgn0000114 aret "arrest" [Drosophila melanogaster (taxid:7227)]

 Score = 256 (95.2 bits), Expect = 7.6e-21, P = 7.6e-21
 Identities = 51/92 (55%), Positives = 62/92 (67%)

Query:     1 MQNLVTLAAMTGAGTMSPTALSGLASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADL 60
             M     L     A  +S + L+ +A S AA  ++GKQ+ GPEG NLFIYHLP EF+D DL
Sbjct:   683 MSTAAGLPQFGSASALSTSPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDL 742

Query:    61 ASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
             AS F PFG V+SAKVFIDKQ + SKCFG + F
Sbjct:   743 ASTFLPFGNVISAKVFIDKQTSLSKCFGFVSF 774

GO:0048477 "oogenesis" evidence=IMP

GO:0007286 "spermatid development" evidence=IMP

GO:0007319 "negative regulation of oskar mRNA translation" evidence=IDA;NAS;TAS

GO:0003729 "mRNA binding" evidence=ISS;NAS;TAS

GO:0005515 "protein binding" evidence=IPI

GO:0030727 "germarium-derived female germ-line cyst formation" evidence=TAS

GO:0042078 "germ-line stem cell division" evidence=NAS

GO:0046011 "regulation of oskar mRNA translation" evidence=TAS

GO:0006378 "mRNA polyadenylation" evidence=TAS

GO:0003730 "mRNA 3'-UTR binding" evidence=IDA;TAS

GO:0017148 "negative regulation of translation" evidence=IMP

GO:0000166 "nucleotide binding" evidence=IEA

GO:0043186 "P granule" evidence=IDA

GO:0005634 "nucleus" evidence=IC

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

GO:0003723 "RNA binding" evidence=IDA

GO:0007281 "germ cell development" evidence=IMP

GO:0031536 "positive regulation of exit from mitosis" evidence=IMP

GO:0002121 "inter-male aggressive behavior" evidence=IMP

GO:0007476 "imaginal disc-derived wing morphogenesis" evidence=IMP

FB|FBgn0262475 bru-2 "bruno-2" [Drosophila melanogaster (taxid:7227)]

 Score = 246 (91.7 bits), Expect = 1.1e-19, P = 1.1e-19
 Identities = 52/88 (59%), Positives = 61/88 (69%)

Query:     5 VTLAAMTGAGTMSPTALSGLASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMF 64
             +T  A  GA +  P   S L +  AA G +GKQ+ GP+G+NLFIYHLP EF D DLAS F
Sbjct:   772 LTNGAAYGAASQ-PVTTSALQA--AAAGVTGKQIEGPDGSNLFIYHLPQEFIDTDLASTF 828

Query:    65 GPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
              PFG VLSAKVFIDKQ N SKCFG + +
Sbjct:   829 LPFGNVLSAKVFIDKQTNLSKCFGFVSY 856

GO:0003729 "mRNA binding" evidence=ISS

GO:0005575 "cellular_component" evidence=ND

GO:0000166 "nucleotide binding" evidence=IEA

GO:0017148 "negative regulation of translation" evidence=ISA

GO:0003723 "RNA binding" evidence=ISA

UNIPROTKB|F1SID9 CELF1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 231 (86.4 bits), Expect = 2.5e-19, P = 2.5e-19
 Identities = 45/76 (59%), Positives = 52/76 (68%)

Query:    13 AGTMSPTALSGLASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLS 72
             A    PT  +    +  ++G++G Q  GPEGANLFIYHLP EF D DL  MF PFG V+S
Sbjct:   225 AAAALPTLYNQNLLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVS 284

Query:    73 AKVFIDKQNNRSKCFG 88
             AKVFIDKQ N SKCFG
Sbjct:   285 AKVFIDKQTNLSKCFG 300

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

GO:0042835 "BRE binding" evidence=IEA

GO:0040018 "positive regulation of multicellular organism growth" evidence=IEA

GO:0031369 "translation initiation factor binding" evidence=IEA

GO:0007286 "spermatid development" evidence=IEA

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

GO:0003729 "mRNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

ZFIN|ZDB-GENE-000501-1 celf1 "cugbp, Elav-like family member 1" [Danio rerio (taxid:7955)]

 Score = 236 (88.1 bits), Expect = 4.7e-19, P = 4.7e-19
 Identities = 51/92 (55%), Positives = 59/92 (64%)

Query:     5 VTLAAMTGAGTMSPTALSGLAS----SNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADL 60
             +T AA +G    +  AL  L S    S   V ++G Q  GPEGANLFIYHLP EF D DL
Sbjct:   407 LTQAAYSGIQQYAAAALPSLYSQSLLSQQNVSAAGSQKEGPEGANLFIYHLPQEFGDQDL 466

Query:    61 ASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
               MF PFG V+SAKVFIDKQ N SKCFG + +
Sbjct:   467 LQMFMPFGNVISAKVFIDKQTNLSKCFGFVSY 498

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0045495 "pole plasm" evidence=IDA

GO:0005737 "cytoplasm" evidence=IEA;IDA

GO:0005634 "nucleus" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

UNIPROTKB|F1ND14 CELF1 "CUGBP Elav-like family member 1" [Gallus gallus (taxid:9031)]

 Score = 234 (87.4 bits), Expect = 5.9e-19, P = 5.9e-19
 Identities = 45/80 (56%), Positives = 54/80 (67%)

Query:    13 AGTMSPTALSGLASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLS 72
             A    PT  +    +  ++G++G Q  GPEGANLFIYHLP EF D DL  MF PFG V+S
Sbjct:   369 AAAALPTLYNQSLLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVS 428

Query:    73 AKVFIDKQNNRSKCFGTIIF 92
             AKVFIDKQ N SKCFG + +
Sbjct:   429 AKVFIDKQTNLSKCFGFVSY 448

GO:0000166 "nucleotide binding" evidence=IEA

GO:0040018 "positive regulation of multicellular organism growth" evidence=IEA

GO:0042835 "BRE binding" evidence=IEA

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

GO:0003729 "mRNA binding" evidence=IEA

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

GO:0007286 "spermatid development" evidence=IEA

GO:0031369 "translation initiation factor binding" evidence=IEA

UNIPROTKB|Q5F3T7 CELF1 "CUGBP Elav-like family member 1" [Gallus gallus (taxid:9031)]

 Score = 234 (87.4 bits), Expect = 6.0e-19, P = 6.0e-19
 Identities = 45/80 (56%), Positives = 54/80 (67%)

Query:    13 AGTMSPTALSGLASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLS 72
             A    PT  +    +  ++G++G Q  GPEGANLFIYHLP EF D DL  MF PFG V+S
Sbjct:   373 AAAALPTLYNQSLLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVS 432

Query:    73 AKVFIDKQNNRSKCFGTIIF 92
             AKVFIDKQ N SKCFG + +
Sbjct:   433 AKVFIDKQTNLSKCFGFVSY 452

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

UNIPROTKB|A7MB95 CUGBP1 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 233 (87.1 bits), Expect = 7.7e-19, P = 7.7e-19
 Identities = 45/80 (56%), Positives = 54/80 (67%)

Query:    13 AGTMSPTALSGLASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLS 72
             A    PT  +    +  ++G++G Q  GPEGANLFIYHLP EF D DL  MF PFG V+S
Sbjct:   370 AAAALPTLYNQNLLAQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVS 429

Query:    73 AKVFIDKQNNRSKCFGTIIF 92
             AKVFIDKQ N SKCFG + +
Sbjct:   430 AKVFIDKQTNLSKCFGFVSY 449

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

GO:0042835 "BRE binding" evidence=IEA

GO:0040018 "positive regulation of multicellular organism growth" evidence=IEA

GO:0031369 "translation initiation factor binding" evidence=IEA

GO:0007286 "spermatid development" evidence=IEA

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

GO:0003729 "mRNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|Q92879 CELF1 "CUGBP Elav-like family member 1" [Homo sapiens (taxid:9606)]

 Score = 233 (87.1 bits), Expect = 7.7e-19, P = 7.7e-19
 Identities = 45/80 (56%), Positives = 54/80 (67%)

Query:    13 AGTMSPTALSGLASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLS 72
             A    PT  +    +  ++G++G Q  GPEGANLFIYHLP EF D DL  MF PFG V+S
Sbjct:   370 AAAALPTLYNQNLLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVS 429

Query:    73 AKVFIDKQNNRSKCFGTIIF 92
             AKVFIDKQ N SKCFG + +
Sbjct:   430 AKVFIDKQTNLSKCFGFVSY 449

GO:0000166 "nucleotide binding" evidence=IEA

GO:0007286 "spermatid development" evidence=IEA

GO:0031369 "translation initiation factor binding" evidence=IEA

GO:0040018 "positive regulation of multicellular organism growth" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

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

GO:0005634 "nucleus" evidence=NAS

GO:0042835 "BRE binding" evidence=IDA

GO:0016246 "RNA interference" evidence=NAS

GO:0007281 "germ cell development" evidence=NAS

GO:0009790 "embryo development" evidence=NAS

GO:0030529 "ribonucleoprotein complex" evidence=NAS

GO:0000900 "translation repressor activity, nucleic acid binding" evidence=NAS

GO:0003723 "RNA binding" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

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

GO:0006397 "mRNA processing" evidence=TAS

GO:0003729 "mRNA binding" evidence=IDA

MGI|MGI:1342295 Celf1 "CUGBP, Elav-like family member 1" [Mus musculus (taxid:10090)]

 Score = 233 (87.1 bits), Expect = 7.7e-19, P = 7.7e-19
 Identities = 45/80 (56%), Positives = 54/80 (67%)

Query:    13 AGTMSPTALSGLASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLS 72
             A    PT  +    +  ++G++G Q  GPEGANLFIYHLP EF D DL  MF PFG V+S
Sbjct:   370 AAAALPTLYNQNLLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVS 429

Query:    73 AKVFIDKQNNRSKCFGTIIF 92
             AKVFIDKQ N SKCFG + +
Sbjct:   430 AKVFIDKQTNLSKCFGFVSY 449

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISO

GO:0003729 "mRNA binding" evidence=ISO

GO:0005634 "nucleus" evidence=IDA;TAS

GO:0005737 "cytoplasm" evidence=IDA;TAS

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

GO:0006397 "mRNA processing" evidence=IEA

GO:0007286 "spermatid development" evidence=IMP

GO:0008380 "RNA splicing" evidence=IEA

GO:0031369 "translation initiation factor binding" evidence=IDA

GO:0040018 "positive regulation of multicellular organism growth" evidence=IMP

GO:0042835 "BRE binding" evidence=ISO

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

RGD|1307721 Celf1 "CUGBP, Elav-like family member 1" [Rattus norvegicus (taxid:10116)]

 Score = 233 (87.1 bits), Expect = 7.7e-19, P = 7.7e-19
 Identities = 45/80 (56%), Positives = 54/80 (67%)

Query:    13 AGTMSPTALSGLASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLS 72
             A    PT  +    +  ++G++G Q  GPEGANLFIYHLP EF D DL  MF PFG V+S
Sbjct:   371 AAAALPTLYNQNLLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVS 430

Query:    73 AKVFIDKQNNRSKCFGTIIF 92
             AKVFIDKQ N SKCFG + +
Sbjct:   431 AKVFIDKQTNLSKCFGFVSY 450

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISO;ISS

GO:0003729 "mRNA binding" evidence=IEA;ISO

GO:0005634 "nucleus" evidence=IEA;ISO

GO:0005737 "cytoplasm" evidence=IEA;ISO

GO:0006376 "mRNA splice site selection" evidence=IEA;ISO

GO:0007286 "spermatid development" evidence=IEA;ISO

GO:0031369 "translation initiation factor binding" evidence=IEA;ISO

GO:0040018 "positive regulation of multicellular organism growth" evidence=IEA;ISO

GO:0042835 "BRE binding" evidence=IEA;ISO

GO:0043484 "regulation of RNA splicing" evidence=ISO;ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q5R995	CELF1_PONAB	No assigned EC number	0.6363	0.5156	0.1286	yes	N/A
P28659	CELF1_MOUSE	No assigned EC number	0.6363	0.5156	0.1358	yes	N/A
Q5F3T7	CELF1_CHICK	No assigned EC number	0.6363	0.5156	0.1349	yes	N/A
Q9IBD0	CELF1_DANRE	No assigned EC number	0.5543	0.6875	0.1756	yes	N/A
Q28HE9	CELF1_XENTR	No assigned EC number	0.6515	0.5156	0.1346	yes	N/A
Q92879	CELF1_HUMAN	No assigned EC number	0.6363	0.5156	0.1358	yes	N/A
Q4QQT3	CELF1_RAT	No assigned EC number	0.6363	0.5156	0.1355	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	128
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	1e-23
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	2e-23
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	3e-23
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	1e-20
smart00360	73	smart00360, RRM, RNA recognition motif	1e-11
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	1e-09
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	1e-09
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	1e-08
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	1e-08
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-08
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	2e-08
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	3e-08
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	4e-08
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	5e-08
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	5e-08
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	8e-08
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	2e-07
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	2e-07
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	6e-07
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	8e-07
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	1e-06
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	1e-06
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	1e-06
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	2e-06
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	4e-06
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	4e-06
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	5e-06
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	7e-06
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	7e-06
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	7e-06
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	7e-06
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	8e-06
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	9e-06
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-05
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	1e-05
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	1e-05
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	3e-05
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	3e-05
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	3e-05
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	3e-05
cd12678	74	cd12678, RRM_SLTM, RNA recognition motif in Scaffo	3e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	4e-05
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	5e-05
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	6e-05
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	7e-05
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	7e-05
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	7e-05
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	8e-05
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	1e-04
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	1e-04
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	1e-04
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	1e-04
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	2e-04
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	2e-04
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	3e-04
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	3e-04
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	3e-04
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	4e-04
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	4e-04
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	4e-04
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	5e-04
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	6e-04
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	6e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	7e-04
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	8e-04
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	8e-04
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	8e-04
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	8e-04
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	8e-04
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	0.001
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	0.001
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	0.001
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	0.002
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	0.002
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	0.002
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	0.002
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	0.003
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	0.004
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	0.004

>gnl|CDD|241083 cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 86.8 bits (215), Expect = 1e-23
 Identities = 36/53 (67%), Positives = 42/53 (79%)

Query: 40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          GPEG NLFIYHLP EF DA+L  MF PFG V+SAKVF+D+  N+SKCFG + F
Sbjct: 1  GPEGCNLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSF 53

This subgroup corresponds to the RRM3 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contains three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. Both, RRM1 and RRM2 of CELF-4, can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 79

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

 Score = 86.2 bits (213), Expect = 2e-23
 Identities = 38/53 (71%), Positives = 42/53 (79%)

Query: 40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          GPEG NLFIYHLP EF+D DLA  F PFG V+SAKVFIDKQ N SKCFG + +
Sbjct: 1  GPEGCNLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSY 53

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

>gnl|CDD|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 86.3 bits (213), Expect = 3e-23
 Identities = 40/56 (71%), Positives = 43/56 (76%)

Query: 37 QLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          Q  GPEGANLFIYHLP EF D DL  MF PFG V+SAKVFIDKQ N SKCFG + +
Sbjct: 1  QKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSY 56

This subgroup corresponds to the RRM3 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. Human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It specifically binds to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contain three highly conserved RRMs. It binds to RNA via the first two RRMs, which are important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. . Length = 92

>gnl|CDD|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 = 78.8 bits (195), Expect = 1e-20
 Identities = 29/43 (67%), Positives = 34/43 (79%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
          LFIYHLP EF+D DL  +F PFG V+SAKVF+DK   +SKCFG
Sbjct: 1  LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFG 43

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|214636 smart00360, RRM, RNA recognition motif

 Score = 55.7 bits (135), Expect = 1e-11
 Identities = 17/48 (35%), Positives = 29/48 (60%)

Query: 45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
           LF+ +LPP+ ++ +L  +F  FG V S ++  DK+  +SK F  + F
Sbjct: 1  TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEF 48

Length = 73

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

 Score = 50.7 bits (122), Expect = 1e-09
 Identities = 19/48 (39%), Positives = 30/48 (62%)

Query: 45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          N++I  LPP  +D DL  +  PFG ++S K  +DK+ N+ K +G + F
Sbjct: 2  NVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDF 49

This subfamily corresponds to the RRM1 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus, they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. Moreover, the family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot. . Length = 71

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

 Score = 50.7 bits (122), Expect = 1e-09
 Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 1/48 (2%)

Query: 45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          N+++ +L  +  D  L  +FG +G + SAKV  D    +SK FG + F
Sbjct: 3  NVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKD-DEGKSKGFGFVNF 49

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

 Score = 48.1 bits (115), Expect = 1e-08
 Identities = 18/46 (39%), Positives = 28/46 (60%)

Query: 43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
          G  +F+Y+LPP+  ++ L  +F PFG V + KV  D   N+ K +G
Sbjct: 1  GWCIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYG 46

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

 Score = 48.4 bits (116), Expect = 1e-08
 Identities = 22/51 (43%), Positives = 28/51 (54%), Gaps = 1/51 (1%)

Query: 43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFM 93
          G NL++ +L     D  L   F PFGT+ SAKV  D +  RSK FG + F 
Sbjct: 1  GVNLYVKNLDDSIDDERLREEFSPFGTITSAKVMTD-EKGRSKGFGFVCFS 50

This subfamily corresponds to the RRM4 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in theThe CD corresponds to the RRM. regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 79

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

 Score = 51.3 bits (123), Expect = 1e-08
 Identities = 17/51 (33%), Positives = 29/51 (56%), Gaps = 1/51 (1%)

Query: 42  EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
           +G NL++ +L    +D  L  +F   G + SAKV +D++   S+ FG + F
Sbjct: 284 QGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEK-GVSRGFGFVCF 333

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

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

 Score = 47.4 bits (113), Expect = 2e-08
 Identities = 18/51 (35%), Positives = 29/51 (56%)

Query: 45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRK 95
          ++F+  L PE     L + F PFG +  A+V  D Q  +SK +G + F++K
Sbjct: 1  HIFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKK 51

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

 Score = 46.8 bits (112), Expect = 3e-08
 Identities = 19/44 (43%), Positives = 29/44 (65%)

Query: 45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
          NL++ +LP   ++ DL  +FG FG V SA+V  D++  RS+ FG
Sbjct: 1  NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFG 44

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|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 49.9 bits (119), Expect = 4e-08
 Identities = 33/108 (30%), Positives = 50/108 (46%), Gaps = 4/108 (3%)

Query: 15  TMSPTALSGLASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAK 74
             SP A  G  +   A G+      G  G  +F+Y+L P+  +  L  +FGPFG V + K
Sbjct: 243 RASPPATDGQTAG-LAAGAQIAASDG-AGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVK 300

Query: 75  VFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNT 121
           +  D   N+ K +G  + M  +    +   + N Y LG   L+ SF T
Sbjct: 301 IIRDLTTNQCKGYG-FVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKT 347

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

 Score = 47.0 bits (111), Expect = 5e-08
 Identities = 29/80 (36%), Positives = 42/80 (52%), Gaps = 2/80 (2%)

Query: 43  GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIR 102
           G  +F+Y+L PE  ++ L  +FGPFG V + KV  D   N+ K FG  + M  +    + 
Sbjct: 1   GWCIFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFG-FVTMTNYDEAAMA 59

Query: 103 FDTANDY-LGQSFLKPSFNT 121
             + N Y LG   L+ SF T
Sbjct: 60  IASLNGYRLGDRVLQVSFKT 79

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

 Score = 46.5 bits (111), Expect = 5e-08
 Identities = 17/47 (36%), Positives = 29/47 (61%), Gaps = 1/47 (2%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          LF+ +LPP+ ++ DL  +F  FG + S ++  DK + +SK F  + F
Sbjct: 1  LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK-DGKSKGFAFVEF 46

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|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 46.4 bits (109), Expect = 8e-08
 Identities = 19/48 (39%), Positives = 29/48 (60%)

Query: 45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          NL+I  LPP  +D DL  +  P+G ++S K  +DK  N+ K +G + F
Sbjct: 9  NLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDF 56

This subgroup corresponds to the RRM1 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 86

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

 Score = 45.5 bits (107), Expect = 2e-07
 Identities = 29/80 (36%), Positives = 42/80 (52%), Gaps = 2/80 (2%)

Query: 43  GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIR 102
           G  +F+Y+L P+  ++ L  MFGPFG V + KV  D   N+ K FG  + M  +    + 
Sbjct: 3   GWCIFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFG-FVTMTNYDEAAMA 61

Query: 103 FDTANDY-LGQSFLKPSFNT 121
             + N Y LG   L+ SF T
Sbjct: 62  IASLNGYRLGDRVLQVSFKT 81

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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 44.5 bits (106), Expect = 2e-07
 Identities = 17/47 (36%), Positives = 28/47 (59%), Gaps = 1/47 (2%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          LF+ +LPP+ ++ DL  +F  FG + S ++  D +  RSK F  + F
Sbjct: 1  LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRD-ETGRSKGFAFVEF 46

(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|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 44.0 bits (103), Expect = 6e-07
 Identities = 19/48 (39%), Positives = 29/48 (60%)

Query: 45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          NL+I  LPP  +D DL  +  P+G ++S K  +DK  N+ K +G + F
Sbjct: 6  NLYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDF 53

This subgroup corresponds to the RRM1 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 80

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

 Score = 46.0 bits (109), Expect = 8e-07
 Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 1/48 (2%)

Query: 45  NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
           NL++ +L P  ++  L  +F  FG + SA V  D  + RS+ F  + F
Sbjct: 180 NLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKD-GSGRSRGFAFVNF 226

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

 Score = 43.5 bits (102), Expect = 1e-06
 Identities = 28/80 (35%), Positives = 42/80 (52%), Gaps = 2/80 (2%)

Query: 43  GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIR 102
           G  +F+Y+L P+  ++ L  +FGPFG V + KV  D   N+ K FG  + M  +    + 
Sbjct: 3   GWCIFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFG-FVTMTNYDEAAMA 61

Query: 103 FDTANDY-LGQSFLKPSFNT 121
             + N Y LG   L+ SF T
Sbjct: 62  IASLNGYRLGDRVLQVSFKT 81

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

 Score = 42.7 bits (101), Expect = 1e-06
 Identities = 13/38 (34%), Positives = 22/38 (57%)

Query: 45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNN 82
          NL+I +LP    + DL +M  P+G V+S ++  D +  
Sbjct: 2  NLYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKGQ 39

This subfamily corresponds to the RRM2 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. Moreover, they family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot. . Length = 79

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

 Score = 43.1 bits (101), Expect = 1e-06
 Identities = 29/80 (36%), Positives = 40/80 (50%), Gaps = 2/80 (2%)

Query: 43  GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIR 102
           G  +FIY+L  +  +  L  MFGPFG V + KV  D   N+ K FG  + M  +    + 
Sbjct: 1   GWCIFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFG-FVTMTNYEEAAMA 59

Query: 103 FDTANDY-LGQSFLKPSFNT 121
             + N Y LG   L+ SF T
Sbjct: 60  IASLNGYRLGDKILQVSFKT 79

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

 Score = 42.3 bits (100), Expect = 2e-06
 Identities = 14/48 (29%), Positives = 26/48 (54%)

Query: 45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          NL++  L      ADL  +F  +G V+ AK+  + ++  ++CFG +  
Sbjct: 1  NLWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTM 48

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

 Score = 41.6 bits (98), Expect = 4e-06
 Identities = 15/47 (31%), Positives = 26/47 (55%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          +F+  LPP+ ++ +    F  FG V+ A++  D    RS+ FG + F
Sbjct: 2  IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTF 48

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

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

 Score = 41.9 bits (99), Expect = 4e-06
 Identities = 18/50 (36%), Positives = 25/50 (50%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRK 95
          LF+  L P  +D DL  +F  FG + S +V  DK+   S  +  I F  K
Sbjct: 6  LFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETK 55

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|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 = 41.5 bits (98), Expect = 5e-06
 Identities = 16/48 (33%), Positives = 27/48 (56%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFM 93
          LF+ +LP   ++ +L  +F  FG +    + +DK+  RSK F  + FM
Sbjct: 2  LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFM 49

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

 Score = 41.1 bits (97), Expect = 7e-06
 Identities = 14/49 (28%), Positives = 28/49 (57%)

Query: 44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          ANL++  LP   +  +L ++F P+G ++++++  D     S+  G I F
Sbjct: 1  ANLYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRF 49

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

 Score = 40.9 bits (96), Expect = 7e-06
 Identities = 16/51 (31%), Positives = 24/51 (47%)

Query: 42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          +   LF+  L  + SD+ L   F  +G +    V +D    RS+ FG I F
Sbjct: 1  QLCKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITF 51

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

 Score = 40.9 bits (96), Expect = 7e-06
 Identities = 19/50 (38%), Positives = 26/50 (52%), Gaps = 4/50 (8%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNR-SKCFGTIIFMR 94
          L + ++P  F D DL  MFG FG +L  ++     N R SK FG + F  
Sbjct: 3  LHVSNIPFRFRDPDLRQMFGQFGPILDVEIIF---NERGSKGFGFVTFAN 49

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

 Score = 43.4 bits (101), Expect = 7e-06
 Identities = 16/57 (28%), Positives = 31/57 (54%)

Query: 36  KQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
           +Q +  E   LF+ +LP + ++ DL  +F  FG V   ++  D++  +S+ F  + F
Sbjct: 108 RQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEF 164

Length = 306

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

 Score = 40.8 bits (95), Expect = 8e-06
 Identities = 17/52 (32%), Positives = 29/52 (55%)

Query: 45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKF 96
          ++F+  L PE +  D+ + F PFG +  A+V  D    +SK +G + F  K+
Sbjct: 3  HVFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKW 54

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|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 = 40.7 bits (96), Expect = 9e-06
 Identities = 14/52 (26%), Positives = 24/52 (46%)

Query: 43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMR 94
          G  LF+  L    ++ +L ++F  FG V    +  D +   S+ FG + F  
Sbjct: 1  GNKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFES 52

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 40.2 bits (95), Expect = 1e-05
 Identities = 13/42 (30%), Positives = 22/42 (52%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCF 87
          L++ +LPP  ++ DL   F P+G V   ++  +K   R   F
Sbjct: 1  LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAF 42

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

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

 Score = 40.6 bits (95), Expect = 1e-05
 Identities = 17/48 (35%), Positives = 28/48 (58%)

Query: 45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          N+F+  L PE +DA L + F  F +   A+V  D ++ RS+ +G + F
Sbjct: 1  NIFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSF 48

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|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 40.1 bits (93), Expect = 1e-05
 Identities = 18/49 (36%), Positives = 28/49 (57%)

Query: 44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
           NL+I  L P  +D DL  +  P+G ++S K  +DK  N+ K +G + F
Sbjct: 2  TNLYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDF 50

This subgroup corresponds to the RRM1 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 75

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

 Score = 39.5 bits (93), Expect = 3e-05
 Identities = 16/50 (32%), Positives = 26/50 (52%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRK 95
          +FI +LP + ++ +L  +F  FG V  A++  DK    SK    + F  K
Sbjct: 3  VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTK 52

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

 Score = 39.1 bits (92), Expect = 3e-05
 Identities = 14/48 (29%), Positives = 22/48 (45%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFM 93
          LFI  L  + ++  L   F  +G V+   +  D    RS+ FG + F 
Sbjct: 1  LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFA 48

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

 Score = 39.1 bits (92), Expect = 3e-05
 Identities = 13/47 (27%), Positives = 26/47 (55%), Gaps = 4/47 (8%)

Query: 51 LPPEFSDADLASMFGPFGTVLSAKVFI--DKQNNRSKCFGTIIFMRK 95
          L  +  + DL  +F PFG +  ++V++  DK+  +S+ F  + F  +
Sbjct: 7  LSEDADEDDLRELFRPFGPI--SRVYLAKDKETGQSRGFAFVTFHTR 51

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

 Score = 39.3 bits (92), Expect = 3e-05
 Identities = 13/44 (29%), Positives = 24/44 (54%)

Query: 45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
          NL + +LP + +  +L S+F   G + S K+  D+   +S  +G
Sbjct: 2  NLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYG 45

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

 Score = 39.3 bits (91), Expect = 3e-05
 Identities = 18/46 (39%), Positives = 29/46 (63%)

Query: 45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTI 90
          NL++  L      ADL ++FG +G VLSAKV  + ++  +KC+G +
Sbjct: 1  NLWVSGLSSNTKAADLKNLFGKYGKVLSAKVVTNARSPGAKCYGIV 46

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

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

 Score = 41.1 bits (96), Expect = 4e-05
 Identities = 18/55 (32%), Positives = 32/55 (58%)

Query: 42  EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKF 96
           +GANL++  LP   +  +L S+F PFG ++++++  D     SK  G I F ++ 
Sbjct: 88  KGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRD 142

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|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score = 38.7 bits (90), Expect = 5e-05
 Identities = 16/48 (33%), Positives = 27/48 (56%), Gaps = 1/48 (2%)

Query: 46 LFIYHLPPEFSDADLASMF-GPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          +F+  L PE +++DL S+F   F +  SAK+  D     S+ +G + F
Sbjct: 4  IFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRF 51

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|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 = 6e-05
 Identities = 16/48 (33%), Positives = 25/48 (52%), Gaps = 1/48 (2%)

Query: 46 LFIYHLPPEFSDADLASMF-GPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          +F+  L P+ +D  L   F   + +V  AKV +D    RSK +G + F
Sbjct: 4  IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRF 51

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|241217 cd12773, RRM2_HuR, RNA recognition motif 2 in vertebrate Hu-antigen R (HuR)

 Score = 38.5 bits (89), Expect = 7e-05
 Identities = 16/52 (30%), Positives = 29/52 (55%)

Query: 44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRK 95
          ANL+I  LP   +  D+  MF  FG +++++V +D+    S+    I F ++
Sbjct: 1  ANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKR 52

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

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

 Score = 38.2 bits (89), Expect = 7e-05
 Identities = 22/65 (33%), Positives = 34/65 (52%), Gaps = 1/65 (1%)

Query: 46  LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDT 105
           ++I HLP  F + +L   F  FGTV + +V   K+   SK +G I F+    +  I   +
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNP-EVAAIAAKS 60

Query: 106 ANDYL 110
            N+YL
Sbjct: 61  MNNYL 65

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

 Score = 38.5 bits (89), Expect = 7e-05
 Identities = 18/52 (34%), Positives = 28/52 (53%)

Query: 45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKF 96
          ++F+  L PE +  D+ S F PFG +  A+V  D    +SK +G + F  K 
Sbjct: 3  HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKL 54

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

 Score = 38.1 bits (89), Expect = 8e-05
 Identities = 14/47 (29%), Positives = 27/47 (57%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          +F+  L PE ++  +   FG FG ++  ++ +DK+ N+ + F  I F
Sbjct: 2  IFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITF 48

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|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 = 37.9 bits (89), Expect = 1e-04
 Identities = 12/44 (27%), Positives = 22/44 (50%), Gaps = 2/44 (4%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSK--CF 87
          LF+  LP   ++ D+ ++F  +G +    +  DK   +SK   F
Sbjct: 2  LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAF 45

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|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 38.4 bits (89), Expect = 1e-04
 Identities = 18/50 (36%), Positives = 26/50 (52%)

Query: 43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
             LF+ +LP + ++  LA  F  FG+V  A   IDK   R+K  G + F
Sbjct: 1  DFTLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCF 50

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

 Score = 37.6 bits (88), Expect = 1e-04
 Identities = 15/57 (26%), Positives = 25/57 (43%)

Query: 46  LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIR 102
           L + +LP EF+D     +  PFG V    +   +    SK +G + +  K   L  +
Sbjct: 2   LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAK 58

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

 Score = 37.4 bits (87), Expect = 1e-04
 Identities = 18/51 (35%), Positives = 28/51 (54%)

Query: 42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          E   LF+ +LP    + DL  +F  FG +    V IDK++ +SK F  ++F
Sbjct: 1  ETGRLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLF 51

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

 Score = 37.3 bits (87), Expect = 2e-04
 Identities = 18/47 (38%), Positives = 24/47 (51%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          +F+  LPP  ++ DL   F  FGTV    V  D +  R + FG I F
Sbjct: 5  IFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITF 51

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

 Score = 37.0 bits (86), Expect = 2e-04
 Identities = 18/48 (37%), Positives = 27/48 (56%)

Query: 45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
           LF+ +L     D  L + F  FGTV+ A+V  D++  RS+ FG + F
Sbjct: 1  TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDF 48

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

 Score = 36.7 bits (85), Expect = 3e-04
 Identities = 12/47 (25%), Positives = 20/47 (42%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          LF+ +L    +  DL   F     +  A V  D +   S+ +G + F
Sbjct: 2  LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTF 48

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

 Score = 37.0 bits (86), Expect = 3e-04
 Identities = 16/48 (33%), Positives = 25/48 (52%)

Query: 45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          NL I +LP   +D +  S+F   G V + K+  DK+   S  FG + +
Sbjct: 2  NLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDY 49

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

 Score = 36.8 bits (85), Expect = 3e-04
 Identities = 13/52 (25%), Positives = 29/52 (55%)

Query: 44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRK 95
          ANL++  LP   +  +L  +F  +G ++++++  D+    S+  G I F ++
Sbjct: 1  ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKR 52

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

 Score = 36.4 bits (85), Expect = 4e-04
 Identities = 16/48 (33%), Positives = 25/48 (52%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFM 93
          +F+  L  E +D  LA  F  + +   AKV  DK+  +SK +G + F 
Sbjct: 9  IFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFS 56

This subfamily corresponds to the RRM of RBM42 which has been identified as a heterogeneous nuclear ribonucleoprotein K (hnRNP K)-binding protein. It also directly binds the 3' untranslated region of p21 mRNA that is one of the target mRNAs for hnRNP K. Both, hnRNP K and RBM42, are components of stress granules (SGs). Under nonstress conditions, RBM42 predominantly localizes within the nucleus and co-localizes with hnRNP K. Under stress conditions, hnRNP K and RBM42 form cytoplasmic foci where the SG marker TIAR localizes, and may play a role in the maintenance of cellular ATP level by protecting their target mRNAs. RBM42 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 83

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

 Score = 38.3 bits (89), Expect = 4e-04
 Identities = 18/64 (28%), Positives = 32/64 (50%)

Query: 29  AAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
           AA  ++ +    P    L++ +L    ++ +L  +F PFG +   ++  D +  RSK FG
Sbjct: 172 AAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFG 231

Query: 89  TIIF 92
            I F
Sbjct: 232 FIQF 235

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

 Score = 36.4 bits (85), Expect = 4e-04
 Identities = 17/45 (37%), Positives = 23/45 (51%), Gaps = 1/45 (2%)

Query: 44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
           N+FI +L     +  L   F  FG +LS KV  D+ N  SK +G
Sbjct: 3  GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVATDE-NGGSKGYG 46

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

 Score = 36.1 bits (84), Expect = 5e-04
 Identities = 20/51 (39%), Positives = 25/51 (49%), Gaps = 1/51 (1%)

Query: 43 GANLFIYHLPPEFSDADLASMFGPFGTVLSA-KVFIDKQNNRSKCFGTIIF 92
          GANLFI +L PE  +  L   F  FG +L   K+  D     SK F  I +
Sbjct: 1  GANLFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISY 51

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

 Score = 36.1 bits (84), Expect = 6e-04
 Identities = 16/50 (32%), Positives = 25/50 (50%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRK 95
          +F+  LP   +D  L   F  FG +  A V  D+Q  +S+ +G + F  K
Sbjct: 3  IFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDK 52

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

 Score = 35.7 bits (83), Expect = 6e-04
 Identities = 11/37 (29%), Positives = 21/37 (56%)

Query: 56 SDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          ++ DL  +F  +G +   +V  D++  RS+ FG + F
Sbjct: 12 TERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYF 48

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

 Score = 37.9 bits (88), Expect = 7e-04
 Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 1/48 (2%)

Query: 45  NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
           N+F+ +L     +  L   F  FG +LS KV  D +N +S+ +G + F
Sbjct: 90  NIFVKNLDKSVDNKALFDTFSKFGNILSCKVATD-ENGKSRGYGFVHF 136

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

 Score = 35.3 bits (82), Expect = 8e-04
 Identities = 15/47 (31%), Positives = 26/47 (55%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          L++ +L    ++ DL  +F PFG +   ++  D +  RSK +G I F
Sbjct: 1  LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQF 47

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

 Score = 35.7 bits (82), Expect = 8e-04
 Identities = 17/47 (36%), Positives = 24/47 (51%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          LF+  L  +  + DL   F  FG V  A+V  DKQ  + + FG + F
Sbjct: 2  LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYF 48

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

 Score = 35.3 bits (82), Expect = 8e-04
 Identities = 19/47 (40%), Positives = 27/47 (57%), Gaps = 1/47 (2%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          +F+ +LP   +  DL  +F   G VL A V  D  + RSK FGT++F
Sbjct: 1  IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTD-NDGRSKGFGTVLF 46

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

 Score = 35.3 bits (82), Expect = 8e-04
 Identities = 14/47 (29%), Positives = 23/47 (48%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          LF+ +LP + +D  L   F   G +    V  DK + + + FG + F
Sbjct: 2  LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTF 48

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

 Score = 35.3 bits (82), Expect = 8e-04
 Identities = 13/47 (27%), Positives = 24/47 (51%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          LF+  L  + ++ DL   F  +G V S ++  DK+  + + F  + F
Sbjct: 2  LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTF 48

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

 Score = 35.1 bits (81), Expect = 0.001
 Identities = 15/52 (28%), Positives = 26/52 (50%)

Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          P+   LF+ +LP + ++ +L   F  FG VL  ++       R   FG ++F
Sbjct: 1  PDSHQLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVF 52

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

 Score = 34.6 bits (80), Expect = 0.001
 Identities = 17/47 (36%), Positives = 23/47 (48%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          LF+ +LP      +L   F  FG V S  V  DK+   SK +G + F
Sbjct: 2  LFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSF 48

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

 Score = 35.1 bits (81), Expect = 0.001
 Identities = 15/52 (28%), Positives = 25/52 (48%)

Query: 42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFM 93
          E   LFI +L    ++ DL  +F  +G +    + IDK   + K F  + +M
Sbjct: 1  ESGRLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYM 52

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

 Score = 34.7 bits (80), Expect = 0.002
 Identities = 16/51 (31%), Positives = 22/51 (43%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKF 96
          LFI  L  E +D  L + F  +G +    V  D    RS+ FG + F    
Sbjct: 2  LFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASAS 52

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|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 34.5 bits (80), Expect = 0.002
 Identities = 9/29 (31%), Positives = 18/29 (62%)

Query: 44 ANLFIYHLPPEFSDADLASMFGPFGTVLS 72
          + L++ + PP F  +D+  +F  +G +LS
Sbjct: 1  STLWVTNFPPSFDQSDIRDLFEQYGEILS 29

This subfamily corresponds to the RRM2 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

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

 Score = 34.5 bits (79), Expect = 0.002
 Identities = 18/47 (38%), Positives = 22/47 (46%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          +FI  L  E +D  L   FG FG V    V  D    RS+ FG + F
Sbjct: 1  MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTF 47

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

 Score = 34.3 bits (78), Expect = 0.002
 Identities = 13/52 (25%), Positives = 30/52 (57%)

Query: 44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRK 95
          ANL++  LP   +  +L  +F  +G ++++++ +D+    S+  G I F ++
Sbjct: 3  ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKR 54

This subgroup corresponds to the RRM2 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells and also regulates the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

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

 Score = 34.0 bits (79), Expect = 0.003
 Identities = 15/39 (38%), Positives = 22/39 (56%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRS 84
          L++  L P+ ++A L  +F P G VLS +V  D    RS
Sbjct: 2  LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRS 40

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

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

 Score = 34.0 bits (77), Expect = 0.004
 Identities = 13/52 (25%), Positives = 30/52 (57%)

Query: 44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRK 95
          ANL++  LP   +  +L  +F  +G ++++++ +D+    S+  G I F ++
Sbjct: 6  ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKR 57

This subgroup corresponds to the RRM2 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 90

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

 Score = 33.8 bits (77), Expect = 0.004
 Identities = 13/52 (25%), Positives = 30/52 (57%)

Query: 44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRK 95
          ANL++  LP   S  ++  +F  +G ++++++ +D+    S+  G I F ++
Sbjct: 2  ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKR 53

This subgroup corresponds to the RRM2 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	128
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.87
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.86
KOG0122|consensus	270		99.84
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.82
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.82
KOG0146|consensus	371		99.82
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.77
KOG0145|consensus	360		99.77
KOG0125|consensus	376		99.77
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.76
KOG0121|consensus	153		99.75
KOG0149|consensus	247		99.74
KOG0148|consensus	321		99.74
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.74
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.73
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.7
KOG0111|consensus	298		99.7
KOG0145|consensus	360		99.7
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.7
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.7
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.69
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.69
PLN03120	260	nucleic acid binding protein; Provisional	99.68
PLN03213	759	repressor of silencing 3; Provisional	99.68
KOG4207|consensus	256		99.68
KOG0126|consensus	219		99.68
KOG0124|consensus	544		99.67
KOG0130|consensus	170		99.67
KOG0108|consensus	435		99.66
KOG0113|consensus	335		99.66
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.66
KOG0117|consensus	506		99.65
KOG0114|consensus	124		99.65
KOG0144|consensus	510		99.64
KOG0107|consensus	195		99.63
KOG0148|consensus	321		99.63
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.63
PLN03121	243	nucleic acid binding protein; Provisional	99.63
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.62
smart00362	72	RRM_2 RNA recognition motif.	99.62
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.61
smart00360	71	RRM RNA recognition motif.	99.6
KOG0144|consensus	510		99.59
KOG0147|consensus	549		99.57
KOG0131|consensus	203		99.57
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.54
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.53
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.52
smart00361	70	RRM_1 RNA recognition motif.	99.5
KOG0105|consensus	241		99.49
KOG4208|consensus	214		99.47
KOG0117|consensus	506		99.47
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.46
KOG0127|consensus	678		99.45
KOG0124|consensus	544		99.45
KOG0131|consensus	203		99.44
KOG0127|consensus	678		99.4
KOG0109|consensus	346		99.38
KOG0415|consensus	479		99.37
KOG0146|consensus	371		99.34
KOG4206|consensus	221		99.31
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.31
KOG0123|consensus	369		99.31
KOG4212|consensus	608		99.31
KOG0109|consensus	346		99.3
KOG0533|consensus	243		99.26
KOG4661|consensus	940		99.26
KOG0132|consensus	894		99.25
KOG4205|consensus	311		99.23
KOG0110|consensus	725		99.21
KOG0151|consensus	877		99.2
KOG0226|consensus	290		99.18
KOG0123|consensus	369		99.16
KOG4212|consensus	608		99.14
KOG0153|consensus	377		99.11
KOG0110|consensus	725		99.09
KOG1548|consensus	382		99.04
KOG0116|consensus	419		99.03
KOG4209|consensus	231		99.0
KOG4205|consensus	311		98.91
KOG1190|consensus	492		98.87
KOG0120|consensus	500		98.86
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.81
KOG1457|consensus	284		98.78
KOG4454|consensus	267		98.7
KOG4660|consensus	549		98.67
KOG0106|consensus	216		98.66
KOG4211|consensus	510		98.57
KOG0147|consensus	549		98.43
KOG1995|consensus	351		98.36
KOG4210|consensus	285		98.36
KOG4211|consensus	510		98.32
COG5175	480	MOT2 Transcriptional repressor [Transcription]	98.3
KOG1457|consensus	284		98.22
KOG4206|consensus	221		98.21
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.12
KOG1456|consensus	494		98.08
KOG4849|consensus	498		98.01
KOG1190|consensus	492		97.99
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.99
KOG2314|consensus	698		97.94
KOG3152|consensus	278		97.75
KOG0106|consensus	216		97.73
KOG4307|consensus	944		97.6
KOG0120|consensus	500		97.59
KOG1855|consensus	484		97.54
KOG1456|consensus	494		97.46
KOG0112|consensus	975		97.42
KOG0128|consensus	881		97.38
KOG1365|consensus	508		97.38
KOG0128|consensus	881		97.36
KOG1548|consensus	382		97.31
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.3
KOG1365|consensus	508		97.25
KOG1996|consensus	378		97.14
KOG0129|consensus	520		97.09
KOG2253|consensus	668		97.05
KOG2193|consensus	584		97.03
KOG2068|consensus	327		97.0
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.93
KOG4307|consensus	944		96.92
KOG0129|consensus	520		96.79
KOG0115|consensus	275		96.75
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	96.63
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.28
KOG2202|consensus	260		96.23
KOG2416|consensus	718		95.83
KOG0105|consensus	241		95.6
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	95.37
KOG0112|consensus	975		95.29
KOG4676|consensus	479		95.05
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	94.69
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	94.49
KOG2591|consensus	684		94.43
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	94.43
KOG2135|consensus	526		94.38
KOG4574|consensus	1007		94.27
KOG2193|consensus	584		93.79
KOG4660|consensus	549		93.37
KOG4210|consensus	285		92.99
KOG4285|consensus	350		91.3
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	91.29
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	88.14
KOG4454|consensus	267		85.88
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	80.59

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

Probab=99.87  E-value=2.1e-21  Score=130.39  Aligned_cols=83  Identities=27%  Similarity=0.330  Sum_probs=77.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ....++|||+|||++++|++|+++|++||.|.+++++.|+.|++++|||||+|.+.+ +|+.|++.||+. ++|+.|+|.
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e-~A~~Al~~lng~~i~Gr~l~V~  109 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEG-AATAAISEMDGKELNGRHIRVN  109 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHH-HHHHHHHHcCCCEECCEEEEEE
Confidence            345779999999999999999999999999999999999999999999999997777 999999999999 999999999


Q ss_pred             ecccc
Q psy8615         119 FNTYV  123 (128)
Q Consensus       119 ~~~~~  123 (128)
                      |.+..
T Consensus       110 ~a~~~  114 (144)
T PLN03134        110 PANDR  114 (144)
T ss_pred             eCCcC
Confidence            98754

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.86  E-value=3.4e-21  Score=145.08  Aligned_cols=82  Identities=30%  Similarity=0.529  Sum_probs=76.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      ..+.+|||+|||+++++++|+++|++||.|.+++++.|+.||+++|||||+|++.+ +|..|++.|||+ ++||.|+|+|
T Consensus       267 ~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~-~A~~Ai~~lnG~~~~gr~i~V~~  345 (352)
T TIGR01661       267 GAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYD-EAAMAILSLNGYTLGNRVLQVSF  345 (352)
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHH-HHHHHHHHhCCCEECCeEEEEEE
Confidence            33558999999999999999999999999999999999999999999999997777 999999999999 9999999999


Q ss_pred             cccc
Q psy8615         120 NTYV  123 (128)
Q Consensus       120 ~~~~  123 (128)
                      ++..
T Consensus       346 ~~~~  349 (352)
T TIGR01661       346 KTNK  349 (352)
T ss_pred             ccCC
Confidence            9853

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

>KOG0122|consensus

Probab=99.84  E-value=5.1e-20  Score=130.29  Aligned_cols=82  Identities=21%  Similarity=0.338  Sum_probs=78.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      .+.++|-|.||+.+++|++|+++|.+||.|.++.+.+|+.||.++|||||.|++.+ +|.+||+.|||+ +.+-.|+|.|
T Consensus       187 ~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRd-dA~rAI~~LnG~gyd~LILrvEw  265 (270)
T KOG0122|consen  187 DDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRD-DAARAIADLNGYGYDNLILRVEW  265 (270)
T ss_pred             CccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHH-HHHHHHHHccCcccceEEEEEEe
Confidence            35678999999999999999999999999999999999999999999999998888 999999999999 9999999999


Q ss_pred             cccc
Q psy8615         120 NTYV  123 (128)
Q Consensus       120 ~~~~  123 (128)
                      +||.
T Consensus       266 skP~  269 (270)
T KOG0122|consen  266 SKPS  269 (270)
T ss_pred             cCCC
Confidence            9986

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.82  E-value=1.5e-19  Score=136.58  Aligned_cols=84  Identities=20%  Similarity=0.287  Sum_probs=78.5

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEE
Q psy8615          38 LTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLK  116 (128)
Q Consensus        38 ~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~  116 (128)
                      ......++|||+|||++++|++|+++|+.||+|.+|+++.|+.|++++|||||+|.+.+ +|++|++.||+. +.+++|+
T Consensus       102 ~~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e-~A~~Ai~~LnG~~l~gr~i~  180 (346)
T TIGR01659       102 DTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEA-DSQRAIKNLNGITVRNKRLK  180 (346)
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHH-HHHHHHHHcCCCccCCceee
Confidence            34566889999999999999999999999999999999999999999999999997776 999999999999 9999999


Q ss_pred             EEeccc
Q psy8615         117 PSFNTY  122 (128)
Q Consensus       117 V~~~~~  122 (128)
                      |.|.++
T Consensus       181 V~~a~p  186 (346)
T TIGR01659       181 VSYARP  186 (346)
T ss_pred             eecccc
Confidence            999875

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.82  E-value=7.1e-20  Score=137.90  Aligned_cols=80  Identities=23%  Similarity=0.348  Sum_probs=76.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecc
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNT  121 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~  121 (128)
                      .++|||+|||.+++|++|+++|++||+|.+|+++.|+.+|+++|||||+|.+.+ +|.+|++.|||. ++|+.|+|.|.+
T Consensus         3 ~~~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         3 KTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPE-DAEKAVNSLNGLRLQNKTIKVSYAR   81 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHH-HHHHHHhhcccEEECCeeEEEEeec
Confidence            679999999999999999999999999999999999999999999999997777 999999999999 999999999987


Q ss_pred             cc
Q psy8615         122 YV  123 (128)
Q Consensus       122 ~~  123 (128)
                      +.
T Consensus        82 ~~   83 (352)
T TIGR01661        82 PS   83 (352)
T ss_pred             cc
Confidence            54

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

>KOG0146|consensus

Probab=99.82  E-value=1.8e-20  Score=134.55  Aligned_cols=94  Identities=43%  Similarity=0.693  Sum_probs=87.1

Q ss_pred             CCCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc
Q psy8615          30 AVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY  109 (128)
Q Consensus        30 ~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~  109 (128)
                      ...-...+++++++|+|||-.||.+..+.+|...|-+||.|.+.++..|+.|.++|+||||.|++.. .++.||..|||+
T Consensus       272 p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~-SaQaAIqAMNGF  350 (371)
T KOG0146|consen  272 PPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPA-SAQAAIQAMNGF  350 (371)
T ss_pred             cchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCch-hHHHHHHHhcch
Confidence            3334556789999999999999999999999999999999999999999999999999999998888 999999999999


Q ss_pred             -CCCeEEEEEeccccc
Q psy8615         110 -LGQSFLKPSFNTYVL  124 (128)
Q Consensus       110 -~~~~~l~V~~~~~~~  124 (128)
                       +|-|.|||++|+|.=
T Consensus       351 QIGMKRLKVQLKRPkd  366 (371)
T KOG0146|consen  351 QIGMKRLKVQLKRPKD  366 (371)
T ss_pred             hhhhhhhhhhhcCccc
Confidence             999999999998753

>PF00076 RRM_1: RNA recognition motif

Probab=99.77  E-value=2.3e-18  Score=101.18  Aligned_cols=69  Identities=22%  Similarity=0.433  Sum_probs=64.9

Q ss_pred             EEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEE
Q psy8615          46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLK  116 (128)
Q Consensus        46 l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~  116 (128)
                      |||+|||.++++++|+++|++||.+..+++..+ .++..+|+|||+|.+.+ +|..|++.++|. ++|+.|+
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-SSGKSKGYAFVEFESEE-DAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHH-HHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHH-HHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999999999988 56999999999997777 999999999999 9999886

(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 ....

>KOG0145|consensus

Probab=99.77  E-value=4.4e-18  Score=121.92  Aligned_cols=84  Identities=25%  Similarity=0.369  Sum_probs=79.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      +...++|.|..||..+++++++.+|+..|+|.+|++++|+-+|++-|||||.|.++. ||++||..|||. +-.|.|||+
T Consensus        38 ~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~-DAe~AintlNGLrLQ~KTIKVS  116 (360)
T KOG0145|consen   38 DESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPK-DAEKAINTLNGLRLQNKTIKVS  116 (360)
T ss_pred             CcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChH-HHHHHHhhhcceeeccceEEEE
Confidence            445789999999999999999999999999999999999999999999999998888 999999999999 999999999


Q ss_pred             eccccc
Q psy8615         119 FNTYVL  124 (128)
Q Consensus       119 ~~~~~~  124 (128)
                      |++|+.
T Consensus       117 yARPSs  122 (360)
T KOG0145|consen  117 YARPSS  122 (360)
T ss_pred             eccCCh
Confidence            999864

>KOG0125|consensus

Probab=99.77  E-value=3.7e-18  Score=125.23  Aligned_cols=81  Identities=22%  Similarity=0.301  Sum_probs=76.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecc
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNT  121 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~  121 (128)
                      ..+|+|+|||++..|.||+.+|++||.|.+|+|+...  ..+||||||+|++.+ ||++|-++|||. +.||.|+|...|
T Consensus        96 pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE--RGSKGFGFVTmen~~-dadRARa~LHgt~VEGRkIEVn~AT  172 (376)
T KOG0125|consen   96 PKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE--RGSKGFGFVTMENPA-DADRARAELHGTVVEGRKIEVNNAT  172 (376)
T ss_pred             CceeEeecCCccccCccHHHHHHhhCceeeEEEEecc--CCCCccceEEecChh-hHHHHHHHhhcceeeceEEEEeccc
Confidence            4689999999999999999999999999999999876  468999999999888 999999999999 999999999999


Q ss_pred             ccccc
Q psy8615         122 YVLMN  126 (128)
Q Consensus       122 ~~~~~  126 (128)
                      ..+||
T Consensus       173 arV~n  177 (376)
T KOG0125|consen  173 ARVHN  177 (376)
T ss_pred             hhhcc
Confidence            99987

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

Probab=99.76  E-value=5.2e-18  Score=135.13  Aligned_cols=84  Identities=17%  Similarity=0.295  Sum_probs=77.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      ...++|||+|||+++++++|+++|++||.|.++++..|+.+|+++|||||+|++.+ +|.+|++.||++ ++|+.|+|.+
T Consensus       202 ~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e-~A~kAI~amNg~elgGr~LrV~k  280 (612)
T TIGR01645       202 KKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQ-SQSEAIASMNLFDLGGQYLRVGK  280 (612)
T ss_pred             cccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHH-HHHHHHHHhCCCeeCCeEEEEEe
Confidence            34579999999999999999999999999999999999999999999999998777 999999999999 9999999999


Q ss_pred             cccccc
Q psy8615         120 NTYVLM  125 (128)
Q Consensus       120 ~~~~~~  125 (128)
                      ......
T Consensus       281 Ai~pP~  286 (612)
T TIGR01645       281 CVTPPD  286 (612)
T ss_pred             cCCCcc
Confidence            876443

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.

>KOG0121|consensus

Probab=99.75  E-value=4.7e-18  Score=110.05  Aligned_cols=79  Identities=8%  Similarity=0.127  Sum_probs=75.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      ...++||||||++-++|++|.++|+++|.|+++-+-.|+.+-...|||||+|...+ +|+.|++-++|. +.+++|+|.|
T Consensus        34 r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~-dA~~AlryisgtrLddr~ir~D~  112 (153)
T KOG0121|consen   34 RKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRD-DAEDALRYISGTRLDDRPIRIDW  112 (153)
T ss_pred             hhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecch-hHHHHHHHhccCcccccceeeec
Confidence            45789999999999999999999999999999999999998889999999999888 999999999999 9999999998


Q ss_pred             c
Q psy8615         120 N  120 (128)
Q Consensus       120 ~  120 (128)
                      +
T Consensus       113 D  113 (153)
T KOG0121|consen  113 D  113 (153)
T ss_pred             c
Confidence            6

>KOG0149|consensus

Probab=99.74  E-value=2.6e-18  Score=121.11  Aligned_cols=79  Identities=23%  Similarity=0.262  Sum_probs=70.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCcCCCeEEEEE
Q psy8615          39 TGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDYLGQSFLKPS  118 (128)
Q Consensus        39 ~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~~~~~~l~V~  118 (128)
                      .+..-|+||||+|+|++..++|+..|++||+|.+..++.|+.||++||||||+|.+.+ .|++|++.-|-.++||.-.+.
T Consensus         8 ~DT~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~-aa~rAc~dp~piIdGR~aNcn   86 (247)
T KOG0149|consen    8 GDTTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAE-AATRACKDPNPIIDGRKANCN   86 (247)
T ss_pred             CCceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHH-HHHHHhcCCCCcccccccccc
Confidence            3445789999999999999999999999999999999999999999999999998877 999999887777777664443

>KOG0148|consensus

Probab=99.74  E-value=5.7e-18  Score=121.59  Aligned_cols=80  Identities=29%  Similarity=0.442  Sum_probs=75.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecc
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNT  121 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~  121 (128)
                      -..+||+.|..+++.++|++.|.+||+|.++++++|..|++++|||||.|-+.+ +|+.||+.|||. ||+|.|+-.|++
T Consensus        62 hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~-dAEnAI~~MnGqWlG~R~IRTNWAT  140 (321)
T KOG0148|consen   62 HFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKE-DAENAIQQMNGQWLGRRTIRTNWAT  140 (321)
T ss_pred             ceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchH-HHHHHHHHhCCeeeccceeeccccc
Confidence            447999999999999999999999999999999999999999999999997777 999999999999 999999999997


Q ss_pred             cc
Q psy8615         122 YV  123 (128)
Q Consensus       122 ~~  123 (128)
                      .-
T Consensus       141 RK  142 (321)
T KOG0148|consen  141 RK  142 (321)
T ss_pred             cC
Confidence            64

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

Probab=99.74  E-value=8.6e-18  Score=133.89  Aligned_cols=80  Identities=16%  Similarity=0.265  Sum_probs=74.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      ...++|||+|||+++++++|+++|++||.|.+++++.|+.||+++|||||+|++.+ +|.+|++.|||. ++|+.|+|.+
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e-~A~~Ai~~lnG~~i~GR~IkV~r  183 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPE-AAQLALEQMNGQMLGGRNIKVGR  183 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHH-HHHHHHHhcCCeEEecceeeecc
Confidence            34679999999999999999999999999999999999999999999999998777 999999999999 9999999986


Q ss_pred             cc
Q psy8615         120 NT  121 (128)
Q Consensus       120 ~~  121 (128)
                      ..
T Consensus       184 p~  185 (612)
T TIGR01645       184 PS  185 (612)
T ss_pred             cc
Confidence            43

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.

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.73  E-value=2.3e-17  Score=124.64  Aligned_cols=81  Identities=17%  Similarity=0.327  Sum_probs=74.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCC--eEEEE
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQ--SFLKP  117 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~--~~l~V  117 (128)
                      ...++|||+|||++++|++|+++|++||.|.+++++.|+.+|+++|||||+|.+.+ +|++||+.||+. +.+  ++|+|
T Consensus       191 ~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e-~A~~Ai~~lng~~~~g~~~~l~V  269 (346)
T TIGR01659       191 IKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKRE-EAQEAISALNNVIPEGGSQPLTV  269 (346)
T ss_pred             cccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHH-HHHHHHHHhCCCccCCCceeEEE
Confidence            34678999999999999999999999999999999999999999999999997777 999999999998 544  78999


Q ss_pred             Eeccc
Q psy8615         118 SFNTY  122 (128)
Q Consensus       118 ~~~~~  122 (128)
                      .|.+.
T Consensus       270 ~~a~~  274 (346)
T TIGR01659       270 RLAEE  274 (346)
T ss_pred             EECCc
Confidence            98864

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).

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

Probab=99.70  E-value=6.9e-17  Score=128.70  Aligned_cols=77  Identities=30%  Similarity=0.458  Sum_probs=73.5

Q ss_pred             CeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecc
Q psy8615          44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNT  121 (128)
Q Consensus        44 ~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~  121 (128)
                      .+|||+|||.+++|++|+++|++||.|.+|++.+|+.|++++|||||+|.+.+ +|++|++.+|+. +.|+.|+|.|..
T Consensus         1 ~sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~-~A~~Al~~ln~~~i~gk~i~i~~s~   78 (562)
T TIGR01628         1 ASLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPA-DAERALETMNFKRLGGKPIRIMWSQ   78 (562)
T ss_pred             CeEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHH-HHHHHHHHhCCCEECCeeEEeeccc
Confidence            37999999999999999999999999999999999999999999999997777 999999999999 999999999975

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

>KOG0111|consensus

Probab=99.70  E-value=1.6e-17  Score=116.55  Aligned_cols=83  Identities=18%  Similarity=0.282  Sum_probs=78.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ....++||||+|..+++|..|...|-+||.|..++++.|..++++||||||+|+..+ +|..||..||+. |.||.|+|.
T Consensus         7 a~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aE-DAaaAiDNMnesEL~GrtirVN   85 (298)
T KOG0111|consen    7 ANQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAE-DAAAAIDNMNESELFGRTIRVN   85 (298)
T ss_pred             cccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccc-hhHHHhhcCchhhhcceeEEEe
Confidence            345779999999999999999999999999999999999999999999999998887 999999999999 999999999


Q ss_pred             ecccc
Q psy8615         119 FNTYV  123 (128)
Q Consensus       119 ~~~~~  123 (128)
                      |++|.
T Consensus        86 ~AkP~   90 (298)
T KOG0111|consen   86 LAKPE   90 (298)
T ss_pred             ecCCc
Confidence            99985

>KOG0145|consensus

Probab=99.70  E-value=2.4e-16  Score=113.06  Aligned_cols=81  Identities=33%  Similarity=0.562  Sum_probs=76.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      ..++.|||-||..+.+|.-|-++|++||.|..+++++|..|.+.+|||||.+.+-+ +|..||..|||+ +|+|.|.|+|
T Consensus       276 ~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYd-EAamAi~sLNGy~lg~rvLQVsF  354 (360)
T KOG0145|consen  276 GGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYD-EAAMAIASLNGYRLGDRVLQVSF  354 (360)
T ss_pred             CCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchH-HHHHHHHHhcCccccceEEEEEE
Confidence            34789999999999999999999999999999999999999999999999996666 999999999999 9999999999


Q ss_pred             ccc
Q psy8615         120 NTY  122 (128)
Q Consensus       120 ~~~  122 (128)
                      ++.
T Consensus       355 Ktn  357 (360)
T KOG0145|consen  355 KTN  357 (360)
T ss_pred             ecC
Confidence            985

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

Probab=99.70  E-value=9.6e-17  Score=127.86  Aligned_cols=81  Identities=25%  Similarity=0.376  Sum_probs=75.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ...+++|||+||++++++++|+++|++||.|.+++++.| .+|+++|||||+|++.+ +|.+|++.|||. ++|++|+|.
T Consensus       282 ~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d-~~g~~~g~gfV~f~~~~-~A~~A~~~~~g~~~~gk~l~V~  359 (562)
T TIGR01628       282 KAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPE-EANRAVTEMHGRMLGGKPLYVA  359 (562)
T ss_pred             ccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEEC-CCCCcCCeEEEEeCCHH-HHHHHHHHhcCCeeCCceeEEE
Confidence            345778999999999999999999999999999999999 56999999999997777 999999999999 999999999


Q ss_pred             eccc
Q psy8615         119 FNTY  122 (128)
Q Consensus       119 ~~~~  122 (128)
                      |++.
T Consensus       360 ~a~~  363 (562)
T TIGR01628       360 LAQR  363 (562)
T ss_pred             eccC
Confidence            9874

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

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.70  E-value=2.2e-16  Score=93.22  Aligned_cols=69  Identities=23%  Similarity=0.423  Sum_probs=63.0

Q ss_pred             EEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEE
Q psy8615          46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLK  116 (128)
Q Consensus        46 l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~  116 (128)
                      |||+|||+++++++|+++|+.||.|.++++..++. |..+|+|||+|.+.+ +|.+|++.+++. ++|+.|+
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-GQSRGFAFVEFSSEE-DAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHH-HHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHH-HHHHHHHHCCCcEECCEEcC
Confidence            79999999999999999999999999999999988 999999999997766 999999999988 9999875

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 ....

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

Probab=99.69  E-value=2e-16  Score=123.05  Aligned_cols=80  Identities=23%  Similarity=0.372  Sum_probs=75.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      ..++|||+|||..+++++|+++|++||.|..+.++.++.+|+++|||||+|.+.+ +|..|++.|||+ ++|+.|+|.|.
T Consensus       185 ~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e-~A~~A~~~l~g~~i~g~~i~v~~a  263 (457)
T TIGR01622       185 NFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAE-EAKEALEVMNGFELAGRPIKVGYA  263 (457)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHH-HHHHHHHhcCCcEECCEEEEEEEc
Confidence            3689999999999999999999999999999999999999999999999997777 999999999999 99999999996


Q ss_pred             cc
Q psy8615         121 TY  122 (128)
Q Consensus       121 ~~  122 (128)
                      +.
T Consensus       264 ~~  265 (457)
T TIGR01622       264 QD  265 (457)
T ss_pred             cC
Confidence            53

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.

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

Probab=99.69  E-value=2.3e-16  Score=124.05  Aligned_cols=80  Identities=14%  Similarity=0.223  Sum_probs=75.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      ..++|||+|||..+++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.+ +|..|++.|||. ++|+.|+|.+.
T Consensus       294 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~-~a~~A~~~l~g~~~~~~~l~v~~a  372 (509)
T TIGR01642       294 SKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPS-VTDVAIAALNGKDTGDNKLHVQRA  372 (509)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHH-HHHHHHHHcCCCEECCeEEEEEEC
Confidence            4579999999999999999999999999999999999999999999999997777 999999999999 99999999997


Q ss_pred             cc
Q psy8615         121 TY  122 (128)
Q Consensus       121 ~~  122 (128)
                      ..
T Consensus       373 ~~  374 (509)
T TIGR01642       373 CV  374 (509)
T ss_pred             cc
Confidence            53

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

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.68  E-value=2.4e-16  Score=113.83  Aligned_cols=74  Identities=5%  Similarity=0.016  Sum_probs=68.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecc
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNT  121 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~  121 (128)
                      .++|||+|||++++|++|+++|+.||.|.+++++.|+.   .+|||||+|.+.+ ++..|+. |||. ++|+.|+|.+..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~e-aAe~All-LnG~~l~gr~V~Vt~a~   78 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQ-GAETALL-LSGATIVDQSVTITPAE   78 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHH-HHHHHHH-hcCCeeCCceEEEEecc
Confidence            57899999999999999999999999999999998864   5799999998777 9999995 9999 999999999986

>PLN03213 repressor of silencing 3; Provisional

Probab=99.68  E-value=2.1e-16  Score=121.61  Aligned_cols=82  Identities=24%  Similarity=0.283  Sum_probs=72.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCH-HHHHHHHHHhcCc-CCCeEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKF-FILTIRFDTANDY-LGQSFLKP  117 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~-~~a~~Ai~~l~g~-~~~~~l~V  117 (128)
                      +..+.+||||||++++++++|+..|+.||.|.++.++  +.||  ||||||+|.... ++..+||..|||. |.|+.|+|
T Consensus         7 ~~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIp--RETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKV   82 (759)
T PLN03213          7 GGGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFV--RTKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRL   82 (759)
T ss_pred             CCcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEe--cccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEE
Confidence            4456899999999999999999999999999999999  5567  999999997762 2789999999999 99999999


Q ss_pred             Eecccccc
Q psy8615         118 SFNTYVLM  125 (128)
Q Consensus       118 ~~~~~~~~  125 (128)
                      .-+++..+
T Consensus        83 NKAKP~YL   90 (759)
T PLN03213         83 EKAKEHYL   90 (759)
T ss_pred             eeccHHHH
Confidence            99887643

>KOG4207|consensus

Probab=99.68  E-value=8.7e-17  Score=111.80  Aligned_cols=82  Identities=21%  Similarity=0.190  Sum_probs=77.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecc
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNT  121 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~  121 (128)
                      -+.|-|-||.+.++.++|+.+|++||.|-+|.|+.|+.|+.++|||||.|.... +|+.|++.|+|. +.|+.|.|++++
T Consensus        13 m~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~-daedA~damDG~~ldgRelrVq~ar   91 (256)
T KOG4207|consen   13 MTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKR-DAEDALDAMDGAVLDGRELRVQMAR   91 (256)
T ss_pred             ceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecc-hHHHHHHhhcceeeccceeeehhhh
Confidence            457999999999999999999999999999999999999999999999999888 999999999999 999999999988


Q ss_pred             cccc
Q psy8615         122 YVLM  125 (128)
Q Consensus       122 ~~~~  125 (128)
                      +--+
T Consensus        92 ygr~   95 (256)
T KOG4207|consen   92 YGRP   95 (256)
T ss_pred             cCCC
Confidence            7544

>KOG0126|consensus

Probab=99.68  E-value=9.2e-18  Score=114.53  Aligned_cols=78  Identities=19%  Similarity=0.389  Sum_probs=72.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      .+..-|||||||++.+|.+|--+|++||+|..+.+++|+.||+++||||..|++-- ....|+..|||+ +.||.|+|..
T Consensus        33 kdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQR-STILAVDN~NGiki~gRtirVDH  111 (219)
T KOG0126|consen   33 KDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQR-STILAVDNLNGIKILGRTIRVDH  111 (219)
T ss_pred             ccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCcc-ceEEEEeccCCceecceeEEeee
Confidence            34568999999999999999999999999999999999999999999999998877 777899999999 9999999974

>KOG0124|consensus

Probab=99.67  E-value=5e-17  Score=121.18  Aligned_cols=75  Identities=17%  Similarity=0.305  Sum_probs=72.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      -|++|||.|.+++.|+.|+..|.+||+|+++.+.+|+.||+++||+||+|+-++ .|+.|++.|||. +|||.|||.
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPE-aAqLAlEqMNg~mlGGRNiKVg  188 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPE-AAQLALEQMNGQMLGGRNIKVG  188 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcH-HHHHHHHHhccccccCcccccc
Confidence            489999999999999999999999999999999999999999999999999888 999999999999 999999997

>KOG0130|consensus

Probab=99.67  E-value=1.3e-16  Score=104.30  Aligned_cols=81  Identities=15%  Similarity=0.228  Sum_probs=76.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEE
Q psy8615          39 TGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKP  117 (128)
Q Consensus        39 ~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V  117 (128)
                      .+..++.|||.++..+.+|+++.+.|..||+|+.+++.+|+.||..+||+.|+|++.. +|+.|+..+||. |-++.++|
T Consensus        68 rSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~k-eAq~A~~~~Ng~~ll~q~v~V  146 (170)
T KOG0130|consen   68 RSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLK-EAQAAIDALNGAELLGQNVSV  146 (170)
T ss_pred             cceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHH-HHHHHHHhccchhhhCCceeE
Confidence            4566899999999999999999999999999999999999999999999999998777 999999999999 88889999


Q ss_pred             Eec
Q psy8615         118 SFN  120 (128)
Q Consensus       118 ~~~  120 (128)
                      .|.
T Consensus       147 Dw~  149 (170)
T KOG0130|consen  147 DWC  149 (170)
T ss_pred             EEE
Confidence            884

>KOG0108|consensus

Probab=99.66  E-value=2.1e-16  Score=121.73  Aligned_cols=78  Identities=23%  Similarity=0.363  Sum_probs=75.0

Q ss_pred             CeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEeccc
Q psy8615          44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNTY  122 (128)
Q Consensus        44 ~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~~  122 (128)
                      +.+||||+|++++|++|..+|+..|.|.+++++.|+.||+.+||||++|.+.+ ++++|++.|||+ ++|+.|+|.|+..
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~-~~~~a~~~lNg~~~~gr~l~v~~~~~   97 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEE-TAERAIRNLNGAEFNGRKLRVNYASN   97 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchh-hHHHHHHhcCCcccCCceEEeecccc
Confidence            89999999999999999999999999999999999999999999999997766 999999999999 9999999999864

>KOG0113|consensus

Probab=99.66  E-value=5.8e-16  Score=112.49  Aligned_cols=88  Identities=16%  Similarity=0.232  Sum_probs=80.2

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEE
Q psy8615          38 LTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLK  116 (128)
Q Consensus        38 ~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~  116 (128)
                      ..+..-++|||+-|+.+++|..|+..|+.||+|..++++.|+.||+++|||||+|+..- +...|.+..+|. +.|+.|-
T Consensus        96 a~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~er-dm~~AYK~adG~~Idgrri~  174 (335)
T KOG0113|consen   96 AIGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHER-DMKAAYKDADGIKIDGRRIL  174 (335)
T ss_pred             ccCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHH-HHHHHHHhccCceecCcEEE
Confidence            33455789999999999999999999999999999999999999999999999997766 999999999999 9999999


Q ss_pred             EEeccccccc
Q psy8615         117 PSFNTYVLMN  126 (128)
Q Consensus       117 V~~~~~~~~~  126 (128)
                      |.+..-.+|.
T Consensus       175 VDvERgRTvk  184 (335)
T KOG0113|consen  175 VDVERGRTVK  184 (335)
T ss_pred             EEeccccccc
Confidence            9998776653

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

Probab=99.66  E-value=4e-16  Score=124.05  Aligned_cols=79  Identities=15%  Similarity=0.370  Sum_probs=71.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-C-CCeEEEEE
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-L-GQSFLKPS  118 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~-~~~~l~V~  118 (128)
                      ..+|+|||+|||++++|++|+++|++||.|.+++++.| .+|+++|||||+|.+.+ +|++||+.||++ + .++.|.|+
T Consensus        56 ~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e-~A~~Ai~~lng~~i~~Gr~l~V~  133 (578)
T TIGR01648        56 GRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKE-EAKEAVKLLNNYEIRPGRLLGVC  133 (578)
T ss_pred             CCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHH-HHHHHHHHcCCCeecCCcccccc
Confidence            34799999999999999999999999999999999999 67999999999997777 999999999998 5 57888887


Q ss_pred             ecc
Q psy8615         119 FNT  121 (128)
Q Consensus       119 ~~~  121 (128)
                      ++.
T Consensus       134 ~S~  136 (578)
T TIGR01648       134 ISV  136 (578)
T ss_pred             ccc
Confidence            653

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.

>KOG0117|consensus

Probab=99.65  E-value=5.4e-16  Score=117.71  Aligned_cols=79  Identities=16%  Similarity=0.389  Sum_probs=74.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc--CCCeEEEEE
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY--LGQSFLKPS  118 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~--~~~~~l~V~  118 (128)
                      +.+|.||||.||.++.|++|..+|++.|+|-+++++.|+.+|.+||||||.|.+.+ +|+.||+.||++  --||.|+|+
T Consensus        81 ~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke-~Aq~Aik~lnn~Eir~GK~igvc  159 (506)
T KOG0117|consen   81 PRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKE-EAQEAIKELNNYEIRPGKLLGVC  159 (506)
T ss_pred             CCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHH-HHHHHHHHhhCccccCCCEeEEE
Confidence            67999999999999999999999999999999999999999999999999997777 999999999999  577999988


Q ss_pred             ec
Q psy8615         119 FN  120 (128)
Q Consensus       119 ~~  120 (128)
                      .+
T Consensus       160 ~S  161 (506)
T KOG0117|consen  160 VS  161 (506)
T ss_pred             Ee
Confidence            64

>KOG0114|consensus

Probab=99.65  E-value=1.9e-15  Score=94.76  Aligned_cols=75  Identities=17%  Similarity=0.369  Sum_probs=68.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecc
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNT  121 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~  121 (128)
                      .+-|||.|||++++.++..++|++||.|+.+++-..+.|   +|-|||.|++-. +|.+|+++|+|+ +.++.|.|-|=+
T Consensus        18 nriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~T---rGTAFVVYedi~-dAk~A~dhlsg~n~~~ryl~vlyyq   93 (124)
T KOG0114|consen   18 NRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKET---RGTAFVVYEDIF-DAKKACDHLSGYNVDNRYLVVLYYQ   93 (124)
T ss_pred             heeEEEecCCccccHHHHHHHhhcccceEEEEecCccCc---CceEEEEehHhh-hHHHHHHHhcccccCCceEEEEecC
Confidence            567999999999999999999999999999999888754   899999998877 999999999999 999999997754

>KOG0144|consensus

Probab=99.64  E-value=1.2e-15  Score=115.48  Aligned_cols=89  Identities=16%  Similarity=0.224  Sum_probs=77.0

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc--CCC--
Q psy8615          37 QLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY--LGQ--  112 (128)
Q Consensus        37 ~~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~--~~~--  112 (128)
                      ...+.+.-++|||.||..++|.||+.+|++||.|.+|.+++|+.||.++|||||.|.+.+ +|.+|+..|+..  +-|  
T Consensus        28 d~~d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk-~a~~a~~Alhn~ktlpG~~  106 (510)
T KOG0144|consen   28 DNPDGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRK-EADEAINALHNQKTLPGMH  106 (510)
T ss_pred             CCCCchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHH-HHHHHHHHhhcccccCCCC
Confidence            333455669999999999999999999999999999999999999999999999998777 999999999986  433  


Q ss_pred             eEEEEEeccccccc
Q psy8615         113 SFLKPSFNTYVLMN  126 (128)
Q Consensus       113 ~~l~V~~~~~~~~~  126 (128)
                      .++.|.|+---..|
T Consensus       107 ~pvqvk~Ad~E~er  120 (510)
T KOG0144|consen  107 HPVQVKYADGERER  120 (510)
T ss_pred             cceeecccchhhhc
Confidence            78899887654444

>KOG0107|consensus

Probab=99.63  E-value=9.6e-16  Score=104.03  Aligned_cols=76  Identities=13%  Similarity=0.130  Sum_probs=68.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      +-.++||||||+.++++.+|+.+|..||++.++-|-..     ..|||||+|+++. +|+.|+..|+|. +.|..|+|.+
T Consensus         8 ~~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn-----PPGfAFVEFed~R-DA~DAvr~LDG~~~cG~r~rVE~   81 (195)
T KOG0107|consen    8 NGNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN-----PPGFAFVEFEDPR-DAEDAVRYLDGKDICGSRIRVEL   81 (195)
T ss_pred             CCCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec-----CCCceEEeccCcc-cHHHHHhhcCCccccCceEEEEe
Confidence            34789999999999999999999999999999876654     3799999999999 999999999999 9999999998


Q ss_pred             ccc
Q psy8615         120 NTY  122 (128)
Q Consensus       120 ~~~  122 (128)
                      .+-
T Consensus        82 S~G   84 (195)
T KOG0107|consen   82 STG   84 (195)
T ss_pred             ecC
Confidence            763

>KOG0148|consensus

Probab=99.63  E-value=1.8e-15  Score=108.87  Aligned_cols=79  Identities=16%  Similarity=0.379  Sum_probs=73.0

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEE
Q psy8615          38 LTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLK  116 (128)
Q Consensus        38 ~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~  116 (128)
                      ..+++.|+|||||++..++|+++++.|++||.|.+|++-.|      +||+||.|++++ .|..||..+|+. ++|+..|
T Consensus       159 Qssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~------qGYaFVrF~tkE-aAahAIv~mNntei~G~~Vk  231 (321)
T KOG0148|consen  159 QSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD------QGYAFVRFETKE-AAAHAIVQMNNTEIGGQLVR  231 (321)
T ss_pred             cCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc------cceEEEEecchh-hHHHHHHHhcCceeCceEEE
Confidence            34578999999999999999999999999999999999877      679999998888 999999999999 9999999


Q ss_pred             EEecccc
Q psy8615         117 PSFNTYV  123 (128)
Q Consensus       117 V~~~~~~  123 (128)
                      -+|.|-.
T Consensus       232 CsWGKe~  238 (321)
T KOG0148|consen  232 CSWGKEG  238 (321)
T ss_pred             EeccccC
Confidence            9998853

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

Probab=99.63  E-value=1.9e-15  Score=117.52  Aligned_cols=78  Identities=17%  Similarity=0.207  Sum_probs=72.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      ..++|||+|||.++++++|+++|++||.|.+|+++.|+.+|+++|||||+|.+.+ +|.+|+. |+|. +.|++|.|.+.
T Consensus        88 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e-~A~~Al~-l~g~~~~g~~i~v~~~  165 (457)
T TIGR01622        88 DDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVE-SVIKALA-LTGQMLLGRPIIVQSS  165 (457)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHH-HHHHHHH-hCCCEECCeeeEEeec
Confidence            3678999999999999999999999999999999999999999999999997776 9999996 8888 99999999885


Q ss_pred             c
Q psy8615         121 T  121 (128)
Q Consensus       121 ~  121 (128)
                      .
T Consensus       166 ~  166 (457)
T TIGR01622       166 Q  166 (457)
T ss_pred             c
Confidence            4

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.

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.63  E-value=2.2e-15  Score=107.46  Aligned_cols=74  Identities=14%  Similarity=0.246  Sum_probs=65.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      +.+++|||+||+++++|++|+++|+.||.|.+|++++|.   +.+|||||+|.++. .++.|+ .|+|. |.+++|.|.-
T Consensus         3 ~~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~-aaetAl-lLnGa~l~d~~I~It~   77 (243)
T PLN03121          3 PGGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAY-ALETAV-LLSGATIVDQRVCITR   77 (243)
T ss_pred             CCceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHH-HHHHHH-hcCCCeeCCceEEEEe
Confidence            357899999999999999999999999999999999884   45689999997777 888887 79998 9998888765

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

Probab=99.62  E-value=2.1e-15  Score=107.55  Aligned_cols=78  Identities=22%  Similarity=0.353  Sum_probs=74.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecc
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNT  121 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~  121 (128)
                      .++|||+|||.++++++|+++|.+||.+.++.+..|+.+|+++|||||+|.+.+ ++..|++.+++. +.|+.|+|.+..
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~-~~~~a~~~~~~~~~~~~~~~v~~~~  193 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEE-SAEKAIEELNGKELEGRPLRVQKAQ  193 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHH-HHHHHHHHcCCCeECCceeEeeccc
Confidence            689999999999999999999999999999999999989999999999997777 999999999999 999999999965

>smart00362 RRM_2 RNA recognition motif

Probab=99.62  E-value=4.1e-15  Score=86.49  Aligned_cols=71  Identities=30%  Similarity=0.470  Sum_probs=65.3

Q ss_pred             eEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        45 ~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      +|||+|||..+++++|+++|.+||.+..+++..++  +.++|+|||+|.+.+ +|..|++.+++. +.|+.|+|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~-~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEE-DAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHH-HHHHHHHHhCCcEECCEEEeeC
Confidence            58999999999999999999999999999988776  788999999998877 999999999998 999998874

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

Probab=99.61  E-value=7e-15  Score=115.54  Aligned_cols=78  Identities=19%  Similarity=0.195  Sum_probs=70.8

Q ss_pred             CCCCCeEEEcCCCC-CCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEE
Q psy8615          40 GPEGANLFIYHLPP-EFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKP  117 (128)
Q Consensus        40 ~~~~~~l~V~nLp~-~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V  117 (128)
                      .+.+++|||+|||+ .+++++|+++|++||.|.+++++.++     +|||||+|.+.+ +|..|++.|||. +.|+.|+|
T Consensus       272 ~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~-----~g~afV~f~~~~-~A~~Ai~~lng~~l~g~~l~v  345 (481)
T TIGR01649       272 GGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK-----KETALIEMADPY-QAQLALTHLNGVKLFGKPLRV  345 (481)
T ss_pred             CCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-----CCEEEEEECCHH-HHHHHHHHhCCCEECCceEEE
Confidence            34578999999998 69999999999999999999998874     689999998777 999999999999 99999999


Q ss_pred             Eecccc
Q psy8615         118 SFNTYV  123 (128)
Q Consensus       118 ~~~~~~  123 (128)
                      ++++..
T Consensus       346 ~~s~~~  351 (481)
T TIGR01649       346 CPSKQQ  351 (481)
T ss_pred             EEcccc
Confidence            998653

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).

>smart00360 RRM RNA recognition motif

Probab=99.60  E-value=4.7e-15  Score=85.92  Aligned_cols=70  Identities=26%  Similarity=0.416  Sum_probs=64.9

Q ss_pred             EcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          48 IYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        48 V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      |+|||..+++++|+.+|.+||.+..+.+..++.++.++|+|||+|.+.+ +|..|++.+++. ++|+.|+|+
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~-~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEE-DAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHH-HHHHHHHHcCCCeeCCcEEEeC
Confidence            5799999999999999999999999999998888999999999997777 999999999998 999998874

>KOG0144|consensus

Probab=99.59  E-value=1.6e-15  Score=114.81  Aligned_cols=91  Identities=47%  Similarity=0.741  Sum_probs=85.1

Q ss_pred             CCCCCCCCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-C
Q psy8615          32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-L  110 (128)
Q Consensus        32 ~~~~~~~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~  110 (128)
                      .....+.+++++.++||.+||.+.-+.+|-..|.+||.|.+.++-.|+.|+-+++|+||.|++.. +|..||..|||+ +
T Consensus       413 ~~~~~q~eGpeGanlfiyhlPqefgdq~l~~~f~pfG~Vlsakvfidk~tnlskcfgfvSyen~~-sa~~aI~amngfQi  491 (510)
T KOG0144|consen  413 MVGNGQVEGPEGANLFIYHLPQEFGDQDLIATFQPFGGVLSAKVFIDKVTNLSKCFGFVSYENAQ-SAQNAISAMNGFQI  491 (510)
T ss_pred             cccCccccCCCccceeeeeCchhhhhHHHHHHhccccceeEEEEEEecccCHhhhcCcccccchh-hhHHHHHHhcchhh
Confidence            34556778899999999999999999999999999999999999999999999999999999999 999999999999 9


Q ss_pred             CCeEEEEEecccc
Q psy8615         111 GQSFLKPSFNTYV  123 (128)
Q Consensus       111 ~~~~l~V~~~~~~  123 (128)
                      |.|.|+|+.+...
T Consensus       492 g~KrlkVQlk~~~  504 (510)
T KOG0144|consen  492 GSKRLKVQLKRDR  504 (510)
T ss_pred             ccccceEEeeecc
Confidence            9999999998754

>KOG0147|consensus

Probab=99.57  E-value=3.2e-15  Score=115.77  Aligned_cols=79  Identities=27%  Similarity=0.415  Sum_probs=74.7

Q ss_pred             eEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecccc
Q psy8615          45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNTYV  123 (128)
Q Consensus        45 ~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~~~  123 (128)
                      +||||||+++++|++|+.+|++||.|..+.+.+|..||+++||||++|...+ +|..|++.|||+ +.|+.|+|+..+..
T Consensus       280 rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~-~ar~a~e~lngfelAGr~ikV~~v~~r  358 (549)
T KOG0147|consen  280 RLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKE-DARKALEQLNGFELAGRLIKVSVVTER  358 (549)
T ss_pred             hhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHH-HHHHHHHHhccceecCceEEEEEeeee
Confidence            3999999999999999999999999999999999999999999999998877 999999999999 99999999987765


Q ss_pred             c
Q psy8615         124 L  124 (128)
Q Consensus       124 ~  124 (128)
                      +
T Consensus       359 ~  359 (549)
T KOG0147|consen  359 V  359 (549)
T ss_pred             c
Confidence            3

>KOG0131|consensus

Probab=99.57  E-value=5.9e-15  Score=100.78  Aligned_cols=81  Identities=16%  Similarity=0.164  Sum_probs=75.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      .....+||||||+..++++.|.++|-+.|+|.+++++.|+.|...+||||++|.+.+ +|+-|++.||.. |-||+|+|.
T Consensus         6 rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~ee-dadYAikiln~VkLYgrpIrv~   84 (203)
T KOG0131|consen    6 RNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEE-DADYAIKILNMVKLYGRPIRVN   84 (203)
T ss_pred             cCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechh-hhHHHHHHHHHHHhcCceeEEE
Confidence            344679999999999999999999999999999999999999999999999996666 999999999987 999999998


Q ss_pred             ecc
Q psy8615         119 FNT  121 (128)
Q Consensus       119 ~~~  121 (128)
                      -..
T Consensus        85 kas   87 (203)
T KOG0131|consen   85 KAS   87 (203)
T ss_pred             ecc
Confidence            765

>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=99.54  E-value=9e-14  Score=81.16  Aligned_cols=73  Identities=32%  Similarity=0.525  Sum_probs=67.1

Q ss_pred             eEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        45 ~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      +|+|+|||..+++++++++|..||.+..+.+..++. +..+|+|||+|.+.+ +|..|++.+++. +.|+.+.|.|
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~-~~~~~~~~v~f~s~~-~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKD-TKSKGFAFVEFEDEE-DAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCC-CCcceEEEEEECCHH-HHHHHHHHhCCCeECCeEEEEeC
Confidence            489999999999999999999999999999998876 477999999997777 999999999999 9999999875

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).

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

Probab=99.53  E-value=3.7e-14  Score=112.90  Aligned_cols=72  Identities=18%  Similarity=0.199  Sum_probs=66.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCC--CceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPF--GTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~--G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      ..+|||+|||++++|++|+++|++|  |.|.+|+++        ++||||+|++.+ +|++|++.||+. ++|+.|+|+|
T Consensus       233 ~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~--------rgfAFVeF~s~e-~A~kAi~~lnG~~i~Gr~I~V~~  303 (578)
T TIGR01648       233 VKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI--------RDYAFVHFEDRE-DAVKAMDELNGKELEGSEIEVTL  303 (578)
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee--------cCeEEEEeCCHH-HHHHHHHHhCCCEECCEEEEEEE
Confidence            4689999999999999999999999  999998765        459999998777 999999999999 9999999999


Q ss_pred             cccc
Q psy8615         120 NTYV  123 (128)
Q Consensus       120 ~~~~  123 (128)
                      +++.
T Consensus       304 Akp~  307 (578)
T TIGR01648       304 AKPV  307 (578)
T ss_pred             ccCC
Confidence            9875

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=99.52  E-value=6.1e-14  Score=110.23  Aligned_cols=81  Identities=26%  Similarity=0.310  Sum_probs=69.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCc--eEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeE---
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGT--VLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSF---  114 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~--i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~---  114 (128)
                      +...+|||+|||+++++++|+++|+.||.  +..+++..++  +..+|+|||+|++.+ +|..|+..||++ ++++.   
T Consensus       392 ~ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~ik~~~~~--~~~~~~gfVeF~~~e-~A~~Al~~ln~~~l~~~~~~~  468 (481)
T TIGR01649       392 PPSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFKFFPKD--NERSKMGLLEWESVE-DAVEALIALNHHQLNEPNGSA  468 (481)
T ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHhcCCccceEEEEecCC--CCcceeEEEEcCCHH-HHHHHHHHhcCCccCCCCCCc
Confidence            34568999999999999999999999998  8888876443  235899999997766 999999999999 98874   


Q ss_pred             ---EEEEeccccc
Q psy8615         115 ---LKPSFNTYVL  124 (128)
Q Consensus       115 ---l~V~~~~~~~  124 (128)
                         |+|+|+++.+
T Consensus       469 ~~~lkv~fs~~~~  481 (481)
T TIGR01649       469 PYHLKVSFSTSRI  481 (481)
T ss_pred             cceEEEEeccCCC
Confidence               9999999864

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).

>smart00361 RRM_1 RNA recognition motif

Probab=99.50  E-value=9.1e-14  Score=82.42  Aligned_cols=61  Identities=23%  Similarity=0.246  Sum_probs=54.8

Q ss_pred             HHHHHhhhc----CCCceEEEE-EEecCCC--CCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          57 DADLASMFG----PFGTVLSAK-VFIDKQN--NRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        57 e~~l~~~f~----~~G~i~~~~-~~~~~~t--g~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      +++|+++|+    +||.|.++. +..++.+  ++++||+||+|.+.+ +|..|++.|||. ++|+.|+++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~-dA~~A~~~l~g~~~~gr~l~~~   70 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSE-DAARAIVDLNGRYFDGRTVKAE   70 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHH-HHHHHHHHhCCCEECCEEEEeC
Confidence            678889998    999999995 8888877  999999999997777 999999999999 999999864

>KOG0105|consensus

Probab=99.49  E-value=8.8e-14  Score=95.54  Aligned_cols=77  Identities=12%  Similarity=0.216  Sum_probs=69.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      ...++|||||||.++.|.+++++|.+||.|+.|.+-..+   ...+||||+|+++- +|+.||..-+|+ ++|..|+|.|
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~---g~ppfafVeFEd~R-DAeDAiygRdGYdydg~rLRVEf   79 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRP---GPPPFAFVEFEDPR-DAEDAIYGRDGYDYDGCRLRVEF   79 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCC---CCCCeeEEEecCcc-chhhhhhcccccccCcceEEEEe
Confidence            346799999999999999999999999999999875543   34679999999999 999999999999 9999999998


Q ss_pred             cc
Q psy8615         120 NT  121 (128)
Q Consensus       120 ~~  121 (128)
                      ..
T Consensus        80 pr   81 (241)
T KOG0105|consen   80 PR   81 (241)
T ss_pred             cc
Confidence            64

>KOG4208|consensus

Probab=99.47  E-value=2.3e-13  Score=94.54  Aligned_cols=80  Identities=23%  Similarity=0.384  Sum_probs=72.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCC-CceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPF-GTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~-G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ....-+|+..+|..+.+..+..+|.+| |.+++.++.+.+.||.++|||||+|++.+ .|..|-+.||+| ++++.|++.
T Consensus        47 ~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~e-VA~IaAETMNNYLl~e~lL~c~  125 (214)
T KOG4208|consen   47 EIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEE-VAKIAAETMNNYLLMEHLLECH  125 (214)
T ss_pred             CCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHH-HHHHHHHHhhhhhhhhheeeeE
Confidence            345578999999999999999999988 78888899899999999999999998887 999999999999 999999987


Q ss_pred             ecc
Q psy8615         119 FNT  121 (128)
Q Consensus       119 ~~~  121 (128)
                      +=-
T Consensus       126 vmp  128 (214)
T KOG4208|consen  126 VMP  128 (214)
T ss_pred             EeC
Confidence            643

>KOG0117|consensus

Probab=99.47  E-value=1.1e-13  Score=105.27  Aligned_cols=70  Identities=20%  Similarity=0.259  Sum_probs=66.5

Q ss_pred             eEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecccc
Q psy8615          45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNTYV  123 (128)
Q Consensus        45 ~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~~~  123 (128)
                      .|||.||+.++||+.|+++|.+||.|.+|+.++|        ||||.|...+ +|.+|++.+||+ +.|..|.|.++||+
T Consensus       261 vLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD--------YaFVHf~eR~-davkAm~~~ngkeldG~~iEvtLAKP~  331 (506)
T KOG0117|consen  261 VLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD--------YAFVHFAERE-DAVKAMKETNGKELDGSPIEVTLAKPV  331 (506)
T ss_pred             eeeeeccchhhhHHHHHHHHHhccceEEeecccc--------eeEEeecchH-HHHHHHHHhcCceecCceEEEEecCCh
Confidence            6999999999999999999999999999988755        9999998888 999999999999 99999999999986

>PF13893 RRM_5: RNA recognition motif

Probab=99.46  E-value=3e-13  Score=76.64  Aligned_cols=55  Identities=25%  Similarity=0.329  Sum_probs=48.3

Q ss_pred             HHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          60 LASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        60 l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      |+++|++||.|.++.+..+.     ++++||+|++.+ +|..|++.|||. ++|++|+|+|+
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-----RGFAFVEFASVE-DAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-----TTEEEEEESSHH-HHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC-----CCEEEEEECCHH-HHHHHHHHhCCCEECCcEEEEEEC
Confidence            67899999999999886553     689999997777 999999999999 99999999985

(a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....

>KOG0127|consensus

Probab=99.45  E-value=2.5e-13  Score=105.58  Aligned_cols=76  Identities=20%  Similarity=0.235  Sum_probs=71.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      .++|.|.||||.+.+.+|+.+|+.||.|.++.|+..+. |+.+|||||.|.... +|..|++.+|+. ++|+++-|.|+
T Consensus       117 k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~d-gklcGFaFV~fk~~~-dA~~Al~~~N~~~i~gR~VAVDWA  193 (678)
T KOG0127|consen  117 KWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKD-GKLCGFAFVQFKEKK-DAEKALEFFNGNKIDGRPVAVDWA  193 (678)
T ss_pred             cceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCC-CCccceEEEEEeeHH-HHHHHHHhccCceecCceeEEeee
Confidence            67999999999999999999999999999999998777 777899999997777 999999999999 99999999996

>KOG0124|consensus

Probab=99.45  E-value=5e-14  Score=105.29  Aligned_cols=81  Identities=17%  Similarity=0.340  Sum_probs=74.0

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEE
Q psy8615          38 LTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLK  116 (128)
Q Consensus        38 ~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~  116 (128)
                      .+.....+|||..++++.+|+||+.+|+.||+|.+|++-+++.++.++||||++|.+.. ....||..||-+ +||+.|+
T Consensus       205 eeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~q-s~~eAiasMNlFDLGGQyLR  283 (544)
T KOG0124|consen  205 EEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQ-SQSEAIASMNLFDLGGQYLR  283 (544)
T ss_pred             HHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEecccc-chHHHhhhcchhhcccceEe
Confidence            33455679999999999999999999999999999999999998999999999998887 888899999999 9999999


Q ss_pred             EEe
Q psy8615         117 PSF  119 (128)
Q Consensus       117 V~~  119 (128)
                      |.-
T Consensus       284 VGk  286 (544)
T KOG0124|consen  284 VGK  286 (544)
T ss_pred             ccc
Confidence            853

>KOG0131|consensus

Probab=99.44  E-value=1.5e-13  Score=93.91  Aligned_cols=85  Identities=27%  Similarity=0.342  Sum_probs=75.2

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEE-EEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeE
Q psy8615          37 QLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLS-AKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSF  114 (128)
Q Consensus        37 ~~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~-~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~  114 (128)
                      +.....+.++||+||.++++|..|.+.|+.||.+.+ -++.+|+.||.++||||+.|.+.+ .+.+|+..+||. +++++
T Consensus        90 ~~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfe-asd~ai~s~ngq~l~nr~  168 (203)
T KOG0131|consen   90 QKNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFE-ASDAAIGSMNGQYLCNRP  168 (203)
T ss_pred             cccccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHH-HHHHHHHHhccchhcCCc
Confidence            344455789999999999999999999999998876 488999999999999999996666 999999999999 99999


Q ss_pred             EEEEeccc
Q psy8615         115 LKPSFNTY  122 (128)
Q Consensus       115 l~V~~~~~  122 (128)
                      +.|+|...
T Consensus       169 itv~ya~k  176 (203)
T KOG0131|consen  169 ITVSYAFK  176 (203)
T ss_pred             eEEEEEEe
Confidence            99998753

>KOG0127|consensus

Probab=99.40  E-value=6.9e-13  Score=103.20  Aligned_cols=83  Identities=19%  Similarity=0.243  Sum_probs=76.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      .+.+|||++||++++.++|.++|+.+|+|..|.++.++.++.+||||||.|.- ++++++|+...++. ++|+.|.|.+.
T Consensus         4 ~g~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam-~ED~qrA~~e~~~~kf~Gr~l~v~~A   82 (678)
T KOG0127|consen    4 SGATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAM-EEDVQRALAETEQSKFEGRILNVDPA   82 (678)
T ss_pred             CCceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeeh-HhHHHHHHHHhhcCcccceecccccc
Confidence            35899999999999999999999999999999999999999999999999954 45999999999998 99999999998


Q ss_pred             ccccc
Q psy8615         121 TYVLM  125 (128)
Q Consensus       121 ~~~~~  125 (128)
                      ++..-
T Consensus        83 ~~R~r   87 (678)
T KOG0127|consen   83 KKRAR   87 (678)
T ss_pred             ccccc
Confidence            87643

>KOG0109|consensus

Probab=99.38  E-value=6.5e-13  Score=96.61  Aligned_cols=71  Identities=23%  Similarity=0.364  Sum_probs=65.5

Q ss_pred             CeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEeccc
Q psy8615          44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNTY  122 (128)
Q Consensus        44 ~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~~  122 (128)
                      .+|||||||.++++.+|+.+|++||+|.+|.|++.        ||||..++.. .++.||+.||++ |.|..|+|.-+|.
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN--------YgFVHiEdkt-aaedairNLhgYtLhg~nInVeaSks   73 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN--------YGFVHIEDKT-AAEDAIRNLHGYTLHGVNINVEASKS   73 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc--------cceEEeeccc-ccHHHHhhcccceecceEEEEEeccc
Confidence            47999999999999999999999999999999854        9999998888 999999999999 9999999988775


Q ss_pred             c
Q psy8615         123 V  123 (128)
Q Consensus       123 ~  123 (128)
                      -
T Consensus        74 K   74 (346)
T KOG0109|consen   74 K   74 (346)
T ss_pred             c
Confidence            4

>KOG0415|consensus

Probab=99.37  E-value=9.7e-13  Score=98.03  Aligned_cols=82  Identities=24%  Similarity=0.395  Sum_probs=77.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      ++...|||..|.+.+++++|.-+|+.||.|.+|.+++|..||.+-.|+||+|++.+ ++++|.=+|++. +.++.|.|.|
T Consensus       237 PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~e-scE~AyFKMdNvLIDDrRIHVDF  315 (479)
T KOG0415|consen  237 PPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKE-SCEQAYFKMDNVLIDDRRIHVDF  315 (479)
T ss_pred             CCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchh-hHHHHHhhhcceeeccceEEeeh
Confidence            55678999999999999999999999999999999999999999999999998877 999999999999 9999999999


Q ss_pred             cccc
Q psy8615         120 NTYV  123 (128)
Q Consensus       120 ~~~~  123 (128)
                      +..+
T Consensus       316 SQSV  319 (479)
T KOG0415|consen  316 SQSV  319 (479)
T ss_pred             hhhh
Confidence            8654

>KOG0146|consensus

Probab=99.34  E-value=3.3e-12  Score=92.24  Aligned_cols=79  Identities=22%  Similarity=0.312  Sum_probs=71.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc--CCC--eEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY--LGQ--SFL  115 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~--~~~--~~l  115 (128)
                      +.+.++||||-|...-.|+|++.+|.+||+|.+|.+.+.+. |.+|||+||.|++.. +|..||..|+|.  +-|  ..|
T Consensus        16 g~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~d-g~sKGCAFVKf~s~~-eAqaAI~aLHgSqTmpGASSSL   93 (371)
T KOG0146|consen   16 GGDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPD-GNSKGCAFVKFSSHA-EAQAAINALHGSQTMPGASSSL   93 (371)
T ss_pred             CccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCC-CCCCCceEEEeccch-HHHHHHHHhcccccCCCCccce
Confidence            34678999999999999999999999999999999999987 999999999998888 999999999996  544  568


Q ss_pred             EEEec
Q psy8615         116 KPSFN  120 (128)
Q Consensus       116 ~V~~~  120 (128)
                      .|.|.
T Consensus        94 VVK~A   98 (371)
T KOG0146|consen   94 VVKFA   98 (371)
T ss_pred             EEEec
Confidence            88875

>KOG4206|consensus

Probab=99.31  E-value=6.8e-12  Score=88.30  Aligned_cols=74  Identities=14%  Similarity=0.335  Sum_probs=66.8

Q ss_pred             eEEEcCCCCCCCHHHHHh----hhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          45 NLFIYHLPPEFSDADLAS----MFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        45 ~l~V~nLp~~~~e~~l~~----~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      +|||.||.+.+..++|+.    +|++||.|.+|...   .|.+.||-|||.|.+.+ .|..|+..|+|+ +-||+++|+|
T Consensus        11 TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~---kt~KmRGQA~VvFk~~~-~As~A~r~l~gfpFygK~mriqy   86 (221)
T KOG4206|consen   11 TLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAF---KTPKMRGQAFVVFKETE-AASAALRALQGFPFYGKPMRIQY   86 (221)
T ss_pred             eEeehhccccccHHHHHHHHHHHHHhhCCeEEEEec---CCCCccCceEEEecChh-HHHHHHHHhcCCcccCchhheec
Confidence            999999999999998887    99999999987654   34788999999997777 999999999999 9999999999


Q ss_pred             ccc
Q psy8615         120 NTY  122 (128)
Q Consensus       120 ~~~  122 (128)
                      ++.
T Consensus        87 A~s   89 (221)
T KOG4206|consen   87 AKS   89 (221)
T ss_pred             ccC
Confidence            875

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

Probab=99.31  E-value=9.9e-12  Score=97.91  Aligned_cols=73  Identities=22%  Similarity=0.330  Sum_probs=58.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCC------------CceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhc
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPF------------GTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTAN  107 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~------------G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~  107 (128)
                      ....++|||||||+++++++|+++|..+            +.|..+.      .+..+|||||+|.+.+ +|..|+ .||
T Consensus       172 ~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~------~~~~kg~afVeF~~~e-~A~~Al-~l~  243 (509)
T TIGR01642       172 TRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVN------INKEKNFAFLEFRTVE-EATFAM-ALD  243 (509)
T ss_pred             CccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEE------ECCCCCEEEEEeCCHH-HHhhhh-cCC
Confidence            4456799999999999999999999864            2333333      2456899999997777 999999 599


Q ss_pred             Cc-CCCeEEEEEec
Q psy8615         108 DY-LGQSFLKPSFN  120 (128)
Q Consensus       108 g~-~~~~~l~V~~~  120 (128)
                      |. +.|++|+|...
T Consensus       244 g~~~~g~~l~v~r~  257 (509)
T TIGR01642       244 SIIYSNVFLKIRRP  257 (509)
T ss_pred             CeEeeCceeEecCc
Confidence            99 99999999743

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

>KOG0123|consensus

Probab=99.31  E-value=6.6e-12  Score=95.77  Aligned_cols=72  Identities=24%  Similarity=0.314  Sum_probs=66.3

Q ss_pred             eEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        45 ~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      .+||.||+.+++..+|+++|+.||+|.+|++..|.. | ++|| ||+|++.+ .|.+||+.+||. +.++.|.|...
T Consensus        78 ~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~-g-~kg~-FV~f~~e~-~a~~ai~~~ng~ll~~kki~vg~~  150 (369)
T KOG0123|consen   78 LVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDEN-G-SKGY-FVQFESEE-SAKKAIEKLNGMLLNGKKIYVGLF  150 (369)
T ss_pred             eeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCC-C-ceee-EEEeCCHH-HHHHHHHHhcCcccCCCeeEEeec
Confidence            399999999999999999999999999999999986 6 9999 99997766 999999999999 99999888543

>KOG4212|consensus

Probab=99.31  E-value=1.4e-11  Score=94.06  Aligned_cols=75  Identities=16%  Similarity=0.274  Sum_probs=69.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhc-CCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          43 GANLFIYHLPPEFSDADLASMFG-PFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~-~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      .+.+||.|||+++.|.+|+++|. +-|+|..|++..|.. |++|||+.|+|++++ .+++|++.||.+ +.|++|+|.=
T Consensus        44 ~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~-GK~rGcavVEFk~~E-~~qKa~E~lnk~~~~GR~l~vKE  120 (608)
T KOG4212|consen   44 DRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDES-GKARGCAVVEFKDPE-NVQKALEKLNKYEVNGRELVVKE  120 (608)
T ss_pred             cceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccC-CCcCCceEEEeeCHH-HHHHHHHHhhhccccCceEEEec
Confidence            34599999999999999999996 789999999999976 999999999998887 999999999999 9999999864

>KOG0109|consensus

Probab=99.30  E-value=3.4e-12  Score=92.89  Aligned_cols=76  Identities=14%  Similarity=0.260  Sum_probs=69.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      ...++|+||||.+.++..+|+..|++||++.+|++++|        |+||.|+..+ +|..|+..||+. +.|++|+|+.
T Consensus        76 k~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd--------y~fvh~d~~e-da~~air~l~~~~~~gk~m~vq~  146 (346)
T KOG0109|consen   76 KASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD--------YAFVHFDRAE-DAVEAIRGLDNTEFQGKRMHVQL  146 (346)
T ss_pred             CCccccccCCCCccccCHHHhhhhcccCCceeeeeecc--------eeEEEEeecc-chHHHHhcccccccccceeeeee
Confidence            34679999999999999999999999999999999855        9999997777 999999999999 9999999999


Q ss_pred             cccccc
Q psy8615         120 NTYVLM  125 (128)
Q Consensus       120 ~~~~~~  125 (128)
                      +|..+-
T Consensus       147 stsrlr  152 (346)
T KOG0109|consen  147 STSRLR  152 (346)
T ss_pred             eccccc
Confidence            998764

>KOG0533|consensus

Probab=99.26  E-value=2.5e-11  Score=87.42  Aligned_cols=84  Identities=21%  Similarity=0.229  Sum_probs=75.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEE
Q psy8615          39 TGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKP  117 (128)
Q Consensus        39 ~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V  117 (128)
                      .+...++|+|.|||..+.+++|+++|+.||.+..+-+.+++. |.+.|.|-|.|...+ +|.+|++.+++. +.|++|++
T Consensus        79 ~~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~-G~s~Gta~v~~~r~~-DA~~avk~~~gv~ldG~~mk~  156 (243)
T KOG0533|consen   79 NETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRA-GRSLGTADVSFNRRD-DAERAVKKYNGVALDGRPMKI  156 (243)
T ss_pred             cCCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCC-CCCCccceeeecchH-hHHHHHHHhcCcccCCceeee
Confidence            344458899999999999999999999999999999999986 999999999997777 999999999999 99999998


Q ss_pred             Eeccccc
Q psy8615         118 SFNTYVL  124 (128)
Q Consensus       118 ~~~~~~~  124 (128)
                      .......
T Consensus       157 ~~i~~~~  163 (243)
T KOG0533|consen  157 EIISSPS  163 (243)
T ss_pred             EEecCcc
Confidence            8765543

>KOG4661|consensus

Probab=99.26  E-value=3.4e-11  Score=94.62  Aligned_cols=83  Identities=19%  Similarity=0.322  Sum_probs=75.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      .-+++|||.+|.-.+...+|+.+|++||.|...+++....+-..++||||++++.. +|.+||++|+.. |.|+.|.|.-
T Consensus       403 ~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~-eAtkCI~hLHrTELHGrmISVEk  481 (940)
T KOG4661|consen  403 TLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSA-EATKCIEHLHRTELHGRMISVEK  481 (940)
T ss_pred             ccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchH-HHHHHHHHhhhhhhcceeeeeee
Confidence            44679999999999999999999999999999999999888888999999997777 999999999999 9999999987


Q ss_pred             ccccc
Q psy8615         120 NTYVL  124 (128)
Q Consensus       120 ~~~~~  124 (128)
                      .|.-+
T Consensus       482 aKNEp  486 (940)
T KOG4661|consen  482 AKNEP  486 (940)
T ss_pred             cccCc
Confidence            76543

>KOG0132|consensus

Probab=99.25  E-value=1.8e-11  Score=98.49  Aligned_cols=72  Identities=17%  Similarity=0.315  Sum_probs=66.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecc
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNT  121 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~  121 (128)
                      .++||||+|+.+++|.+|..+|+.||+|.++.++..      +|||||.+.+.. +|++|+.+|+.+ +.++.|+|.|+-
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~------R~cAfI~M~~Rq-dA~kalqkl~n~kv~~k~Iki~Wa~  493 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP------RGCAFIKMVRRQ-DAEKALQKLSNVKVADKTIKIAWAV  493 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeeccC------CceeEEEEeehh-HHHHHHHHHhcccccceeeEEeeec
Confidence            479999999999999999999999999999987744      789999998888 999999999999 999999999973

>KOG4205|consensus

Probab=99.23  E-value=1.3e-11  Score=91.95  Aligned_cols=76  Identities=26%  Similarity=0.374  Sum_probs=62.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCcCCCeEEEEE
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDYLGQSFLKPS  118 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~~~~~~l~V~  118 (128)
                      +.+++|||+|+|+++++.|++.|++||+|.+|.+++|+.|++++||+||+|.+.+ ....++..-.-.+.++.+.+.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~-~v~~vl~~~~h~~dgr~ve~k   80 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPE-GVDAVLNARTHKLDGRSVEPK   80 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCc-chheeecccccccCCccccce
Confidence            6889999999999999999999999999999999999999999999999997565 544444333323666665443

>KOG0110|consensus

Probab=99.21  E-value=1.1e-11  Score=98.81  Aligned_cols=80  Identities=18%  Similarity=0.269  Sum_probs=73.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecc
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNT  121 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~  121 (128)
                      .++|+|.|||+..+-.+++.+|..||.+++|+++.....+.++|||||+|-++. +|..|+++|.+. +-|+.|.+.|++
T Consensus       613 ~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~-ea~nA~~al~STHlyGRrLVLEwA~  691 (725)
T KOG0110|consen  613 GTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPR-EAKNAFDALGSTHLYGRRLVLEWAK  691 (725)
T ss_pred             cceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcH-HHHHHHHhhcccceechhhheehhc
Confidence            689999999999999999999999999999999887555778999999998888 999999999988 999999999987


Q ss_pred             cc
Q psy8615         122 YV  123 (128)
Q Consensus       122 ~~  123 (128)
                      .-
T Consensus       692 ~d  693 (725)
T KOG0110|consen  692 SD  693 (725)
T ss_pred             cc
Confidence            54

>KOG0151|consensus

Probab=99.20  E-value=7.7e-11  Score=94.19  Aligned_cols=90  Identities=21%  Similarity=0.335  Sum_probs=79.1

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecC---CCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCe
Q psy8615          38 LTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDK---QNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQS  113 (128)
Q Consensus        38 ~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~---~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~  113 (128)
                      ..++..+++||+||++.++|+.|-..|+.||++.+++++..+   ...+.+-||||.|.+.. ++++|++.|+|. +.+.
T Consensus       169 dgDP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~-D~era~k~lqg~iv~~~  247 (877)
T KOG0151|consen  169 DGDPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRA-DAERALKELQGIIVMEY  247 (877)
T ss_pred             CCCCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhh-hHHHHHHHhcceeeeee
Confidence            335667899999999999999999999999999999998765   22445679999998777 999999999999 9999


Q ss_pred             EEEEEeccccccccC
Q psy8615         114 FLKPSFNTYVLMNVI  128 (128)
Q Consensus       114 ~l~V~~~~~~~~~~~  128 (128)
                      .+++.|++.|..|.|
T Consensus       248 e~K~gWgk~V~ip~~  262 (877)
T KOG0151|consen  248 EMKLGWGKAVPIPNI  262 (877)
T ss_pred             eeeeccccccccCCc
Confidence            999999999988765

>KOG0226|consensus

Probab=99.18  E-value=2e-11  Score=87.48  Aligned_cols=78  Identities=26%  Similarity=0.300  Sum_probs=72.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      +.+..+||+|.|..+++++.|-..|.+|-.-...++++|+.||+++|||||.|.+.. +..+|+..|+|. +|.++|+..
T Consensus       187 ~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pa-d~~rAmrem~gkyVgsrpiklR  265 (290)
T KOG0226|consen  187 DEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPA-DYVRAMREMNGKYVGSRPIKLR  265 (290)
T ss_pred             ccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHH-HHHHHHHhhcccccccchhHhh
Confidence            355679999999999999999999999999999999999999999999999998887 999999999999 999998753

>KOG0123|consensus

Probab=99.16  E-value=1.2e-10  Score=88.97  Aligned_cols=73  Identities=26%  Similarity=0.300  Sum_probs=67.9

Q ss_pred             CeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEeccc
Q psy8615          44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNTY  122 (128)
Q Consensus        44 ~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~~  122 (128)
                      ..||||   ++++|.+|+++|+++|++.++++-+|. |  +-|||||.|.++. +|++|++.+|.. +.|++++|-|+..
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t--slgy~yvnf~~~~-da~~A~~~~n~~~~~~~~~rim~s~r   74 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T--SLGYAYVNFQQPA-DAERALDTMNFDVLKGKPIRIMWSQR   74 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecC-C--ccceEEEecCCHH-HHHHHHHHcCCcccCCcEEEeehhcc
Confidence            368998   999999999999999999999999998 6  9999999998888 999999999999 9999999999864


Q ss_pred             c
Q psy8615         123 V  123 (128)
Q Consensus       123 ~  123 (128)
                      .
T Consensus        75 d   75 (369)
T KOG0123|consen   75 D   75 (369)
T ss_pred             C
Confidence            3

>KOG4212|consensus

Probab=99.14  E-value=1.5e-10  Score=88.47  Aligned_cols=75  Identities=23%  Similarity=0.284  Sum_probs=67.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ..+.|+|||.|||+++||..|++-|..||.+....++   +.|+++|  .|.|.+++ +|++|+..|++. +.|+.|+|.
T Consensus       533 arKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadim---e~GkskG--VVrF~s~e-dAEra~a~Mngs~l~Gr~I~V~  606 (608)
T KOG4212|consen  533 ARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIM---ENGKSKG--VVRFFSPE-DAERACALMNGSRLDGRNIKVT  606 (608)
T ss_pred             cccccEEEEecCCccccHHHHHHHHHhccceehhhhh---ccCCccc--eEEecCHH-HHHHHHHHhccCcccCceeeee
Confidence            3557899999999999999999999999999999883   2388888  78997777 999999999999 999999998


Q ss_pred             ec
Q psy8615         119 FN  120 (128)
Q Consensus       119 ~~  120 (128)
                      |.
T Consensus       607 y~  608 (608)
T KOG4212|consen  607 YF  608 (608)
T ss_pred             eC
Confidence            83

>KOG0153|consensus

Probab=99.11  E-value=4.3e-10  Score=83.62  Aligned_cols=79  Identities=15%  Similarity=0.158  Sum_probs=67.9

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc--CCCeE
Q psy8615          37 QLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY--LGQSF  114 (128)
Q Consensus        37 ~~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~--~~~~~  114 (128)
                      ..++..-++|||++|-..++|.+|++.|.+||+|+++.+...      +++|||+|-+.. .|+.|.+..-..  +.|+.
T Consensus       222 pPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~-aAE~Aae~~~n~lvI~G~R  294 (377)
T KOG0153|consen  222 PPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFTTRE-AAEKAAEKSFNKLVINGFR  294 (377)
T ss_pred             CCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc------cccceeeehhhH-HHHHHHHhhcceeeecceE
Confidence            344555679999999999999999999999999999988765      459999997777 888888776666  99999


Q ss_pred             EEEEeccc
Q psy8615         115 LKPSFNTY  122 (128)
Q Consensus       115 l~V~~~~~  122 (128)
                      |+|.|+.+
T Consensus       295 l~i~Wg~~  302 (377)
T KOG0153|consen  295 LKIKWGRP  302 (377)
T ss_pred             EEEEeCCC
Confidence            99999987

>KOG0110|consensus

Probab=99.09  E-value=3e-10  Score=90.72  Aligned_cols=78  Identities=23%  Similarity=0.265  Sum_probs=68.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCC---CcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNN---RSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg---~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      .++|||.||+++++.+++...|.+.|.|.++.|...+...   -+.|||||+|.+.+ +|+.|++.|+|. +.|+.|.|.
T Consensus       515 ~t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e-~A~~a~k~lqgtvldGH~l~lk  593 (725)
T KOG0110|consen  515 ETKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPE-SAQAALKALQGTVLDGHKLELK  593 (725)
T ss_pred             chhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHH-HHHHHHHHhcCceecCceEEEE
Confidence            4559999999999999999999999999999887665421   24499999998777 999999999999 999999998


Q ss_pred             ecc
Q psy8615         119 FNT  121 (128)
Q Consensus       119 ~~~  121 (128)
                      ++-
T Consensus       594 ~S~  596 (725)
T KOG0110|consen  594 ISE  596 (725)
T ss_pred             ecc
Confidence            876

>KOG1548|consensus

Probab=99.04  E-value=2.5e-09  Score=79.62  Aligned_cols=82  Identities=12%  Similarity=0.265  Sum_probs=72.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEE--------EEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-C
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLS--------AKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-L  110 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~--------~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~  110 (128)
                      ....+.|||+|||.++|.+++.++|++||-|.+        |++.++.. |+.+|=|.+.|-..+ ....|++.|++. +
T Consensus       131 ~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~-G~lKGDaLc~y~K~E-SVeLA~~ilDe~~~  208 (382)
T KOG1548|consen  131 PKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQ-GKLKGDALCCYIKRE-SVELAIKILDEDEL  208 (382)
T ss_pred             cccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCC-CCccCceEEEeeccc-HHHHHHHHhCcccc
Confidence            344678999999999999999999999998744        78888887 999999999997766 999999999999 9


Q ss_pred             CCeEEEEEecccc
Q psy8615         111 GQSFLKPSFNTYV  123 (128)
Q Consensus       111 ~~~~l~V~~~~~~  123 (128)
                      .|+.|+|+=+++.
T Consensus       209 rg~~~rVerAkfq  221 (382)
T KOG1548|consen  209 RGKKLRVERAKFQ  221 (382)
T ss_pred             cCcEEEEehhhhh
Confidence            9999999877664

>KOG0116|consensus

Probab=99.03  E-value=1.3e-09  Score=84.12  Aligned_cols=79  Identities=20%  Similarity=0.419  Sum_probs=67.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCcCCCeEEEEEeccc
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDYLGQSFLKPSFNTY  122 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~~~~~~l~V~~~~~  122 (128)
                      ...|||.|||+++++.+|+++|.+||.|+...|......++..+||||+|.+.. .++.||++---.+|++.|.|.-+++
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~-~~~~~i~Asp~~ig~~kl~Veek~~  366 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAA-AVQNAIEASPLEIGGRKLNVEEKRP  366 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecc-hhhhhhhcCccccCCeeEEEEeccc
Confidence            456999999999999999999999999999888665533566699999998888 9999998884339999999988775

>KOG4209|consensus

Probab=99.00  E-value=8.9e-10  Score=79.24  Aligned_cols=83  Identities=10%  Similarity=0.122  Sum_probs=75.1

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEE
Q psy8615          38 LTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLK  116 (128)
Q Consensus        38 ~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~  116 (128)
                      ....+...+||+|+.+.++-+++...|+.||.+..+.+..|+.+|+++||+||+|.+.. ..+.++. ||+. +.++.++
T Consensus        96 ~~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~-~~~~ay~-l~gs~i~~~~i~  173 (231)
T KOG4209|consen   96 QKEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYE-LVEEAYK-LDGSEIPGPAIE  173 (231)
T ss_pred             hhccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHh-hhHHHhh-cCCcccccccce
Confidence            34556789999999999999999999999999999999999999999999999997777 9999999 9999 9999999


Q ss_pred             EEeccc
Q psy8615         117 PSFNTY  122 (128)
Q Consensus       117 V~~~~~  122 (128)
                      |.+++=
T Consensus       174 vt~~r~  179 (231)
T KOG4209|consen  174 VTLKRT  179 (231)
T ss_pred             eeeeee
Confidence            998753

>KOG4205|consensus

Probab=98.91  E-value=5e-09  Score=78.15  Aligned_cols=79  Identities=19%  Similarity=0.329  Sum_probs=65.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecc
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNT  121 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~  121 (128)
                      ..++||++||.+++++++++.|++||.|..+.++.|..+.+.+||+||.|++.+ ... -+....-+ +.++.++|.-+.
T Consensus        97 tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~-sVd-kv~~~~f~~~~gk~vevkrA~  174 (311)
T KOG4205|consen   97 TKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSED-SVD-KVTLQKFHDFNGKKVEVKRAI  174 (311)
T ss_pred             eeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEecccc-ccc-eecccceeeecCceeeEeecc
Confidence            348999999999999999999999999999999999999999999999996554 443 34444445 888888776655


Q ss_pred             cc
Q psy8615         122 YV  123 (128)
Q Consensus       122 ~~  123 (128)
                      +.
T Consensus       175 pk  176 (311)
T KOG4205|consen  175 PK  176 (311)
T ss_pred             ch
Confidence            44

>KOG1190|consensus

Probab=98.87  E-value=2.7e-08  Score=75.66  Aligned_cols=77  Identities=17%  Similarity=0.209  Sum_probs=68.5

Q ss_pred             CCeEEEcCCC-CCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          43 GANLFIYHLP-PEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        43 ~~~l~V~nLp-~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      .+.|.|.||. ..+|.+.|..+|+.||.|.++++.+.+     +--|.|.|.+.. .|+.|+++|+|. +.|+.|+|.++
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nk-----kd~ALIQmsd~~-qAqLA~~hL~g~~l~gk~lrvt~S  370 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNK-----KDNALIQMSDGQ-QAQLAMEHLEGHKLYGKKLRVTLS  370 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecC-----Ccceeeeecchh-HHHHHHHHhhcceecCceEEEeec
Confidence            5678899986 569999999999999999999998776     347899999988 999999999999 99999999999


Q ss_pred             ccccc
Q psy8615         121 TYVLM  125 (128)
Q Consensus       121 ~~~~~  125 (128)
                      |..-+
T Consensus       371 KH~~v  375 (492)
T KOG1190|consen  371 KHTNV  375 (492)
T ss_pred             cCccc
Confidence            97644

>KOG0120|consensus

Probab=98.86  E-value=5.1e-09  Score=82.02  Aligned_cols=80  Identities=16%  Similarity=0.229  Sum_probs=74.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecc
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNT  121 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~  121 (128)
                      ..++||++||...++.+++++...||+++..+++.|..+|-++||+|.+|-++. ....|+..|||. +|++.|.|+.+-
T Consensus       289 ~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dps-vtd~A~agLnGm~lgd~~lvvq~A~  367 (500)
T KOG0120|consen  289 PNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPS-VTDQAIAGLNGMQLGDKKLVVQRAI  367 (500)
T ss_pred             cchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCc-chhhhhcccchhhhcCceeEeehhh
Confidence            568999999999999999999999999999999999999999999999999998 999999999999 999999998765


Q ss_pred             cc
Q psy8615         122 YV  123 (128)
Q Consensus       122 ~~  123 (128)
                      .-
T Consensus       368 ~g  369 (500)
T KOG0120|consen  368 VG  369 (500)
T ss_pred             cc
Confidence            43

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

Probab=98.81  E-value=4.6e-08  Score=61.36  Aligned_cols=78  Identities=13%  Similarity=0.141  Sum_probs=67.0

Q ss_pred             CeEEEcCCCCCCCHHHHHhhhcC--CCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CC----CeEEE
Q psy8615          44 ANLFIYHLPPEFSDADLASMFGP--FGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LG----QSFLK  116 (128)
Q Consensus        44 ~~l~V~nLp~~~~e~~l~~~f~~--~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~----~~~l~  116 (128)
                      |+|.+.|||...+.++|.+++..  .|...-+.++.|..++-+.|||||.|-+++ .+.+=.+.++|. +.    .|...
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~-~~~~F~~~f~g~~w~~~~s~Kvc~   80 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQ-AAIRFYKAFNGKKWPNFNSKKVCE   80 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHH-HHHHHHHHHcCCccccCCCCcEEE
Confidence            78999999999999999988864  367777889999999999999999997777 888888999997 53    58888


Q ss_pred             EEeccc
Q psy8615         117 PSFNTY  122 (128)
Q Consensus       117 V~~~~~  122 (128)
                      |+|++-
T Consensus        81 i~yAri   86 (97)
T PF04059_consen   81 ISYARI   86 (97)
T ss_pred             EehhHh
Confidence            888763

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

>KOG1457|consensus

Probab=98.78  E-value=1.8e-07  Score=66.44  Aligned_cols=80  Identities=15%  Similarity=0.167  Sum_probs=62.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEe-cCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-C---CCeEEE
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFI-DKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-L---GQSFLK  116 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~-~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~---~~~~l~  116 (128)
                      .-++|||.+||.++...+|+.+|..|..-..+.+-. ++.....+-+||++|.+.. +|..|++.|||. +   -+..|+
T Consensus        33 ~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q-~A~aamnaLNGvrFDpE~~stLh  111 (284)
T KOG1457|consen   33 AVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQ-FALAAMNALNGVRFDPETGSTLH  111 (284)
T ss_pred             ccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchH-HHHHHHHHhcCeeeccccCceeE
Confidence            357999999999999999999999985555544432 3322234579999998888 999999999997 3   347899


Q ss_pred             EEeccc
Q psy8615         117 PSFNTY  122 (128)
Q Consensus       117 V~~~~~  122 (128)
                      |.++|.
T Consensus       112 iElAKS  117 (284)
T KOG1457|consen  112 IELAKS  117 (284)
T ss_pred             eeehhc
Confidence            998874

>KOG4454|consensus

Probab=98.70  E-value=7.4e-09  Score=73.09  Aligned_cols=75  Identities=15%  Similarity=0.198  Sum_probs=68.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      .++|||+|+...++|+-|.++|-+-|+|.++.|..++. ++.+ |+||.|.+.. ...-|++-+||. +.++.++|.+-
T Consensus         9 drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d-~~~k-Fa~v~f~~E~-sv~~a~~L~ng~~l~~~e~q~~~r   84 (267)
T KOG4454|consen    9 DRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQD-QEQK-FAYVFFPNEN-SVQLAGQLENGDDLEEDEEQRTLR   84 (267)
T ss_pred             hhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCcc-CCCc-eeeeeccccc-chhhhhhhcccchhccchhhcccc
Confidence            56899999999999999999999999999999988876 7777 9999997777 889999999999 99999888764

>KOG4660|consensus

Probab=98.67  E-value=2.8e-08  Score=77.80  Aligned_cols=71  Identities=15%  Similarity=0.290  Sum_probs=62.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLK  116 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~  116 (128)
                      +....+|+|-|||..+++++|+.+|+.||+|+.++     .|-..+|..||+|.+-- +|++|++.|++. +.|+.|+
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir-----~t~~~~~~~~v~FyDvR-~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIR-----ETPNKRGIVFVEFYDVR-DAERALKALNRREIAGKRIK  143 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhh-----cccccCceEEEEEeehH-hHHHHHHHHHHHHhhhhhhc
Confidence            34456899999999999999999999999999864     34556899999999998 999999999998 8888877

>KOG0106|consensus

Probab=98.66  E-value=2e-08  Score=71.23  Aligned_cols=69  Identities=17%  Similarity=0.209  Sum_probs=61.5

Q ss_pred             CeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecc
Q psy8615          44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNT  121 (128)
Q Consensus        44 ~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~  121 (128)
                      ..+|||+||+.+.+.++..+|..||.+.++.+.        .||+||+|++.. +|..|+..+|+. +++-.+.|.|.+
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk--------~gf~fv~fed~r-da~Dav~~l~~~~l~~e~~vve~~r   71 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMK--------NGFGFVEFEDPR-DADDAVHDLDGKELCGERLVVEHAR   71 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceee--------cccceeccCchh-hhhcccchhcCceecceeeeeeccc
Confidence            468999999999999999999999999987643        568999999988 999999999999 777558998877

>KOG4211|consensus

Probab=98.57  E-value=3e-07  Score=71.36  Aligned_cols=78  Identities=10%  Similarity=0.178  Sum_probs=63.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCcCCCeEEEEEec
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDYLGQSFLKPSFN  120 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~~~~~~l~V~~~  120 (128)
                      .....|-+.+|||++|+++|.++|+.++ |..+.+.  +.+|+..|-|||+|.+.+ +++.|++.-...++.+.|.|-=.
T Consensus         8 ~~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~--r~~Gr~sGeA~Ve~~see-dv~~AlkkdR~~mg~RYIEVf~~   83 (510)
T KOG4211|consen    8 STAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIP--RRNGRPSGEAYVEFTSEE-DVEKALKKDRESMGHRYIEVFTA   83 (510)
T ss_pred             CcceEEEecCCCccccHHHHHHHHhcCc-eeEEEEe--ccCCCcCcceEEEeechH-HHHHHHHhhHHHhCCceEEEEcc
Confidence            3455677899999999999999999997 6765444  446999999999996666 99999988776699999998655


Q ss_pred             cc
Q psy8615         121 TY  122 (128)
Q Consensus       121 ~~  122 (128)
                      +.
T Consensus        84 ~~   85 (510)
T KOG4211|consen   84 GG   85 (510)
T ss_pred             CC
Confidence            43

>KOG0147|consensus

Probab=98.43  E-value=1.1e-07  Score=74.38  Aligned_cols=79  Identities=16%  Similarity=0.226  Sum_probs=69.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      +.+.+++|+..++...++.+|.++|+.+|.|+.++++.|+.++.++|.+||+|.+.+ ....|| .|.|. +.|-+|.|.
T Consensus       176 ERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~-sVp~ai-aLsGqrllg~pv~vq  253 (549)
T KOG0147|consen  176 ERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQ-SVPLAI-ALSGQRLLGVPVIVQ  253 (549)
T ss_pred             HHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEeccc-chhhHh-hhcCCcccCceeEec
Confidence            344678999999999999999999999999999999999999999999999998776 666666 88888 888898887


Q ss_pred             ec
Q psy8615         119 FN  120 (128)
Q Consensus       119 ~~  120 (128)
                      ..
T Consensus       254 ~s  255 (549)
T KOG0147|consen  254 LS  255 (549)
T ss_pred             cc
Confidence            53

>KOG1995|consensus

Probab=98.36  E-value=7.3e-07  Score=66.83  Aligned_cols=83  Identities=16%  Similarity=0.228  Sum_probs=73.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEE--------EEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-C
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLS--------AKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-L  110 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~--------~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~  110 (128)
                      ....-++||-+||..+++.++.++|.++|.|..        +.+-+|+.|+..+|-|.|.|+++. .|+.||..+++. +
T Consensus        63 ~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~-~akaai~~~agkdf  141 (351)
T KOG1995|consen   63 KSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPP-AAKAAIEWFAGKDF  141 (351)
T ss_pred             ccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChh-hhhhhhhhhccccc
Confidence            444668999999999999999999999998743        667889999999999999999999 999999999999 8


Q ss_pred             CCeEEEEEecccc
Q psy8615         111 GQSFLKPSFNTYV  123 (128)
Q Consensus       111 ~~~~l~V~~~~~~  123 (128)
                      .+..|+|++....
T Consensus       142 ~gn~ikvs~a~~r  154 (351)
T KOG1995|consen  142 CGNTIKVSLAERR  154 (351)
T ss_pred             cCCCchhhhhhhc
Confidence            8899999887654

>KOG4210|consensus

Probab=98.36  E-value=3.3e-07  Score=67.92  Aligned_cols=79  Identities=18%  Similarity=0.225  Sum_probs=69.7

Q ss_pred             CCeEE-EcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          43 GANLF-IYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        43 ~~~l~-V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      ..++| |+++++++++++|+..|..+|.|..+++..++.+|..+||++++|.... +...++.. +.. ++++++.+.+.
T Consensus       184 s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~-~~~~~~~~-~~~~~~~~~~~~~~~  261 (285)
T KOG4210|consen  184 SDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGN-SKKLALND-QTRSIGGRPLRLEED  261 (285)
T ss_pred             cccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhch-hHHHHhhc-ccCcccCcccccccC
Confidence            34555 9999999999999999999999999999999999999999999997776 77777776 666 99999999998


Q ss_pred             ccc
Q psy8615         121 TYV  123 (128)
Q Consensus       121 ~~~  123 (128)
                      .+.
T Consensus       262 ~~~  264 (285)
T KOG4210|consen  262 EPR  264 (285)
T ss_pred             CCC
Confidence            876

>KOG4211|consensus

Probab=98.32  E-value=4e-06  Score=65.22  Aligned_cols=77  Identities=13%  Similarity=0.216  Sum_probs=63.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEE-EEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCcCCCeEEEEEecc
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLS-AKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDYLGQSFLKPSFNT  121 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~-~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~~~~~~l~V~~~~  121 (128)
                      ...|-+.+||+.+++++|.++|+.--.+.. +-++.|+. |++.|-|||.|++.+ .+++|+......+|.+.|.|-=++
T Consensus       103 d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~r-gR~tGEAfVqF~sqe-~ae~Al~rhre~iGhRYIEvF~Ss  180 (510)
T KOG4211|consen  103 DGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQR-GRPTGEAFVQFESQE-SAEIALGRHRENIGHRYIEVFRSS  180 (510)
T ss_pred             CceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCC-CCcccceEEEecCHH-HHHHHHHHHHHhhccceEEeehhH
Confidence            346778999999999999999997654444 55677776 889999999997777 999998887766999999885443

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=98.30  E-value=2.2e-06  Score=64.20  Aligned_cols=78  Identities=21%  Similarity=0.335  Sum_probs=60.2

Q ss_pred             CCeEEEcCCCCCCCHHH----H--HhhhcCCCceEEEEEEecCCCCCc-ce-EE-EEEEecCHHHHHHHHHHhcCc-CCC
Q psy8615          43 GANLFIYHLPPEFSDAD----L--ASMFGPFGTVLSAKVFIDKQNNRS-KC-FG-TIIFMRKFFILTIRFDTANDY-LGQ  112 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~----l--~~~f~~~G~i~~~~~~~~~~tg~~-~g-~~-fv~f~~~~~~a~~Ai~~l~g~-~~~  112 (128)
                      ..-+||-+||+.+..|+    |  .++|++||.|.++.+.+...+-.+ .+ +| |+.|++.+ +|.+||...+|. ++|
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~ke-dAarcIa~vDgs~~DG  192 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKE-DAARCIAEVDGSLLDG  192 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchH-HHHHHHHHhccccccC
Confidence            34679999988776665    3  378999999999876554322222 23 33 89997777 999999999999 999


Q ss_pred             eEEEEEecc
Q psy8615         113 SFLKPSFNT  121 (128)
Q Consensus       113 ~~l~V~~~~  121 (128)
                      |.|+.+|++
T Consensus       193 r~lkatYGT  201 (480)
T COG5175         193 RVLKATYGT  201 (480)
T ss_pred             ceEeeecCc
Confidence            999999986

>KOG1457|consensus

Probab=98.22  E-value=1.6e-06  Score=61.71  Aligned_cols=61  Identities=15%  Similarity=0.145  Sum_probs=49.7

Q ss_pred             CeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc
Q psy8615          44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY  109 (128)
Q Consensus        44 ~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~  109 (128)
                      .+|||.||..+++|++|+.+|+.|.....+++...   | .-..+|++|++-+ .|..|+.+|+|.
T Consensus       211 stlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~---~-g~~vaf~~~~~~~-~at~am~~lqg~  271 (284)
T KOG1457|consen  211 STLFIANLGPNCTEDELKQLLSRYPGFHILKIRAR---G-GMPVAFADFEEIE-QATDAMNHLQGN  271 (284)
T ss_pred             hhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecC---C-CcceEeecHHHHH-HHHHHHHHhhcc
Confidence            48999999999999999999999976666554322   2 2458999997666 999999999986

>KOG4206|consensus

Probab=98.21  E-value=1.1e-05  Score=57.24  Aligned_cols=76  Identities=13%  Similarity=0.289  Sum_probs=64.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CC-CeEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LG-QSFLKP  117 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~-~~~l~V  117 (128)
                      .+....+|+.|||.+++.+.+..+|.+|..-++++++...     ++.+||+|.+.. .+..|.+.++++ +- ...++|
T Consensus       143 ~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~-----~~iAfve~~~d~-~a~~a~~~lq~~~it~~~~m~i  216 (221)
T KOG4206|consen  143 APPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPR-----SGIAFVEFLSDR-QASAAQQALQGFKITKKNTMQI  216 (221)
T ss_pred             CCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCC-----CceeEEecchhh-hhHHHhhhhccceeccCceEEe
Confidence            3445679999999999999999999999988998877543     679999997666 788999999998 55 788999


Q ss_pred             Eecc
Q psy8615         118 SFNT  121 (128)
Q Consensus       118 ~~~~  121 (128)
                      .|.+
T Consensus       217 ~~a~  220 (221)
T KOG4206|consen  217 TFAK  220 (221)
T ss_pred             cccC
Confidence            8875

>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=98.12  E-value=1.6e-05  Score=48.34  Aligned_cols=67  Identities=18%  Similarity=0.175  Sum_probs=45.6

Q ss_pred             CeEEEcCCCCCCCHHH----HHhhhcCCC-ceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEE
Q psy8615          44 ANLFIYHLPPEFSDAD----LASMFGPFG-TVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKP  117 (128)
Q Consensus        44 ~~l~V~nLp~~~~e~~----l~~~f~~~G-~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V  117 (128)
                      +.|||.|||.+.+...    |+.++..|| .|.++          +.+-|++.|.+.+ .|.+|.+.|+|- ..|+.|.|
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v----------~~~tAilrF~~~~-~A~RA~KRmegEdVfG~kI~v   71 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV----------SGGTAILRFPNQE-FAERAQKRMEGEDVFGNKISV   71 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHH-HHHHHHHHHTT--SSSS--EE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE----------eCCEEEEEeCCHH-HHHHHHHhhcccccccceEEE
Confidence            4689999999988765    566777886 55543          2468999996666 999999999999 77778899


Q ss_pred             Eecc
Q psy8615         118 SFNT  121 (128)
Q Consensus       118 ~~~~  121 (128)
                      +|..
T Consensus        72 ~~~~   75 (90)
T PF11608_consen   72 SFSP   75 (90)
T ss_dssp             ESS-
T ss_pred             EEcC
Confidence            9873

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

>KOG1456|consensus

Probab=98.08  E-value=7.1e-05  Score=56.94  Aligned_cols=79  Identities=16%  Similarity=0.187  Sum_probs=68.5

Q ss_pred             CCCCCCCeEEEcCCCCC-CCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEE
Q psy8615          38 LTGPEGANLFIYHLPPE-FSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFL  115 (128)
Q Consensus        38 ~~~~~~~~l~V~nLp~~-~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l  115 (128)
                      ....+++.+.|.+|+.. .+-+.|..+|-.||.|.++++++.+     .|-|.|++.+.. ..++|+.+||+. +.|..|
T Consensus       282 ~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-----~gtamVemgd~~-aver~v~hLnn~~lfG~kl  355 (494)
T KOG1456|consen  282 GGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-----PGTAMVEMGDAY-AVERAVTHLNNIPLFGGKL  355 (494)
T ss_pred             CCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-----cceeEEEcCcHH-HHHHHHHHhccCccccceE
Confidence            34466899999999876 5557899999999999999999776     578999998888 999999999999 888899


Q ss_pred             EEEeccc
Q psy8615         116 KPSFNTY  122 (128)
Q Consensus       116 ~V~~~~~  122 (128)
                      .|+++|-
T Consensus       356 ~v~~SkQ  362 (494)
T KOG1456|consen  356 NVCVSKQ  362 (494)
T ss_pred             EEeeccc
Confidence            9999874

>KOG4849|consensus

Probab=98.01  E-value=9.9e-06  Score=61.04  Aligned_cols=80  Identities=18%  Similarity=0.167  Sum_probs=63.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCCC--ceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCC-eEEEE
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPFG--TVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQ-SFLKP  117 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~G--~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~-~~l~V  117 (128)
                      ....+|||||-|.++++||.+.+...|  .+.++++...+.+|+++||+.+.. .++....+-++.|-.+ +.| .+...
T Consensus        79 rk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~-~SdAa~Kq~MeiLP~k~iHGQ~P~V~  157 (498)
T KOG4849|consen   79 RKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVL-NSDAAVKQTMEILPTKTIHGQSPTVL  157 (498)
T ss_pred             ceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEe-cchHHHHHHHHhcccceecCCCCeee
Confidence            345789999999999999998887766  566778888888999999999999 5554666777778777 544 67777


Q ss_pred             Eeccc
Q psy8615         118 SFNTY  122 (128)
Q Consensus       118 ~~~~~  122 (128)
                      +|+|-
T Consensus       158 ~~NK~  162 (498)
T KOG4849|consen  158 SYNKT  162 (498)
T ss_pred             ccchh
Confidence            77763

>KOG1190|consensus

Probab=97.99  E-value=2e-05  Score=60.40  Aligned_cols=78  Identities=22%  Similarity=0.323  Sum_probs=63.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCC-eEEEEE
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQ-SFLKPS  118 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~-~~l~V~  118 (128)
                      ++..++...|+|.+++|++++..|..-|...+...-.    ++.+-++.+.+++.+ +|..|+..++.+ +|. ..|+|+
T Consensus       412 PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff----~kd~kmal~q~~sve-eA~~ali~~hnh~lgen~hlRvS  486 (492)
T KOG1190|consen  412 PPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFF----QKDRKMALPQLESVE-EAIQALIDLHNHYLGENHHLRVS  486 (492)
T ss_pred             CchhheeeccCCcccchhHHHHhhhcCCceEEeeeec----CCCcceeecccCChh-HhhhhccccccccCCCCceEEEE
Confidence            4455899999999999999999999888766543222    344669999997777 999999999998 777 489999


Q ss_pred             ecccc
Q psy8615         119 FNTYV  123 (128)
Q Consensus       119 ~~~~~  123 (128)
                      |+|.-
T Consensus       487 FSks~  491 (492)
T KOG1190|consen  487 FSKST  491 (492)
T ss_pred             eeccc
Confidence            99864

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=97.99  E-value=2.1e-05  Score=50.07  Aligned_cols=59  Identities=19%  Similarity=0.184  Sum_probs=37.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcC
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTAND  108 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g  108 (128)
                      |+.|++.+++..++-++|++.|++||.|..|.+.....      -|||.|.+++ .|+.|+..+..
T Consensus         1 G~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~------~g~VRf~~~~-~A~~a~~~~~~   59 (105)
T PF08777_consen    1 GCILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDT------EGYVRFKTPE-AAQKALEKLKE   59 (105)
T ss_dssp             --EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-S------EEEEEESS----HHHHHHHHHH
T ss_pred             CeEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCC------EEEEEECCcc-hHHHHHHHHHh
Confidence            46788999999999999999999999999887765433      7899998777 88888877653

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

>KOG2314|consensus

Probab=97.94  E-value=4.9e-05  Score=60.39  Aligned_cols=76  Identities=11%  Similarity=0.009  Sum_probs=61.2

Q ss_pred             CCCCeEEEcCCCCCCCH------HHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc--CCC
Q psy8615          41 PEGANLFIYHLPPEFSD------ADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY--LGQ  112 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e------~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~--~~~  112 (128)
                      ...+.|+|.|+|.--..      ..|..+|+++|++....++.+.. |..+||.|++|.+.. +|..|++.+||+  .-+
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~-ggtkG~lf~E~~~~~-~A~~aVK~l~G~~ldkn  133 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEE-GGTKGYLFVEYASMR-DAKKAVKSLNGKRLDKN  133 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCcc-CCeeeEEEEEecChh-hHHHHHHhcccceeccc
Confidence            34568899999864322      24678899999999999998988 559999999998888 999999999998  445


Q ss_pred             eEEEEE
Q psy8615         113 SFLKPS  118 (128)
Q Consensus       113 ~~l~V~  118 (128)
                      +...|.
T Consensus       134 Htf~v~  139 (698)
T KOG2314|consen  134 HTFFVR  139 (698)
T ss_pred             ceEEee
Confidence            666654

>KOG3152|consensus

Probab=97.75  E-value=2.3e-05  Score=56.65  Aligned_cols=70  Identities=14%  Similarity=0.244  Sum_probs=58.5

Q ss_pred             CeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCC--------CCcce----EEEEEEecCHHHHHHHHHHhcCc-C
Q psy8615          44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQN--------NRSKC----FGTIIFMRKFFILTIRFDTANDY-L  110 (128)
Q Consensus        44 ~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~t--------g~~~g----~~fv~f~~~~~~a~~Ai~~l~g~-~  110 (128)
                      -.||+++||+.+....|+.+|+.||.|-+|.+.....+        |.++.    -|+|+|.+.. .|.+....||+. +
T Consensus        75 GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~Kr-vAK~iAe~Lnn~~I  153 (278)
T KOG3152|consen   75 GVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKR-VAKRIAELLNNTPI  153 (278)
T ss_pred             eEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHH-HHHHHHHHhCCCcc
Confidence            37999999999999999999999999999988765544        33333    3679998877 999999999999 9


Q ss_pred             CCeE
Q psy8615         111 GQSF  114 (128)
Q Consensus       111 ~~~~  114 (128)
                      ||+.
T Consensus       154 ggkk  157 (278)
T KOG3152|consen  154 GGKK  157 (278)
T ss_pred             CCCC
Confidence            9864

>KOG0106|consensus

Probab=97.73  E-value=2.3e-05  Score=55.76  Aligned_cols=68  Identities=18%  Similarity=0.177  Sum_probs=58.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEE
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKP  117 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V  117 (128)
                      ...+.+.|.+++..+.+.+|.+.|.++|.+.....        .++++||+|+..+ ++.+|+..+++. +.++.|.+
T Consensus        97 ~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--------~~~~~~v~Fs~~~-da~ra~~~l~~~~~~~~~l~~  165 (216)
T KOG0106|consen   97 RTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--------RRNFAFVEFSEQE-DAKRALEKLDGKKLNGRRISV  165 (216)
T ss_pred             cccceeeeccchhhhhHHHHhhhhcccCCCchhhh--------hccccceeehhhh-hhhhcchhccchhhcCceeee
Confidence            34678999999999999999999999999843322        3679999997776 999999999999 99999887

>KOG4307|consensus

Probab=97.60  E-value=0.00082  Score=54.88  Aligned_cols=75  Identities=8%  Similarity=0.073  Sum_probs=62.6

Q ss_pred             CC-eEEEcCCCCCCCHHHHHhhhcCCCceEE-EEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          43 GA-NLFIYHLPPEFSDADLASMFGPFGTVLS-AKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        43 ~~-~l~V~nLp~~~~e~~l~~~f~~~G~i~~-~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      ++ .|-+.|.|++++-+|+.++|..|-.+.. |++-+. +-|+..|-|-|.|++.+ +|.+|...+++. ++++.+++.+
T Consensus       866 Gp~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~n-d~G~pTGe~mvAfes~~-eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  866 GPRVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRN-DDGVPTGECMVAFESQE-EARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             CCeEEEecCCCccccHHHHHHHhcccccCCCceeEeec-CCCCcccceeEeecCHH-HHHhhhhccccCcccceeEEEEe
Confidence            44 7789999999999999999999965543 333333 34999999999998888 999999999999 9999988764

>KOG0120|consensus

Probab=97.59  E-value=0.00019  Score=56.78  Aligned_cols=60  Identities=12%  Similarity=0.082  Sum_probs=47.8

Q ss_pred             HHHhhhcCCCceEEEEEEecCCCCC---cceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          59 DLASMFGPFGTVLSAKVFIDKQNNR---SKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        59 ~l~~~f~~~G~i~~~~~~~~~~tg~---~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      +++..+++||.|.+|.+..+-..+.   ..|--||+|.+.+ ++++|.+.|+|. +.|+++..+|
T Consensus       425 dvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~e-d~qrA~~~L~GrKF~nRtVvtsY  488 (500)
T KOG0120|consen  425 DVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTE-DSQRAMEELTGRKFANRTVVASY  488 (500)
T ss_pred             HHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChH-HHHHHHHHccCceeCCcEEEEEe
Confidence            4556677999999999988732222   2455699998877 999999999999 9999988776

>KOG1855|consensus

Probab=97.54  E-value=9.8e-05  Score=56.93  Aligned_cols=73  Identities=14%  Similarity=0.139  Sum_probs=57.4

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEec---CCC--CCc--------ceEEEEEEecCHHHHHHH
Q psy8615          36 KQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFID---KQN--NRS--------KCFGTIIFMRKFFILTIR  102 (128)
Q Consensus        36 ~~~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~---~~t--g~~--------~g~~fv~f~~~~~~a~~A  102 (128)
                      ...++...++|.+-|||.+-.-+.|.++|+.+|.|..|++...   +..  |..        +-+|+|+|+..+ .|.+|
T Consensus       224 ~~~eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~-~A~KA  302 (484)
T KOG1855|consen  224 FDEEELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVE-AARKA  302 (484)
T ss_pred             ccccccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhH-HHHHH
Confidence            3444556889999999999999999999999999999997554   211  221        458899998777 99999


Q ss_pred             HHHhcCc
Q psy8615         103 FDTANDY  109 (128)
Q Consensus       103 i~~l~g~  109 (128)
                      .+.++..
T Consensus       303 ~e~~~~e  309 (484)
T KOG1855|consen  303 RELLNPE  309 (484)
T ss_pred             HHhhchh
Confidence            9998653

>KOG1456|consensus

Probab=97.46  E-value=0.00089  Score=51.14  Aligned_cols=71  Identities=20%  Similarity=0.142  Sum_probs=60.2

Q ss_pred             CCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc---CCCeEEEEEeccccccccC
Q psy8615          52 PPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY---LGQSFLKPSFNTYVLMNVI  128 (128)
Q Consensus        52 p~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~---~~~~~l~V~~~~~~~~~~~  128 (128)
                      -..++-+.|..+--+.|+|.++.+...  +|.   -|.|+|++.+ .|++|.+.|||.   -|.-.|||.|+||--+||+
T Consensus       131 ~YpItvDVly~Icnp~GkVlRIvIfkk--ngV---QAmVEFdsv~-~AqrAk~alNGADIYsGCCTLKIeyAkP~rlnV~  204 (494)
T KOG1456|consen  131 QYPITVDVLYTICNPQGKVLRIVIFKK--NGV---QAMVEFDSVE-VAQRAKAALNGADIYSGCCTLKIEYAKPTRLNVQ  204 (494)
T ss_pred             ccccchhhhhhhcCCCCceEEEEEEec--cce---eeEEeechhH-HHHHHHhhcccccccccceeEEEEecCcceeeee
Confidence            356888999999999999999876644  343   5899997777 999999999996   5779999999999999885

>KOG0112|consensus

Probab=97.42  E-value=0.00047  Score=57.42  Aligned_cols=78  Identities=14%  Similarity=0.075  Sum_probs=66.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCC--eEE
Q psy8615          39 TGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQ--SFL  115 (128)
Q Consensus        39 ~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~--~~l  115 (128)
                      .....+.+|+++|...+....|...|..||.|..|.+-      +..-|+++.|++.. .++.|++.|.|+ +|+  +.|
T Consensus       451 kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~------hgq~yayi~yes~~-~aq~a~~~~rgap~G~P~~r~  523 (975)
T KOG0112|consen  451 KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYR------HGQPYAYIQYESPP-AAQAATHDMRGAPLGGPPRRL  523 (975)
T ss_pred             ccccceeeccCCCCCCChHHHHHHHhhccCcceeeecc------cCCcceeeecccCc-cchhhHHHHhcCcCCCCCccc
Confidence            34456789999999999999999999999999986542      22459999999888 999999999999 887  779


Q ss_pred             EEEecccc
Q psy8615         116 KPSFNTYV  123 (128)
Q Consensus       116 ~V~~~~~~  123 (128)
                      .|.|...+
T Consensus       524 rvdla~~~  531 (975)
T KOG0112|consen  524 RVDLASPP  531 (975)
T ss_pred             ccccccCC
Confidence            99998754

>KOG0128|consensus

Probab=97.38  E-value=7.1e-05  Score=61.73  Aligned_cols=78  Identities=10%  Similarity=0.034  Sum_probs=69.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecc
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNT  121 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~  121 (128)
                      ...++|.|.|+..|.+.++.++..+|.+.+.+++..+. |+.+|-+||.|.... ++.++....+.. +.-+.+.|+.++
T Consensus       736 K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~-gkpkg~a~v~y~~ea-~~s~~~~s~d~~~~rE~~~~v~vsn  813 (881)
T KOG0128|consen  736 KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRA-GKPKGKARVDYNTEA-DASRKVASVDVAGKRENNGEVQVSN  813 (881)
T ss_pred             hhhhheeCCCCCCchHHHHhhccccCCccccchhhhhc-cccccceeccCCCcc-hhhhhcccchhhhhhhcCccccccC
Confidence            35789999999999999999999999999999888887 999999999997666 899898888887 777778888866


Q ss_pred             c
Q psy8615         122 Y  122 (128)
Q Consensus       122 ~  122 (128)
                      |
T Consensus       814 p  814 (881)
T KOG0128|consen  814 P  814 (881)
T ss_pred             C
Confidence            5

>KOG1365|consensus

Probab=97.38  E-value=0.00035  Score=53.46  Aligned_cols=73  Identities=15%  Similarity=0.223  Sum_probs=56.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCC----CceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCcCCCeEEEE
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPF----GTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDYLGQSFLKP  117 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~----G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~~~~~~l~V  117 (128)
                      .-.|-+.+||+++++.++.++|.+-    |....+-++..++ |+..|-|||.|...+ +|..|+.+-.+.+|.|.|++
T Consensus       161 qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpd-grpTGdAFvlfa~ee-~aq~aL~khrq~iGqRYIEl  237 (508)
T KOG1365|consen  161 QVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPD-GRPTGDAFVLFACEE-DAQFALRKHRQNIGQRYIEL  237 (508)
T ss_pred             ceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCC-CCcccceEEEecCHH-HHHHHHHHHHHHHhHHHHHH
Confidence            3356788999999999999999742    3455666676665 999999999996665 99999988766677766543

>KOG0128|consensus

Probab=97.36  E-value=1.6e-05  Score=65.45  Aligned_cols=67  Identities=22%  Similarity=0.418  Sum_probs=59.0

Q ss_pred             CeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CC
Q psy8615          44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LG  111 (128)
Q Consensus        44 ~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~  111 (128)
                      +++||+||+..+.+++|...|+++|.+..+++......++.||.|+++|..+. ++.+|+...++. +|
T Consensus       668 ~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~-~~~aaV~f~d~~~~g  735 (881)
T KOG0128|consen  668 IKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPE-HAGAAVAFRDSCFFG  735 (881)
T ss_pred             HHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCC-chhhhhhhhhhhhhh
Confidence            57899999999999999999999998888776666677999999999998888 999999888876 44

>KOG1548|consensus

Probab=97.31  E-value=0.00093  Score=50.41  Aligned_cols=72  Identities=19%  Similarity=0.206  Sum_probs=55.1

Q ss_pred             CCeEEEcCC--C--CCCC-------HHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-C
Q psy8615          43 GANLFIYHL--P--PEFS-------DADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-L  110 (128)
Q Consensus        43 ~~~l~V~nL--p--~~~~-------e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~  110 (128)
                      .++|.+.|+  |  +..+       +++|++--++||.|+++.+ .|   .++.|.+-|.|.+++ +|..||+.|+|. +
T Consensus       265 ~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv-~d---~hPdGvvtV~f~n~e-eA~~ciq~m~GR~f  339 (382)
T KOG1548|consen  265 DRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVV-YD---RHPDGVVTVSFRNNE-EADQCIQTMDGRWF  339 (382)
T ss_pred             CcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEE-ec---cCCCceeEEEeCChH-HHHHHHHHhcCeee
Confidence            467778887  2  2344       3456666789999999864 44   355789999998887 999999999999 9


Q ss_pred             CCeEEEEEe
Q psy8615         111 GQSFLKPSF  119 (128)
Q Consensus       111 ~~~~l~V~~  119 (128)
                      +||.|..+.
T Consensus       340 dgRql~A~i  348 (382)
T KOG1548|consen  340 DGRQLTASI  348 (382)
T ss_pred             cceEEEEEE
Confidence            999987654

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

Probab=97.30  E-value=0.00051  Score=38.32  Aligned_cols=52  Identities=13%  Similarity=0.245  Sum_probs=38.8

Q ss_pred             CeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHH
Q psy8615          44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRF  103 (128)
Q Consensus        44 ~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai  103 (128)
                      +.|-|.+.+.+..+..|+ .|..||+|.+..+...      .-+.++.|.+.. +|++|+
T Consensus         2 ~wI~V~Gf~~~~~~~vl~-~F~~fGeI~~~~~~~~------~~~~~l~y~~~~-~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEEVLE-HFASFGEIVDIYVPES------TNWMYLKYKSRK-DAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHHHHH-HHHhcCCEEEEEcCCC------CcEEEEEECCHH-HHHhhC
Confidence            346677888777766555 7888999999876522      348999998777 888874

>KOG1365|consensus

Probab=97.25  E-value=0.0011  Score=50.84  Aligned_cols=74  Identities=12%  Similarity=0.119  Sum_probs=60.5

Q ss_pred             eEEEcCCCCCCCHHHHHhhhcCCC-ceEE--EEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          45 NLFIYHLPPEFSDADLASMFGPFG-TVLS--AKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        45 ~l~V~nLp~~~~e~~l~~~f~~~G-~i~~--~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      .|-+.+||++.+.+++-++|..|. .|+.  ++++...+ |+..|-|||+|.+.+ +|..|....+.. ...+.|+|--.
T Consensus       282 cvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~q-GrPSGeAFIqm~nae-~a~aaaqk~hk~~mk~RYiEvfp~  359 (508)
T KOG1365|consen  282 CVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNGQ-GRPSGEAFIQMRNAE-RARAAAQKCHKKLMKSRYIEVFPC  359 (508)
T ss_pred             eeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcCC-CCcChhhhhhhhhhH-HHHHHHHHHHHhhcccceEEEeec
Confidence            566889999999999999999885 3333  77788877 999999999996665 999999999888 55788887543

>KOG1996|consensus

Probab=97.14  E-value=0.0013  Score=48.83  Aligned_cols=63  Identities=13%  Similarity=0.075  Sum_probs=50.2

Q ss_pred             HHHHhhhcCCCceEEEEEEecCCCCCcc-eEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecc
Q psy8615          58 ADLASMFGPFGTVLSAKVFIDKQNNRSK-CFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNT  121 (128)
Q Consensus        58 ~~l~~~f~~~G~i~~~~~~~~~~tg~~~-g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~  121 (128)
                      ++.++..++||.|..|-+..++.--..+ ---||+|++.+ .|.+|+-.|||. +||+..+.+|-+
T Consensus       301 de~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e-~aiKA~VdlnGRyFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  301 DETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVE-SAIKAVVDLNGRYFGGRVVSACFYN  365 (378)
T ss_pred             HHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHH-HHHHHHHhcCCceecceeeeheecc
Confidence            4566778899999999887776433333 34699997777 999999999999 999999988754

>KOG0129|consensus

Probab=97.09  E-value=0.0035  Score=49.54  Aligned_cols=53  Identities=21%  Similarity=0.355  Sum_probs=38.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCC-C--CCcce---EEEEEEecCH
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQ-N--NRSKC---FGTIIFMRKF   96 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~-t--g~~~g---~~fv~f~~~~   96 (128)
                      .++||||+||++++|+.|...|..||.+. +.+..... .  -..+|   |.|..|++..
T Consensus       259 S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~  317 (520)
T KOG0129|consen  259 SRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDER  317 (520)
T ss_pred             ccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchH
Confidence            56899999999999999999999999753 34432111 0  22356   9999995544

>KOG2253|consensus

Probab=97.05  E-value=0.00068  Score=54.79  Aligned_cols=69  Identities=17%  Similarity=0.089  Sum_probs=57.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      .+...++||+|+...+.++-++.++..||.|.+++...         |||+.|.... ...+|+..++.. ++|+-|.+.
T Consensus        37 ~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~-~~~ra~r~~t~~~~~~~kl~~~  106 (668)
T KOG2253|consen   37 LPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHI-GDLRASRLLTELNIDDQKLIEN  106 (668)
T ss_pred             CCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHH-HHHHHHHHhcccCCCcchhhcc
Confidence            34466899999999999999999999999998875432         9999998777 888899999988 877665443

>KOG2193|consensus

Probab=97.03  E-value=0.0006  Score=52.82  Aligned_cols=70  Identities=17%  Similarity=0.145  Sum_probs=54.2

Q ss_pred             CeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc--CCCeEEEEEec
Q psy8615          44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY--LGQSFLKPSFN  120 (128)
Q Consensus        44 ~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~--~~~~~l~V~~~  120 (128)
                      .++|++||.+..+..+|+.+|...-      +......-...||+||.+.+.. .|.+|++.++|.  +.|+.+.|.+.
T Consensus         2 nklyignL~p~~~psdl~svfg~ak------~~~~g~fl~k~gyafvd~pdq~-wa~kaie~~sgk~elqGkr~e~~~s   73 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAK------IPGSGQFLVKSGYAFVDCPDQQ-WANKAIETLSGKVELQGKRQEVEHS   73 (584)
T ss_pred             CcccccccCCCCChHHHHHHhcccc------CCCCcceeeecceeeccCCchh-hhhhhHHhhchhhhhcCceeeccch
Confidence            3689999999999999999998541      1111111123679999997666 999999999998  99999988764

>KOG2068|consensus

Probab=97.00  E-value=0.0003  Score=52.72  Aligned_cols=79  Identities=19%  Similarity=0.279  Sum_probs=59.1

Q ss_pred             CeEEEcCCCCCCCHHH-HH--hhhcCCCceEEEEEEecCC--CCCc-ceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEE
Q psy8615          44 ANLFIYHLPPEFSDAD-LA--SMFGPFGTVLSAKVFIDKQ--NNRS-KCFGTIIFMRKFFILTIRFDTANDY-LGQSFLK  116 (128)
Q Consensus        44 ~~l~V~nLp~~~~e~~-l~--~~f~~~G~i~~~~~~~~~~--tg~~-~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~  116 (128)
                      ..+||-+|+....++. |+  +.|++||.|.++....++.  .+.. ..-++|.|+..+ +|..||...+|+ +.|+.|+
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~e-da~rci~~v~g~~~dg~~lk  156 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEE-DADRCIDDVDGFVDDGRALK  156 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchH-hhhhHHHHhhhHHhhhhhhH
Confidence            3568888887765544 44  6688999999988777662  1221 123799996655 999999999999 9999999


Q ss_pred             EEecccc
Q psy8615         117 PSFNTYV  123 (128)
Q Consensus       117 V~~~~~~  123 (128)
                      .++++..
T Consensus       157 a~~gttk  163 (327)
T KOG2068|consen  157 ASLGTTK  163 (327)
T ss_pred             HhhCCCc
Confidence            9988754

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

Probab=96.93  E-value=0.0041  Score=41.73  Aligned_cols=58  Identities=16%  Similarity=0.127  Sum_probs=39.6

Q ss_pred             HHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEeccccccc
Q psy8615          59 DLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNTYVLMN  126 (128)
Q Consensus        59 ~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~~~~~~  126 (128)
                      +|-+.|..||.+.-++++-+        --+|+|.+.. .|.+| -.++|. ++|+.|+|+.|++--++
T Consensus        52 ~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~-sALaa-ls~dg~~v~g~~l~i~LKtpdW~~  110 (146)
T PF08952_consen   52 ELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQ-SALAA-LSLDGIQVNGRTLKIRLKTPDWLK  110 (146)
T ss_dssp             HHHHHHHCCS-ECEEEEETT--------CEEEEESSCH-HHHHH-HHGCCSEETTEEEEEEE-------
T ss_pred             HHHHHHHhCCceEEEEEeCC--------eEEEEECccH-HHHHH-HccCCcEECCEEEEEEeCCccHHH
Confidence            56677889999988887754        4589997776 77755 567777 99999999999987654

; PDB: 1UFW_A 2DNR_A.

>KOG4307|consensus

Probab=96.92  E-value=0.0017  Score=53.06  Aligned_cols=77  Identities=10%  Similarity=0.115  Sum_probs=63.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEE-EEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLS-AKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~-~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      .-+..|||-.||..+++.++.++|..--.|.+ |.+.+.+. ++.++.|||.|-... .+..|...-+.+ +|.+.|+|.
T Consensus       432 ~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P~-~~~~~~afv~F~~~~-a~~~a~~~~~k~y~G~r~irv~  509 (944)
T KOG4307|consen  432 GAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLPT-DLLRPAAFVAFIHPT-APLTASSVKTKFYPGHRIIRVD  509 (944)
T ss_pred             CccceEEeccCCccccccchhhhhhhhhhhhheeEeccCCc-ccccchhhheecccc-ccchhhhcccccccCceEEEee
Confidence            34668999999999999999999998777766 77766664 888999999996655 777777777777 999999986


Q ss_pred             e
Q psy8615         119 F  119 (128)
Q Consensus       119 ~  119 (128)
                      -
T Consensus       510 s  510 (944)
T KOG4307|consen  510 S  510 (944)
T ss_pred             c
Confidence            4

>KOG0129|consensus

Probab=96.79  E-value=0.0046  Score=48.87  Aligned_cols=62  Identities=21%  Similarity=0.292  Sum_probs=53.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhc-CCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHH
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFG-PFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFD  104 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~-~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~  104 (128)
                      ...+||||+||.-++.++|-.+|+ -||.|.-+.|-.|++-...+|-|-|.|++.. .=.+||.
T Consensus       369 prrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqq-sYi~AIs  431 (520)
T KOG0129|consen  369 PRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQ-AYIKAIS  431 (520)
T ss_pred             ccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccH-HHHHHHh
Confidence            356899999999999999999999 7999999999999777899999999996665 4445554

>KOG0115|consensus

Probab=96.75  E-value=0.0019  Score=46.97  Aligned_cols=63  Identities=21%  Similarity=0.265  Sum_probs=55.5

Q ss_pred             CeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcC
Q psy8615          44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTAND  108 (128)
Q Consensus        44 ~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g  108 (128)
                      ..|||.||+.-++.+.+...|+.||+|.+.-+..|.. ++..+-++|.|.... .+..|....+-
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r-~k~t~eg~v~~~~k~-~a~~a~rr~~~   94 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDR-GKPTREGIVEFAKKP-NARKAARRCRE   94 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeeccc-ccccccchhhhhcch-hHHHHHHHhcc
Confidence            6799999999999999999999999999877777765 899999999998888 88888887753

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

Probab=96.63  E-value=0.031  Score=34.11  Aligned_cols=53  Identities=17%  Similarity=0.376  Sum_probs=39.1

Q ss_pred             eEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhc
Q psy8615          45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTAN  107 (128)
Q Consensus        45 ~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~  107 (128)
                      ..|++ .|.++...||..+|++||.|. |.++.|.       -|||...+.+ .+..++..+.
T Consensus        11 VFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~dT-------SAfV~l~~r~-~~~~v~~~~~   63 (87)
T PF08675_consen   11 VFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWINDT-------SAFVALHNRD-QAKVVMNTLK   63 (87)
T ss_dssp             EEEEE---TT--HHHHHHHCCCCCCEE-EEEECTT-------EEEEEECCCH-HHHHHHHHHT
T ss_pred             EEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcCC-------cEEEEeecHH-HHHHHHHHhc
Confidence            45564 999999999999999999864 5666664       6999998888 8888887776

; 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.

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

Probab=96.28  E-value=0.022  Score=32.77  Aligned_cols=56  Identities=13%  Similarity=0.176  Sum_probs=43.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCC---CceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHh
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPF---GTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTA  106 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~---G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l  106 (128)
                      ...+|+|.+++ +.+.++++.+|..|   ....+++++.|..       |-|.|.+.. .|.+|+.+|
T Consensus         4 rpeavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDtS-------cNvvf~d~~-~A~~AL~~L   62 (62)
T PF10309_consen    4 RPEAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDTS-------CNVVFKDEE-TAARALVAL   62 (62)
T ss_pred             eeceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCCc-------EEEEECCHH-HHHHHHHcC
Confidence            45689999985 47888899999887   2457889998863       568897777 999998764

>KOG2202|consensus

Probab=96.23  E-value=0.0016  Score=47.24  Aligned_cols=61  Identities=10%  Similarity=0.075  Sum_probs=45.6

Q ss_pred             HHHHhhhc-CCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          58 ADLASMFG-PFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        58 ~~l~~~f~-~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      +++...|+ +||+|.++.+ .+...-...|-.+|.|. .+++|++|++.||+. ++|++|...+.
T Consensus        83 Ed~f~E~~~kygEiee~~V-c~Nl~~hl~GNVYV~f~-~Ee~ae~a~~~lnnRw~~G~pi~ae~~  145 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNV-CDNLGDHLVGNVYVKFR-SEEDAEAALEDLNNRWYNGRPIHAELS  145 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhh-hcccchhhhhhhhhhcc-cHHHHHHHHHHHcCccccCCcceeeec
Confidence            34555555 8999998754 33332455899999995 455999999999998 99999876654

>KOG2416|consensus

Probab=95.83  E-value=0.0081  Score=48.44  Aligned_cols=76  Identities=16%  Similarity=0.119  Sum_probs=58.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcC-CCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc----CCCeE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGP-FGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY----LGQSF  114 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~-~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~----~~~~~  114 (128)
                      ......|||.||-.-.|.-+|+.++++ +|.|.+. ++ |    +.+..|||.|.+. ++|..-+.+|||.    -+.|.
T Consensus       441 ~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~-Wm-D----kIKShCyV~yss~-eEA~atr~AlhnV~WP~sNPK~  513 (718)
T KOG2416|consen  441 KEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF-WM-D----KIKSHCYVSYSSV-EEAAATREALHNVQWPPSNPKH  513 (718)
T ss_pred             CCccceEeeecccccchHHHHHHHHhhccCchHHH-HH-H----HhhcceeEecccH-HHHHHHHHHHhccccCCCCCce
Confidence            344568999999999999999999995 5555554 22 3    3477999999554 4999999999996    34588


Q ss_pred             EEEEeccc
Q psy8615         115 LKPSFNTY  122 (128)
Q Consensus       115 l~V~~~~~  122 (128)
                      |.+.|.+.
T Consensus       514 L~adf~~~  521 (718)
T KOG2416|consen  514 LIADFVRA  521 (718)
T ss_pred             eEeeecch
Confidence            99999764

>KOG0105|consensus

Probab=95.60  E-value=0.052  Score=38.06  Aligned_cols=59  Identities=25%  Similarity=0.260  Sum_probs=51.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY  109 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~  109 (128)
                      ..++.|.+||.+-++++|++....-|.|....+.+|       |.+.|+|-..+ +.+-|+..|+..
T Consensus       115 e~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-------g~GvV~~~r~e-DMkYAvr~ld~~  173 (241)
T KOG0105|consen  115 EYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-------GVGVVEYLRKE-DMKYAVRKLDDQ  173 (241)
T ss_pred             ceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-------cceeeeeeehh-hHHHHHHhhccc
Confidence            357899999999999999999999999998887766       37889997777 999999998874

>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=95.37  E-value=0.069  Score=33.66  Aligned_cols=77  Identities=13%  Similarity=0.188  Sum_probs=45.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecC-------CCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCe-
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDK-------QNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQS-  113 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~-------~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~-  113 (128)
                      .+-|.|-+.|.. ....+-..|++||.|.+..-....       .......+-.+.|+++. +|.+|+.. ||. ++|. 
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~-~A~rAL~~-NG~i~~g~~   82 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPL-SAQRALQK-NGTIFSGSL   82 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHH-HHHHHHTT-TTEEETTCE
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHH-HHHHHHHh-CCeEEcCcE
Confidence            445677788888 445566779999999876410000       00122447889998877 99999764 566 7765 


Q ss_pred             EEEEEeccc
Q psy8615         114 FLKPSFNTY  122 (128)
Q Consensus       114 ~l~V~~~~~  122 (128)
                      .+.|.+-++
T Consensus        83 mvGV~~~~~   91 (100)
T PF05172_consen   83 MVGVKPCDP   91 (100)
T ss_dssp             EEEEEE-HH
T ss_pred             EEEEEEcHH
Confidence            456777643

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.

>KOG0112|consensus

Probab=95.29  E-value=0.0038  Score=52.23  Aligned_cols=77  Identities=9%  Similarity=0.178  Sum_probs=62.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      ...+||+|||+..+++.+++..|..+|.+.++.+-...- +.-.-|+|+.|.... .+-.|...+.+. ++.-.+++-+.
T Consensus       371 atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~-~~esa~~f~~~~n~d-mtp~ak~e~s~~~I~~g~~r~glG  448 (975)
T KOG0112|consen  371 ATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHI-KTESAYAFVSLLNTD-MTPSAKFEESGPLIGNGTHRIGLG  448 (975)
T ss_pred             hhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCC-Ccccchhhhhhhccc-cCcccchhhcCCccccCccccccc
Confidence            356899999999999999999999999999988765543 444569999998877 777888888887 66666666665

>KOG4676|consensus

Probab=95.05  E-value=0.053  Score=41.92  Aligned_cols=77  Identities=9%  Similarity=0.229  Sum_probs=57.0

Q ss_pred             eEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecC---CCCCcceEEEEEEecCHHHHHHHHHHhcCc--CCCeEEEEEe
Q psy8615          45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDK---QNNRSKCFGTIIFMRKFFILTIRFDTANDY--LGQSFLKPSF  119 (128)
Q Consensus        45 ~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~---~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~--~~~~~l~V~~  119 (128)
                      .|.|.||.+.++.++++.+|+-.|.|..+++....   ......-.|||-|.+.. .+. +-++|..+  ++.-.|.+-|
T Consensus         9 vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~-sv~-vaQhLtntvfvdraliv~p~   86 (479)
T KOG4676|consen    9 VIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQ-SVT-VAQHLTNTVFVDRALIVRPY   86 (479)
T ss_pred             eeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCc-cee-HHhhhccceeeeeeEEEEec
Confidence            78999999999999999999999999998875422   11334558999997776 555 55777776  5555556666


Q ss_pred             cccc
Q psy8615         120 NTYV  123 (128)
Q Consensus       120 ~~~~  123 (128)
                      ...+
T Consensus        87 ~~~~   90 (479)
T KOG4676|consen   87 GDEV   90 (479)
T ss_pred             CCCC
Confidence            5544

>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=94.69  E-value=0.14  Score=35.55  Aligned_cols=68  Identities=18%  Similarity=0.172  Sum_probs=42.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcC-CCce---EEEEEEecCCCCC--cceEEEEEEecCHHHHHHHHHHhcCc
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGP-FGTV---LSAKVFIDKQNNR--SKCFGTIIFMRKFFILTIRFDTANDY  109 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~-~G~i---~~~~~~~~~~tg~--~~g~~fv~f~~~~~~a~~Ai~~l~g~  109 (128)
                      ..+++|-|++||+.++|+++.+.+++ ++.-   ..+....+..+-+  ...-||+.|.+.+ +...=.+.++|+
T Consensus         5 ~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~-~~~~F~~~~~g~   78 (176)
T PF03467_consen    5 KEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPE-DLLEFRDRFDGH   78 (176)
T ss_dssp             ----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCH-HHHHHHHHCTTE
T ss_pred             ccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHH-HHHHHHHhcCCc
Confidence            34679999999999999999998887 5544   3333223222222  2456899997777 888888889986

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

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

Probab=94.49  E-value=0.14  Score=35.86  Aligned_cols=62  Identities=10%  Similarity=0.021  Sum_probs=42.6

Q ss_pred             CHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhc--Cc-CCCeEEEEEeccccc
Q psy8615          56 SDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTAN--DY-LGQSFLKPSFNTYVL  124 (128)
Q Consensus        56 ~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~--g~-~~~~~l~V~~~~~~~  124 (128)
                      ....|+++|..|+.+........      -+-..|.|.+.+ .|.+|...++  +. +.|+.+++-|+....
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s------FrRi~v~f~~~~-~A~~~r~~l~~~~~~~~g~~l~~yf~~~~~   72 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS------FRRIRVVFESPE-SAQRARQLLHWDGTSFNGKRLRVYFGQPTP   72 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT------TTEEEEE-SSTT-HHHHHHHTST--TSEETTEE-EEE----SS
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC------CCEEEEEeCCHH-HHHHHHHHhcccccccCCCceEEEEccccc
Confidence            34789999999998887765533      235678998888 9999999999  88 999999999986543

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

Probab=94.43  E-value=0.12  Score=41.68  Aligned_cols=73  Identities=8%  Similarity=0.056  Sum_probs=56.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhc--CCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc---CCCeEE
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFG--PFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY---LGQSFL  115 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~--~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~---~~~~~l  115 (128)
                      .+.|.+.+.-||..+-.|+++.+|.  .|..+.+|.+-...       -=||+|++.. ||+.|...|...   +-||+|
T Consensus       173 ~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~-------nWyITfesd~-DAQqAykylreevk~fqgKpI  244 (684)
T KOG2591|consen  173 HKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND-------NWYITFESDT-DAQQAYKYLREEVKTFQGKPI  244 (684)
T ss_pred             cceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC-------ceEEEeecch-hHHHHHHHHHHHHHhhcCcch
Confidence            3457788999999999999999997  47788888764432       1279997776 999999888764   888887


Q ss_pred             EEEecc
Q psy8615         116 KPSFNT  121 (128)
Q Consensus       116 ~V~~~~  121 (128)
                      ...+|.
T Consensus       245 mARIKa  250 (684)
T KOG2591|consen  245 MARIKA  250 (684)
T ss_pred             hhhhhh
Confidence            666553

>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=94.43  E-value=0.38  Score=28.34  Aligned_cols=64  Identities=11%  Similarity=0.158  Sum_probs=36.8

Q ss_pred             eEEEcCC--CCCCCHHHHHhhhcCCC-----ceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEE
Q psy8615          45 NLFIYHL--PPEFSDADLASMFGPFG-----TVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLK  116 (128)
Q Consensus        45 ~l~V~nL--p~~~~e~~l~~~f~~~G-----~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~  116 (128)
                      ++|| |+  -..++..+|..++..-+     .|-.+++...        |.||+- ..+ .+...++.|++. +.|+.++
T Consensus         2 rl~i-n~Gr~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~~--------~S~vev-~~~-~a~~v~~~l~~~~~~gk~v~   70 (74)
T PF03880_consen    2 RLFI-NVGRKDGLTPRDIVGAICNEAGIPGRDIGRIDIFDN--------FSFVEV-PEE-VAEKVLEALNGKKIKGKKVR   70 (74)
T ss_dssp             EEEE-S-SGGGT--HHHHHHHHHTCTTB-GGGEEEEEE-SS---------EEEEE--TT--HHHHHHHHTT--SSS----
T ss_pred             EEEE-EcccccCCCHHHHHHHHHhccCCCHHhEEEEEEeee--------EEEEEE-CHH-HHHHHHHHhcCCCCCCeeEE
Confidence            4555 33  34678888888887654     3445554322        889998 455 799999999999 9999999


Q ss_pred             EEe
Q psy8615         117 PSF  119 (128)
Q Consensus       117 V~~  119 (128)
                      |..
T Consensus        71 ve~   73 (74)
T PF03880_consen   71 VER   73 (74)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            874

; PDB: 2G0C_A 3MOJ_B.

>KOG2135|consensus

Probab=94.38  E-value=0.021  Score=44.96  Aligned_cols=73  Identities=18%  Similarity=0.213  Sum_probs=52.7

Q ss_pred             CeEEEcCCCCCCCH-HHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecc
Q psy8615          44 ANLFIYHLPPEFSD-ADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNT  121 (128)
Q Consensus        44 ~~l~V~nLp~~~~e-~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~  121 (128)
                      +.|-+.-.|+.... .+|..-|.+||.|..|.+-+...      .|.|+|.+.. +|-.| ...++. |.++.|||.|.|
T Consensus       373 s~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~~~------~a~vTF~t~a-eag~a-~~s~~avlnnr~iKl~whn  444 (526)
T KOG2135|consen  373 SPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYSSL------HAVVTFKTRA-EAGEA-YASHGAVLNNRFIKLFWHN  444 (526)
T ss_pred             chhhhhccCCCCchHhhhhhhhhhcCccccccccCchh------hheeeeeccc-cccch-hccccceecCceeEEEEec
Confidence            33444445555444 68999999999999998755533      6789997776 66445 345556 999999999999


Q ss_pred             ccc
Q psy8615         122 YVL  124 (128)
Q Consensus       122 ~~~  124 (128)
                      +..
T Consensus       445 ps~  447 (526)
T KOG2135|consen  445 PSP  447 (526)
T ss_pred             CCc
Confidence            853

>KOG4574|consensus

Probab=94.27  E-value=0.024  Score=47.46  Aligned_cols=74  Identities=16%  Similarity=0.185  Sum_probs=60.3

Q ss_pred             eEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc---CCCeEEEEEecc
Q psy8615          45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY---LGQSFLKPSFNT  121 (128)
Q Consensus        45 ~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~---~~~~~l~V~~~~  121 (128)
                      +.++.|.+-..+...|..+++.||.+.+....+|-.      .+.|+|...+ .|..|.+.++|+   .-|-+-+|.|++
T Consensus       300 ~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~N------~alvs~~s~~-sai~a~dAl~gkevs~~g~Ps~V~~ak  372 (1007)
T KOG4574|consen  300 KQSLENNAVNLTSSSLATLCSDYGSVASAWTLRDLN------MALVSFSSVE-SAILALDALQGKEVSVTGAPSRVSFAK  372 (1007)
T ss_pred             hhhhhcccccchHHHHHHHHHhhcchhhheeccccc------chhhhhHHHH-HHHHhhhhhcCCcccccCCceeEEecc
Confidence            345556666788889999999999999988777754      7899996666 999999999997   566678999998


Q ss_pred             cccc
Q psy8615         122 YVLM  125 (128)
Q Consensus       122 ~~~~  125 (128)
                      ...|
T Consensus       373 ~~~~  376 (1007)
T KOG4574|consen  373 TLPM  376 (1007)
T ss_pred             cccc
Confidence            7665

>KOG2193|consensus

Probab=93.79  E-value=0.0023  Score=49.69  Aligned_cols=73  Identities=18%  Similarity=0.260  Sum_probs=59.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEE-EecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKV-FIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~-~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      .+++-+.|+|+...++.|..++..||.+..|.. ..|++|-.-    -|.|...+ .+..||++++|. +.+..++|.|-
T Consensus        80 srk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~etavv----nvty~~~~-~~~~ai~kl~g~Q~en~~~k~~Yi  154 (584)
T KOG2193|consen   80 SRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSETAVV----NVTYSAQQ-QHRQAIHKLNGPQLENQHLKVGYI  154 (584)
T ss_pred             hhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchHHHHH----HHHHHHHH-HHHHHHHhhcchHhhhhhhhcccC
Confidence            457889999999999999999999999998864 445543322    26775666 999999999999 99988888873

>KOG4660|consensus

Probab=93.37  E-value=0.18  Score=40.44  Aligned_cols=55  Identities=13%  Similarity=0.023  Sum_probs=42.1

Q ss_pred             CCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-----CCCeEEEEEeccc
Q psy8615          67 FGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-----LGQSFLKPSFNTY  122 (128)
Q Consensus        67 ~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-----~~~~~l~V~~~~~  122 (128)
                      .|.-..+.++.|..+-.+-|||||-|-+++ .+....++.||+     ...|+.++.|++-
T Consensus       413 ~gtYDFlYLPiDF~nkcNvGYAFINm~sp~-ai~~F~kAFnGk~W~~FnS~Kia~itYArI  472 (549)
T KOG4660|consen  413 KGTYDFLYLPIDFKNKCNVGYAFINMTSPE-AIIRFYKAFNGKKWEKFNSEKIASITYARI  472 (549)
T ss_pred             cCccceEEeccccccccccceeEEeecCHH-HHHHHHHHHcCCchhhhcceeeeeeehhhh
Confidence            344455677788776677899999997777 888899999995     3458888888753

>KOG4210|consensus

Probab=92.99  E-value=0.045  Score=40.83  Aligned_cols=81  Identities=14%  Similarity=0.092  Sum_probs=64.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      ..+++|++++.+...+.....++..+|...............++|++.+.|...+ .+..++.....+ +.+..+...++
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks-~~~~~l~~s~~~~~~~~~~~~dl~  165 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKS-QFFAALEESGSKVLDGNKGEKDLN  165 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHH-HHHHHHHhhhccccccccccCccc
Confidence            3678999999999999988888999998888877776677889999999997777 888787777665 66655555555


Q ss_pred             ccc
Q psy8615         121 TYV  123 (128)
Q Consensus       121 ~~~  123 (128)
                      +..
T Consensus       166 ~~~  168 (285)
T KOG4210|consen  166 TRR  168 (285)
T ss_pred             ccc
Confidence            443

>KOG4285|consensus

Probab=91.30  E-value=2.4  Score=31.98  Aligned_cols=63  Identities=10%  Similarity=0.210  Sum_probs=40.8

Q ss_pred             EcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCcCCCeE-EEEE
Q psy8615          48 IYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDYLGQSF-LKPS  118 (128)
Q Consensus        48 V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~~~~~~-l~V~  118 (128)
                      |-+.|+.-..- +-..|++||.|.+...      +...-|-+|.|+... +|.+|+..-...++|.. |.|.
T Consensus       202 VfGFppg~~s~-vL~~F~~cG~Vvkhv~------~~ngNwMhirYssr~-~A~KALskng~ii~g~vmiGVk  265 (350)
T KOG4285|consen  202 VFGFPPGQVSI-VLNLFSRCGEVVKHVT------PSNGNWMHIRYSSRT-HAQKALSKNGTIIDGDVMIGVK  265 (350)
T ss_pred             EeccCccchhH-HHHHHHhhCeeeeeec------CCCCceEEEEecchh-HHHHhhhhcCeeeccceEEeee
Confidence            44556554443 4567999999987432      222348899998888 99999876443366644 4443

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=91.29  E-value=0.85  Score=30.77  Aligned_cols=73  Identities=12%  Similarity=0.196  Sum_probs=50.0

Q ss_pred             CCCCCeEEEcCCCCCCCH-HHHH---hhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCcCCCeEE
Q psy8615          40 GPEGANLFIYHLPPEFSD-ADLA---SMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDYLGQSFL  115 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e-~~l~---~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~~~~~~l  115 (128)
                      ++.-.+|.|.=|..++.. +|++   ..++.||+|.++..-     |  +--|.|.|.+.. .|-.|+.+++...-|..+
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c-----G--rqsavVvF~d~~-SAC~Av~Af~s~~pgtm~  154 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC-----G--RQSAVVVFKDIT-SACKAVSAFQSRAPGTMF  154 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec-----C--CceEEEEehhhH-HHHHHHHhhcCCCCCceE
Confidence            455567778777666443 4444   557789999997532     2  236889998777 888899988887555566


Q ss_pred             EEEec
Q psy8615         116 KPSFN  120 (128)
Q Consensus       116 ~V~~~  120 (128)
                      .-+|-
T Consensus       155 qCsWq  159 (166)
T PF15023_consen  155 QCSWQ  159 (166)
T ss_pred             Eeecc
Confidence            66553

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=88.14  E-value=2.7  Score=24.40  Aligned_cols=55  Identities=11%  Similarity=0.063  Sum_probs=39.7

Q ss_pred             CCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEE
Q psy8615          53 PEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKP  117 (128)
Q Consensus        53 ~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V  117 (128)
                      ..++-++++..+..|+-. +  +..|+ ||    | ||.|.+.. +|+++....+|. +.+..|.+
T Consensus        10 ~~~~v~d~K~~Lr~y~~~-~--I~~d~-tG----f-YIvF~~~~-Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   10 HGVTVEDFKKRLRKYRWD-R--IRDDR-TG----F-YIVFNDSK-EAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CCccHHHHHHHHhcCCcc-e--EEecC-CE----E-EEEECChH-HHHHHHHhcCCCEEEEEEEEe
Confidence            357778999999999743 2  33443 23    2 79997777 999999999998 76665543

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

>KOG4454|consensus

Probab=85.88  E-value=0.17  Score=36.44  Aligned_cols=83  Identities=19%  Similarity=0.224  Sum_probs=61.8

Q ss_pred             CCCeEEEcC----CCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcC---------
Q psy8615          42 EGANLFIYH----LPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTAND---------  108 (128)
Q Consensus        42 ~~~~l~V~n----Lp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g---------  108 (128)
                      ...+++.|+    |...++++.+...|+.-|++..+++..+.. |+++-++|+.+...+ ..-.+.....+         
T Consensus        79 ~q~~~r~G~shapld~r~~~ei~~~v~s~a~p~~~~R~~~~~d-~rnrn~~~~~~qr~~-~~P~~~~~y~~l~~~~~~~~  156 (267)
T KOG4454|consen   79 EQRTLRCGNSHAPLDERVTEEILYEVFSQAGPIEGVRIPTDND-GRNRNFGFVTYQRLC-AVPFALDLYQGLELFQKKVT  156 (267)
T ss_pred             hhcccccCCCcchhhhhcchhhheeeecccCCCCCcccccccc-CCccCccchhhhhhh-cCcHHhhhhcccCcCCCCcc
Confidence            356778888    888999999999999999999999988877 899999999986655 44445555443         


Q ss_pred             ---cCCCeEEEEEeccccccc
Q psy8615         109 ---YLGQSFLKPSFNTYVLMN  126 (128)
Q Consensus       109 ---~~~~~~l~V~~~~~~~~~  126 (128)
                         +.||++|--++.+|+..|
T Consensus       157 ~ggk~Gg~~lpqsgfsPs~~~  177 (267)
T KOG4454|consen  157 IGGKQGGKQLPQSGFSPSAYN  177 (267)
T ss_pred             cccccCCCcCCcccCCccccc
Confidence               145566665665555443

>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=80.59  E-value=12  Score=23.86  Aligned_cols=64  Identities=14%  Similarity=0.088  Sum_probs=44.0

Q ss_pred             CCeEE-EcCCCCCCCHHHHHhhhcCC-CceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc
Q psy8615          43 GANLF-IYHLPPEFSDADLASMFGPF-GTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY  109 (128)
Q Consensus        43 ~~~l~-V~nLp~~~~e~~l~~~f~~~-G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~  109 (128)
                      ++.+. +...|.-++-++|..+.+++ ..|..+++++|..  .++-...+.|.+.. .|..=.+.+||.
T Consensus        12 ~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~--pnrymVLikF~~~~-~Ad~Fy~~fNGk   77 (110)
T PF07576_consen   12 RSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGT--PNRYMVLIKFRDQE-SADEFYEEFNGK   77 (110)
T ss_pred             CceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCC--CceEEEEEEECCHH-HHHHHHHHhCCC
Confidence            34444 43445556666776666665 4567788888753  35667899997776 888888999996

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	128
2cpz_A	115	Solution Structure Of Rna Binding Domain 3 In Cug T		1e-20
2khc_A	118	Bruno Rrm3+ Length = 118		6e-20
2d9p_A	103	Solution Structure Of Rna Binding Domain 4 In Polya		5e-06
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		2e-05
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		3e-05
1x4e_A	85	Solution Structure Of Rrm Domain In Rna Binding Mot		8e-05

>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet Repeat Rna-Binding Protein 1 Length = 115

Iteration: 1
 Score = 94.4 bits (233), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 45/71 (63%), Positives = 53/71 (74%), Gaps = 2/71 (2%)
Query: 22 SGLASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQN 81
          SGL  +  ++G++G Q  GPEGANLFIYHLP EF D DL  MF PFG V+SAKVFIDKQ 
Sbjct: 6  SGL--TQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQT 63
Query: 82 NRSKCFGTIIF 92
          N SKCFG + +
Sbjct: 64 NLSKCFGFVSY 74

>pdb|2KHC|A Chain A, Bruno Rrm3+ Length = 118

Iteration: 1
 Score = 92.4 bits (228), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 42/58 (72%), Positives = 47/58 (81%)
Query: 35 GKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          GKQ+ GPEG NLFIYHLP EF+D DLAS F PFG V+SAKVFIDKQ + SKCFG + F
Sbjct: 32 GKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSF 89

>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In Polyadenylation Binding Protein 3 Length = 103

Iteration: 1
 Score = 46.2 bits (108), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 25/61 (40%), Positives = 35/61 (57%), Gaps = 2/61 (3%)
Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTII 91
          GSSG ++T  +  NL++ +L     D  L   F PFGT+ SAKV +  +  RSK FG + 
Sbjct: 4  GSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMM--EGGRSKGFGFVC 61
Query: 92 F 92
          F
Sbjct: 62 F 62

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/90 (27%), Positives = 42/90 (46%)
Query: 32  GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTII 91
           GSSG++       ++F+  L PE +  D+ S F PFG +  A+V  D    +SK +G + 
Sbjct: 4   GSSGQKKDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVS 63
Query: 92  FMRKFFILTIRFDTANDYLGQSFLKPSFNT 121
           F  K             +LG   ++ ++ T
Sbjct: 64  FYNKLDAENAIVHMGGQWLGGRQIRTNWAT 93

>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 = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 24/90 (26%), Positives = 43/90 (47%)
Query: 32  GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTII 91
           GSSG++       ++F+  L PE +  D+ + F PFG +  A+V  D    +SK +G + 
Sbjct: 4   GSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVS 63
Query: 92  FMRKFFILTIRFDTANDYLGQSFLKPSFNT 121
           F  K+            +LG   ++ ++ T
Sbjct: 64  FFNKWDAENAIQQMGGQWLGGRQIRTNWAT 93

>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif, Single-Stranded Interacting Protein 2 Length = 85

Iteration: 1
 Score = 42.0 bits (97), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 17/49 (34%), Positives = 28/49 (57%)
Query: 44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          + L+I  L P  +D DL  +  P+G ++S K  +DK  N+ K +G + F
Sbjct: 6  SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDF 54

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	128
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	7e-27
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	4e-26
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	2e-20
1x4e_A	85	RNA binding motif, single-stranded interacting pro	4e-20
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-16
1x5o_A	114	RNA binding motif, single-stranded interacting pro	4e-16
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	6e-16
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	3e-15
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	2e-14
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-13
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	2e-13
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	6e-12
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	4e-13
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	4e-13
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	4e-11
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	5e-13
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-09
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-04
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	6e-13
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	1e-12
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	2e-12
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	2e-12
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	3e-12
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	8e-12
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	1e-11
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	1e-09
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-11
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	3e-11
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	4e-11
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-09
1x5p_A	97	Negative elongation factor E; structure genomics,	4e-11
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-11
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-05
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	7e-11
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	8e-11
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	1e-07
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	9e-11
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-10
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	1e-10
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	2e-10
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-10
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	2e-10
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	3e-10
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	6e-10
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-08
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	7e-10
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-06
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	8e-10
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	1e-09
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-09
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	9e-09
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-07
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	2e-09
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	2e-09
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	2e-09
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	3e-09
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	4e-09
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	5e-09
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	7e-09
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	7e-09
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	3e-05
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	7e-09
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-04
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	8e-09
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	8e-09
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	1e-08
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	1e-08
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	1e-08
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	2e-08
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	2e-08
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	2e-08
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	2e-08
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	2e-08
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	2e-08
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	2e-08
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	3e-08
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-08
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	3e-08
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	4e-08
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-07
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	4e-08
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	4e-08
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	5e-08
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	5e-08
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	5e-08
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	6e-08
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	6e-08
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	6e-08
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-06
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	8e-08
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	8e-08
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	9e-08
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	9e-08
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	1e-07
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-07
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-05
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	1e-07
2div_A	99	TRNA selenocysteine associated protein; structural	1e-07
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	1e-07
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	2e-07
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	3e-07
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	3e-07
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	3e-07
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	4e-07
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	4e-07
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	5e-07
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	5e-07
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	8e-07
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	8e-07
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	8e-07
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	1e-06
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	1e-06
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	1e-06
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	1e-06
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-06
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	2e-06
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	2e-06
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	2e-06
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	2e-06
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-06
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	2e-06
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	3e-06
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	4e-06
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-06
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-05
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	6e-06
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	8e-06
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	9e-06
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	9e-06
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	1e-05
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	2e-05
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	2e-05
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	4e-05
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	4e-04
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	6e-05
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	6e-05
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	8e-05
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	2e-04
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	2e-04
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	2e-04
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	2e-04
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	2e-04
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-04
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	3e-04
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	4e-04
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	5e-04
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	8e-04

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

 Score = 95.5 bits (238), Expect = 7e-27
 Identities = 48/79 (60%), Positives = 58/79 (73%)

Query: 10 MTGAGTMSPTALSGLASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGT 69
             A  +S + L+ +A S AA  ++GKQ+ GPEG NLFIYHLP EF+D DLAS F PFG 
Sbjct: 7  FGSASALSTSPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGN 66

Query: 70 VLSAKVFIDKQNNRSKCFG 88
          V+SAKVFIDKQ + SKCFG
Sbjct: 67 VISAKVFIDKQTSLSKCFG 85

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 93.5 bits (233), Expect = 4e-26
 Identities = 42/64 (65%), Positives = 48/64 (75%)

Query: 25 ASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRS 84
            +  ++G++G Q  GPEGANLFIYHLP EF D DL  MF PFG V+SAKVFIDKQ N S
Sbjct: 7  GLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLS 66

Query: 85 KCFG 88
          KCFG
Sbjct: 67 KCFG 70

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 79.8 bits (197), Expect = 2e-20
 Identities = 11/73 (15%), Positives = 27/73 (36%)

Query: 16 MSPTALSGLASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKV 75
           +             +  +          NL + ++P    +  L  +F  +G + S K+
Sbjct: 15 QTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKI 74

Query: 76 FIDKQNNRSKCFG 88
            D++  +S+ +G
Sbjct: 75 VCDRETRQSRGYG 87

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 77.2 bits (191), Expect = 4e-20
 Identities = 17/53 (32%), Positives = 28/53 (52%)

Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFM 93
             + L+I  L P  +D DL  +  P+G ++S K  +DK  N+ K +G + F 
Sbjct: 3  SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFD 55

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 69.3 bits (170), Expect = 1e-16
 Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 1/64 (1%)

Query: 29 AAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
           + GSSG    G  G+ +F+ +L  +     L  +F   G V+ A +  DK + +S+  G
Sbjct: 1  GSSGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIG 59

Query: 89 TIIF 92
          T+ F
Sbjct: 60 TVTF 63

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 67.7 bits (166), Expect = 4e-16
 Identities = 15/56 (26%), Positives = 28/56 (50%), Gaps = 1/56 (1%)

Query: 33 SSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
          +   +    +  NL+I +LP    + +L +M  PFG V+S ++  D  +  S+  G
Sbjct: 15 AQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVG 69

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 67.2 bits (165), Expect = 6e-16
 Identities = 24/57 (42%), Positives = 33/57 (57%), Gaps = 2/57 (3%)

Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
          GSSG ++T  +  NL++ +L     D  L   F PFGT+ SAKV ++    RSK FG
Sbjct: 4  GSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFG 58

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 65.7 bits (161), Expect = 3e-15
 Identities = 20/50 (40%), Positives = 26/50 (52%), Gaps = 3/50 (6%)

Query: 40 GPEG-ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
          GP G  N+FI +L     +  L   F  FG +LS KV  D+  N SK +G
Sbjct: 1  GPLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYG 48

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 63.1 bits (154), Expect = 2e-14
 Identities = 18/61 (29%), Positives = 27/61 (44%), Gaps = 1/61 (1%)

Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTII 91
          GSSG +  G     LF+  L  + S+ D+  +F PFG +    V     +  SK    + 
Sbjct: 4  GSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVK 62

Query: 92 F 92
          F
Sbjct: 63 F 63

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 61.1 bits (149), Expect = 1e-13
 Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 6/61 (9%)

Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTII 91
          GSSG          +F+ +LP +F+   L   F   G VL A + ++  N +SK  G + 
Sbjct: 1  GSSGS----SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVK 54

Query: 92 F 92
          F
Sbjct: 55 F 55

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 62.2 bits (152), Expect = 2e-13
 Identities = 13/58 (22%), Positives = 27/58 (46%)

Query: 31  VGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
           V  +       +  NL++ +LP   +D  L ++FG +G+++   +  DK   R +   
Sbjct: 77  VSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVA 134

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 58.4 bits (142), Expect = 6e-12
 Identities = 10/47 (21%), Positives = 23/47 (48%)

Query: 42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
             NL + +LP + +D +L ++F   G + + ++  D +   S  + 
Sbjct: 2  SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYA 48

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 60.0 bits (146), Expect = 4e-13
 Identities = 20/60 (33%), Positives = 30/60 (50%), Gaps = 2/60 (3%)

Query: 29 AAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
           + GSSG   +      L + ++P  F D DL  MFG FG +L  ++  ++    SK FG
Sbjct: 1  GSSGSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFG 58

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 61.4 bits (150), Expect = 4e-13
 Identities = 12/58 (20%), Positives = 28/58 (48%)

Query: 31  VGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
           V  +         ANL++  LP   +  +L  +F  +G ++++++ +D+    S+  G
Sbjct: 76  VSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVG 133

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 56.0 bits (136), Expect = 4e-11
 Identities = 14/45 (31%), Positives = 23/45 (51%)

Query: 44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
           NL + +LP   +  +  S+FG  G + S K+  DK   +S  +G
Sbjct: 3  TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYG 47

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 62.7 bits (153), Expect = 5e-13
 Identities = 15/64 (23%), Positives = 31/64 (48%), Gaps = 3/64 (4%)

Query: 35  GKQLT---GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTII 91
            ++L+    P  A L + +LPP  +      +  PFG++    +   ++  +SK +G   
Sbjct: 84  ERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAE 143

Query: 92  FMRK 95
           +M+K
Sbjct: 144 YMKK 147

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 52.3 bits (126), Expect = 3e-09
 Identities = 11/52 (21%), Positives = 20/52 (38%), Gaps = 2/52 (3%)

Query: 42  EGANLFIYHLPPEFSDAD-LASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
               L +  LPP F+D D L        +    ++    Q+ + K F  + +
Sbjct: 183 HSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACG-QDGQLKGFAVLEY 233

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 38.4 bits (90), Expect = 2e-04
 Identities = 5/52 (9%), Positives = 17/52 (32%), Gaps = 7/52 (13%)

Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
               + I  LP + ++ ++  +   +  +    V      ++ K    +  
Sbjct: 20 RNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTL 64

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 59.7 bits (145), Expect = 6e-13
 Identities = 19/60 (31%), Positives = 32/60 (53%)

Query: 29 AAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
           + GSSG++       ++F+  L PE +  D+ + F PFG +  A+V  D    +SK +G
Sbjct: 1  GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYG 60

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score = 58.9 bits (143), Expect = 1e-12
 Identities = 16/62 (25%), Positives = 25/62 (40%), Gaps = 1/62 (1%)

Query: 32 GSSG-KQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTI 90
          GSSG   +   +   LFI  +P    + DL  +F  FG +    V  D+     K    +
Sbjct: 1  GSSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFL 60

Query: 91 IF 92
           +
Sbjct: 61 TY 62

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 58.1 bits (141), Expect = 2e-12
 Identities = 20/64 (31%), Positives = 28/64 (43%), Gaps = 1/64 (1%)

Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTII 91
             G       G  L + +L    SDAD+  +F  FGT+  A V  D+ + RS     + 
Sbjct: 18 SGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVH 76

Query: 92 FMRK 95
          F RK
Sbjct: 77 FERK 80

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 58.5 bits (142), Expect = 2e-12
 Identities = 19/64 (29%), Positives = 29/64 (45%), Gaps = 2/64 (3%)

Query: 25 ASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRS 84
          +S     GS        +   L + ++P  F D DL  MFG FG +L  ++  ++    S
Sbjct: 11 SSGLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGS 68

Query: 85 KCFG 88
          K FG
Sbjct: 69 KGFG 72

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 57.6 bits (140), Expect = 3e-12
 Identities = 17/60 (28%), Positives = 29/60 (48%)

Query: 29 AAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
           + GSSG      + A + + +L  +  + DL  +F PFG++    +  DK   +SK F 
Sbjct: 1  GSSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFA 60

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 56.0 bits (136), Expect = 8e-12
 Identities = 19/51 (37%), Positives = 29/51 (56%), Gaps = 2/51 (3%)

Query: 40 GPEG--ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
          GP G   ++F+  L PE + A +A+ F PFG +  A+V  D    +SK +G
Sbjct: 1  GPLGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYG 51

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 58.1 bits (141), Expect = 1e-11
 Identities = 14/68 (20%), Positives = 26/68 (38%)

Query: 25  ASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRS 84
               A                +++  +  + SD D+ S+F  FG + SA +  D    + 
Sbjct: 107 NIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKH 166

Query: 85  KCFGTIIF 92
           K +G I +
Sbjct: 167 KGYGFIEY 174

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 53.1 bits (128), Expect = 1e-09
 Identities = 10/56 (17%), Positives = 23/56 (41%)

Query: 33 SSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
          ++ +Q      + +++  +  E  +  +   F PFG + S  +  D    + K F 
Sbjct: 18 AAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFA 73

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 54.8 bits (133), Expect = 2e-11
 Identities = 15/45 (33%), Positives = 20/45 (44%)

Query: 44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
           NLF+  L     D  L + F  F + LS  V  D Q   S+ +G
Sbjct: 2  FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYG 46

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 55.5 bits (134), Expect = 3e-11
 Identities = 20/64 (31%), Positives = 29/64 (45%), Gaps = 1/64 (1%)

Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTII 91
             G       GA L + +L    SDAD+  +F  FGT+  A V  D+ + RS     + 
Sbjct: 24 SGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVH 82

Query: 92 FMRK 95
          F R+
Sbjct: 83 FERR 86

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

 Score = 56.1 bits (136), Expect = 4e-11
 Identities = 10/56 (17%), Positives = 23/56 (41%), Gaps = 1/56 (1%)

Query: 33  SSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
           +  ++    E   LFI  +  + ++ D+  MF  FG +   ++     +  S+   
Sbjct: 85  ADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCA 139

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

 Score = 52.2 bits (126), Expect = 1e-09
 Identities = 14/50 (28%), Positives = 24/50 (48%), Gaps = 2/50 (4%)

Query: 45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNN--RSKCFGTIIF 92
           +F+  +P  +S+ DL  +F  +G V    V  D+  N  +SK    + F
Sbjct: 5  KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTF 54

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 54.2 bits (131), Expect = 4e-11
 Identities = 12/64 (18%), Positives = 26/64 (40%), Gaps = 8/64 (12%)

Query: 29 AAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
           + GSSG++    +G  L++Y    + +   L   F PFG ++   +         +   
Sbjct: 1  GSSGSSGERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCA 52

Query: 89 TIIF 92
           + +
Sbjct: 53 FVTY 56

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 55.6 bits (135), Expect = 5e-11
 Identities = 16/56 (28%), Positives = 24/56 (42%)

Query: 33  SSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
              +Q +  +  NLF+  L     D  L + F  F + LS  V  D Q   S+ +G
Sbjct: 77  FQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYG 132

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 40.2 bits (95), Expect = 3e-05
 Identities = 11/43 (25%), Positives = 22/43 (51%), Gaps = 1/43 (2%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
          L++ +L    ++  L   F   G + + K+ IDK NN++  + 
Sbjct: 3  LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYA 44

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 54.2 bits (131), Expect = 7e-11
 Identities = 16/57 (28%), Positives = 27/57 (47%)

Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
          GSSG      +   LF+  L  + ++  L  +F  +G +    V  D++  RS+ FG
Sbjct: 1  GSSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFG 57

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 56.2 bits (136), Expect = 8e-11
 Identities = 17/50 (34%), Positives = 23/50 (46%), Gaps = 1/50 (2%)

Query: 43  GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
           GA L + +L P  S+  L   F  FG V  A V +D    R+   G + F
Sbjct: 96  GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEF 144

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 47.4 bits (113), Expect = 1e-07
 Identities = 12/53 (22%), Positives = 23/53 (43%), Gaps = 6/53 (11%)

Query: 36 KQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
           + T  +   LF+ +LP + ++ D   +F  +G      +      NR + FG
Sbjct: 15 GEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFI------NRDRGFG 61

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 55.2 bits (133), Expect = 9e-11
 Identities = 23/83 (27%), Positives = 33/83 (39%), Gaps = 1/83 (1%)

Query: 13  AGTMSPTALSGLASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLS 72
           A    P  L      +      G       GA L + +L    SDAD+  +F  FGT+  
Sbjct: 58  APYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKK 117

Query: 73  AKVFIDKQNNRSKCFGTIIFMRK 95
           A V  D+ + RS     + F R+
Sbjct: 118 AAVDYDR-SGRSLGTADVHFERR 139

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 56.8 bits (136), Expect = 1e-10
 Identities = 7/50 (14%), Positives = 23/50 (46%)

Query: 46  LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRK 95
           LF+  +  + +++ L   F  +G +    +   K++ + + +  I +  +
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHE 154

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 53.0 bits (128), Expect = 1e-10
 Identities = 15/57 (26%), Positives = 27/57 (47%)

Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
          GSSG +        L ++ L    ++ DL  +F  +G +    +  D+Q+ RS+ F 
Sbjct: 4  GSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 60

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 53.4 bits (129), Expect = 2e-10
 Identities = 12/53 (22%), Positives = 20/53 (37%)

Query: 40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          G     L++ +L P  ++ DL S+F  F       +       R +    I F
Sbjct: 22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITF 74

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 53.2 bits (128), Expect = 2e-10
 Identities = 6/52 (11%), Positives = 16/52 (30%)

Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
               +    L     +  L  M   +G V   ++ +  +  +      ++F
Sbjct: 4  IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLF 55

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 53.0 bits (128), Expect = 2e-10
 Identities = 15/57 (26%), Positives = 25/57 (43%)

Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
          GSSG          L++  L  E  D  L + F PFG +   ++ +D +  + + F 
Sbjct: 1  GSSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFA 57

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score = 54.7 bits (131), Expect = 3e-10
 Identities = 16/87 (18%), Positives = 27/87 (31%), Gaps = 2/87 (2%)

Query: 8   AAMTGAGTMSPTALSGLASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPF 67
            A      M     +           +       +   L+I +L    +D DL       
Sbjct: 33  DAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSL 92

Query: 68  GT--VLSAKVFIDKQNNRSKCFGTIIF 92
           G   +L  K F ++ N +SK F  +  
Sbjct: 93  GVNDILEIKFFENRANGQSKGFALVGV 119

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 53.8 bits (130), Expect = 6e-10
 Identities = 21/76 (27%), Positives = 28/76 (36%), Gaps = 13/76 (17%)

Query: 33  SSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
                L      N+FI +L     +  L   F  FG +LS KV  D   N SK +G   F
Sbjct: 93  QRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYG---F 147

Query: 93  MRKFFILTIRFDTAND 108
                   + F+T   
Sbjct: 148 --------VHFETQEA 155

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 50.0 bits (120), Expect = 1e-08
 Identities = 17/60 (28%), Positives = 27/60 (45%)

Query: 29 AAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
            +GS          A+L++  L P+ ++A L   F P G +LS +V  D    RS  + 
Sbjct: 1  GPLGSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYA 60

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 53.0 bits (128), Expect = 7e-10
 Identities = 14/52 (26%), Positives = 21/52 (40%), Gaps = 1/52 (1%)

Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
              NLFI +L P  S A+L              V +D +   ++ FG + F
Sbjct: 11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAV-VDVRTGTNRKFGYVDF 61

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 44.5 bits (106), Expect = 1e-06
 Identities = 9/57 (15%), Positives = 17/57 (29%), Gaps = 5/57 (8%)

Query: 36  KQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
                     L   +L    ++ +L  +F     +         Q+ +SK    I F
Sbjct: 92  DSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRL-----VSQDGKSKGIAYIEF 143

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 51.5 bits (124), Expect = 8e-10
 Identities = 17/63 (26%), Positives = 30/63 (47%)

Query: 26 SSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSK 85
          S  AA  ++  Q        L++  L    ++  L  +F PFG + S ++ +D +  RSK
Sbjct: 9  SHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSK 68

Query: 86 CFG 88
           +G
Sbjct: 69 GYG 71

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 50.7 bits (122), Expect = 1e-09
 Identities = 16/62 (25%), Positives = 30/62 (48%), Gaps = 2/62 (3%)

Query: 27 SNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKC 86
          S+ + G SG     P  + +++ +LP   ++ DL  +F  +G V+   +  DK   +SK 
Sbjct: 2  SSGSSGMSGGL--APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKG 59

Query: 87 FG 88
            
Sbjct: 60 VA 61

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 53.1 bits (128), Expect = 1e-09
 Identities = 8/49 (16%), Positives = 19/49 (38%)

Query: 44  ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
             L++ + PP ++  ++  +      V  +      + N S+ F  I  
Sbjct: 118 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDV 166

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 50.8 bits (122), Expect = 9e-09
 Identities = 13/53 (24%), Positives = 25/53 (47%), Gaps = 2/53 (3%)

Query: 42  EGANLFIYHLPPEFSDAD-LASMFGPFGTVLSAKVFID-KQNNRSKCFGTIIF 92
           EG  + I +L  E  D + L   F  FG++    +    K+++ + C   ++F
Sbjct: 209 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVF 261

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 46.9 bits (112), Expect = 2e-07
 Identities = 7/47 (14%), Positives = 16/47 (34%)

Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCF 87
           E   + + +LP  ++   +   F   G ++   V    + N     
Sbjct: 39 RELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFAR 85

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 50.4 bits (121), Expect = 2e-09
 Identities = 15/57 (26%), Positives = 23/57 (40%)

Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
          GSSG      EG  +FI +L  +  +  L  +   FG +   +V +      SK   
Sbjct: 4  GSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCA 60

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 50.4 bits (121), Expect = 2e-09
 Identities = 14/53 (26%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
                LFI  L  E ++  L ++FG  G +    +  D+  ++S+ F  I F
Sbjct: 4  ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITF 55

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 50.9 bits (122), Expect = 2e-09
 Identities = 14/72 (19%), Positives = 28/72 (38%)

Query: 17  SPTALSGLASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVF 76
           +    +       + GS G   +      L++  L  E  D  L + F PFG +   ++ 
Sbjct: 37  TCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIP 96

Query: 77  IDKQNNRSKCFG 88
           +D +  + + F 
Sbjct: 97  LDYETEKHRGFA 108

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 50.5 bits (121), Expect = 3e-09
 Identities = 13/73 (17%), Positives = 28/73 (38%)

Query: 16 MSPTALSGLASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKV 75
              +++G           G +        L ++ L    ++ DL  +F  +G +    +
Sbjct: 19 SHMASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSI 78

Query: 76 FIDKQNNRSKCFG 88
            D+Q+ RS+ F 
Sbjct: 79 VYDQQSRRSRGFA 91

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 49.1 bits (118), Expect = 4e-09
 Identities = 11/44 (25%), Positives = 23/44 (52%)

Query: 45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
          N+++ +L    +   +  +F  FG V + K+  D++  + K FG
Sbjct: 3  NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFG 46

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Length = 165

 Score = 50.6 bits (121), Expect = 5e-09
 Identities = 10/48 (20%), Positives = 23/48 (47%)

Query: 41  PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
            EG  LF+  +  E  + ++   F  +G + +  + +D++   SK + 
Sbjct: 70  VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYA 117

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 48.7 bits (117), Expect = 7e-09
 Identities = 18/61 (29%), Positives = 28/61 (45%), Gaps = 2/61 (3%)

Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTII 91
          GSSG   +G +   +F+  +P    + +L   F  FG V    +  D +  R + FG I 
Sbjct: 1  GSSGS--SGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFIT 58

Query: 92 F 92
          F
Sbjct: 59 F 59

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 50.4 bits (121), Expect = 7e-09
 Identities = 12/64 (18%), Positives = 22/64 (34%)

Query: 25  ASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRS 84
            + +  V      +       LFI  LP   +D  +  +   FG + +  +  D     S
Sbjct: 96  ENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLS 155

Query: 85  KCFG 88
           K + 
Sbjct: 156 KGYA 159

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 40.8 bits (96), Expect = 3e-05
 Identities = 7/48 (14%), Positives = 17/48 (35%), Gaps = 5/48 (10%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLS-----AKVFIDKQNNRSKCFG 88
          L++ ++P   ++  +   F     +           +  Q N+ K F 
Sbjct: 7  LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFA 54

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 50.3 bits (121), Expect = 7e-09
 Identities = 12/48 (25%), Positives = 19/48 (39%)

Query: 41  PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
           P    LFI  LP   +D  +  +   FG + +  +  D     SK + 
Sbjct: 92  PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYA 139

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 38.7 bits (91), Expect = 1e-04
 Identities = 7/53 (13%), Positives = 17/53 (32%), Gaps = 5/53 (9%)

Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLS-----AKVFIDKQNNRSKCFG 88
               L++ ++P   ++  +   F     +           +  Q N+ K F 
Sbjct: 2  GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFA 54

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 48.3 bits (116), Expect = 8e-09
 Identities = 12/48 (25%), Positives = 22/48 (45%)

Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
             + L++  L    ++  L  +F PFG + +  +  D    RSK +G
Sbjct: 3  SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYG 50

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 48.8 bits (117), Expect = 8e-09
 Identities = 19/70 (27%), Positives = 30/70 (42%), Gaps = 4/70 (5%)

Query: 23 GLASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNN 82
          G + S+   GS            +F+  LP   +DA L   F  FG +  A V  D+Q  
Sbjct: 1  GSSGSSGMHGSQK----DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTG 56

Query: 83 RSKCFGTIIF 92
          +S+ +G +  
Sbjct: 57 KSRGYGFVTM 66

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 48.6 bits (116), Expect = 1e-08
 Identities = 15/75 (20%), Positives = 29/75 (38%), Gaps = 8/75 (10%)

Query: 29 AAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLS--------AKVFIDKQ 80
           + GSSG      + + +++  L    +  DLA  F   G V            +++DK+
Sbjct: 1  GSSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE 60

Query: 81 NNRSKCFGTIIFMRK 95
            + K   T+ +   
Sbjct: 61 TGKPKGDATVSYEDP 75

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 48.4 bits (116), Expect = 1e-08
 Identities = 15/55 (27%), Positives = 23/55 (41%), Gaps = 2/55 (3%)

Query: 35 GKQLTGPEGANLFIYHLPPEFSDADLASMFG-PFGTVLSAKVFIDKQNNRSKCFG 88
          G   +     +LF+  L P+  D  L   F   + +    KV +D Q   SK +G
Sbjct: 1  GSSGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD-QTGVSKGYG 54

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 48.0 bits (115), Expect = 1e-08
 Identities = 9/45 (20%), Positives = 22/45 (48%)

Query: 44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
            +++  +P + ++  +  +    G V++ K+  D Q  RSK + 
Sbjct: 3  RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYA 47

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 48.6 bits (116), Expect = 2e-08
 Identities = 13/85 (15%), Positives = 28/85 (32%)

Query: 8  AAMTGAGTMSPTALSGLASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPF 67
          + +   G+   +   G      ++             +L + +L    S   L  +F  +
Sbjct: 12 SGLVPRGSHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKY 71

Query: 68 GTVLSAKVFIDKQNNRSKCFGTIIF 92
          G V    +  D+    S+ F  + F
Sbjct: 72 GRVGDVYIPRDRYTKESRGFAFVRF 96

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 47.6 bits (114), Expect = 2e-08
 Identities = 13/60 (21%), Positives = 28/60 (46%)

Query: 29 AAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
           + GSSG      + A +++  L  + S+  L  +F   G V++  +  D+   + + +G
Sbjct: 1  GSSGSSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYG 60

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

 Score = 47.4 bits (113), Expect = 2e-08
 Identities = 14/57 (24%), Positives = 21/57 (36%), Gaps = 3/57 (5%)

Query: 32 GSSGKQLTGPE---GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSK 85
          GSSG   + P+      L I ++PP      L S+   +G V S +           
Sbjct: 1  GSSGSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVV 57

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 47.6 bits (114), Expect = 2e-08
 Identities = 14/58 (24%), Positives = 27/58 (46%), Gaps = 5/58 (8%)

Query: 39 TGPEGA----NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          + PEG      +F+  +     + ++ S F  +G+V   K+  D+    SK +G + F
Sbjct: 1  SLPEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 57

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 47.6 bits (114), Expect = 2e-08
 Identities = 18/58 (31%), Positives = 25/58 (43%), Gaps = 8/58 (13%)

Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLS-AKVFIDKQNNRSKCFG 88
          GSSG        + +FI +L PE  +  L   F  FG +L   K+  D     SK + 
Sbjct: 1  GSSGS-------SGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYA 51

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 47.6 bits (114), Expect = 2e-08
 Identities = 12/51 (23%), Positives = 19/51 (37%), Gaps = 3/51 (5%)

Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDK---QNNRSKCFG 88
             + LFI +L    ++  L  +F   G + S  +   K       S  FG
Sbjct: 3  SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFG 53

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 47.6 bits (114), Expect = 2e-08
 Identities = 13/48 (27%), Positives = 19/48 (39%), Gaps = 1/48 (2%)

Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
              NLFI +L P  S A+L              V +D +   ++ FG
Sbjct: 15 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAV-VDVRTGTNRKFG 61

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 47.2 bits (113), Expect = 3e-08
 Identities = 14/61 (22%), Positives = 23/61 (37%), Gaps = 5/61 (8%)

Query: 32 GSSGKQLTGP----EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCF 87
          GSSG     P        +F+ +L     +  L  +F   G +    +  D+   + K F
Sbjct: 1  GSSGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSF 59

Query: 88 G 88
          G
Sbjct: 60 G 60

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 46.8 bits (112), Expect = 3e-08
 Identities = 14/53 (26%), Positives = 22/53 (41%)

Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFM 93
               LF+ +L    S+ DL  +F  +G +      ID    + K F  + FM
Sbjct: 6  SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFM 58

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 48.0 bits (114), Expect = 3e-08
 Identities = 9/69 (13%), Positives = 23/69 (33%), Gaps = 2/69 (2%)

Query: 26  SSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGT--VLSAKVFIDKQNNR 83
           ++                A +++       +D  L  +    G   V+  K   ++ N +
Sbjct: 38  NNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQ 97

Query: 84  SKCFGTIIF 92
           SK +  ++ 
Sbjct: 98  SKGYAEVVV 106

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 48.3 bits (116), Expect = 4e-08
 Identities = 17/51 (33%), Positives = 26/51 (50%)

Query: 42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          E   +FI  L  + ++ +L   FG +GTV   K+  D    RS+ FG + F
Sbjct: 2  ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSF 52

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 46.8 bits (112), Expect = 1e-07
 Identities = 11/52 (21%), Positives = 27/52 (51%)

Query: 41  PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
            +   +F+  + P+    +    F  +GT++ A++ +DK   +S+ FG + +
Sbjct: 85  DKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTY 136

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 46.4 bits (111), Expect = 4e-08
 Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 2/46 (4%)

Query: 45 NLFIYHLPPEFSDADLASMFGPFGT--VLSAKVFIDKQNNRSKCFG 88
           L+I +L    +D DL       G   +L  K F ++ N +SK F 
Sbjct: 3  ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFA 48

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Length = 126

 Score = 47.4 bits (113), Expect = 4e-08
 Identities = 10/48 (20%), Positives = 23/48 (47%)

Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
           EG  LF+  +  E ++ D+   F  +G + +  + +D++    K + 
Sbjct: 20 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYT 67

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 46.8 bits (112), Expect = 5e-08
 Identities = 21/65 (32%), Positives = 30/65 (46%), Gaps = 4/65 (6%)

Query: 32 GSSGKQLTGPEGAN----LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCF 87
          GSSG       GA+    LF+  L    +   L S F  +G V+   +  DK  N+S+ F
Sbjct: 1  GSSGSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGF 60

Query: 88 GTIIF 92
          G + F
Sbjct: 61 GFVKF 65

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 46.5 bits (111), Expect = 5e-08
 Identities = 16/62 (25%), Positives = 26/62 (41%), Gaps = 3/62 (4%)

Query: 29 AAVGSSG--KQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKC 86
           + GSSG  +  T  E   LFI  LP   +  +L  +    GTV   ++  ++   + K 
Sbjct: 1  GSSGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKG 59

Query: 87 FG 88
            
Sbjct: 60 LA 61

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 46.5 bits (111), Expect = 5e-08
 Identities = 21/61 (34%), Positives = 32/61 (52%)

Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTII 91
          GSSG +    + ++L +  LP + ++ DL   F  FG VL  +V  D +   SK FG + 
Sbjct: 4  GSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVR 63

Query: 92 F 92
          F
Sbjct: 64 F 64

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 46.5 bits (111), Expect = 6e-08
 Identities = 10/48 (20%), Positives = 23/48 (47%)

Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
           EG  LF+  +  E  + ++   F  +G + +  + +D++   SK + 
Sbjct: 24 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYA 71

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 46.5 bits (111), Expect = 6e-08
 Identities = 10/48 (20%), Positives = 23/48 (47%)

Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
           EG  LF+  +  E ++ D+   F  +G + +  + +D++    K + 
Sbjct: 21 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYT 68

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 48.1 bits (115), Expect = 6e-08
 Identities = 17/52 (32%), Positives = 24/52 (46%)

Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
           +   LFI  L  E +D  L S F  +GT+    V  D    RS+ FG + +
Sbjct: 11 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 62

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 44.2 bits (105), Expect = 1e-06
 Identities = 7/47 (14%), Positives = 21/47 (44%)

Query: 46  LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
           +F+  +  +  +  L   F  +G +   ++  D+ + + + F  + F
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 45.6 bits (109), Expect = 8e-08
 Identities = 11/48 (22%), Positives = 21/48 (43%)

Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
               L++  L  E  D  L + F PFG +   ++ +D +  + + F 
Sbjct: 5  TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFA 52

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 46.1 bits (110), Expect = 8e-08
 Identities = 14/48 (29%), Positives = 27/48 (56%)

Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDK 79
          GSSG + T  + + LF+ +LPP+ ++ ++  +F  +G      +  DK
Sbjct: 4  GSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK 51

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 46.1 bits (110), Expect = 9e-08
 Identities = 10/61 (16%), Positives = 27/61 (44%), Gaps = 1/61 (1%)

Query: 29 AAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDK-QNNRSKCF 87
           + GSSG+       + + + ++P + +  ++  +F  FG + + ++          + F
Sbjct: 1  GSSGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGF 60

Query: 88 G 88
          G
Sbjct: 61 G 61

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 47.1 bits (112), Expect = 9e-08
 Identities = 10/47 (21%), Positives = 18/47 (38%)

Query: 42  EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
              +L + +L    S   L  +F  +G V    +  D+    S+ F 
Sbjct: 69  GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFA 115

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 45.7 bits (109), Expect = 1e-07
 Identities = 16/47 (34%), Positives = 21/47 (44%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          +FI  L  + +   L   FG FG V    V  D    RS+ FG + F
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 74

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 47.4 bits (112), Expect = 1e-07
 Identities = 7/61 (11%), Positives = 18/61 (29%)

Query: 32  GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTII 91
             + K         L  ++ P E ++ +   +    G      V +    +     G + 
Sbjct: 112 EQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLE 171

Query: 92  F 92
           +
Sbjct: 172 W 172

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 41.2 bits (96), Expect = 2e-05
 Identities = 10/52 (19%), Positives = 17/52 (32%), Gaps = 1/52 (1%)

Query: 40 GPEGANLFIYHLPPEFSDAD-LASMFGPFGTVLSAKVFIDKQNNRSKCFGTI 90
          G +   L +Y L     + D + ++F  +G V   K    K           
Sbjct: 1  GADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADG 52

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 45.7 bits (109), Expect = 1e-07
 Identities = 13/56 (23%), Positives = 25/56 (44%)

Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCF 87
          GSSG      +   L++ +L  + ++  +  +F   G   S K+  +  +N   CF
Sbjct: 4  GSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCF 59

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 45.4 bits (108), Expect = 1e-07
 Identities = 12/59 (20%), Positives = 25/59 (42%), Gaps = 1/59 (1%)

Query: 35 GKQLTGPEGANLFIYHLPPEFSDADLASMFGPFG-TVLSAKVFIDKQNNRSKCFGTIIF 92
          G   +    A+L++  L P   +  ++  F   G TV+S K+  ++       +  + F
Sbjct: 1  GSSGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEF 59

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 45.2 bits (108), Expect = 1e-07
 Identities = 7/53 (13%), Positives = 22/53 (41%), Gaps = 1/53 (1%)

Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQN-NRSKCFGTIIF 92
           +   + I  L    +   +  +F  +G +    + +++ + + SK +  + F
Sbjct: 2  MKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEF 54

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 45.2 bits (107), Expect = 2e-07
 Identities = 15/51 (29%), Positives = 26/51 (50%)

Query: 29 AAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDK 79
           + GSSG ++ G     L I  LP E ++ ++ ++  PFG V +  +   K
Sbjct: 1  GSSGSSGDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK 51

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 44.9 bits (107), Expect = 3e-07
 Identities = 15/64 (23%), Positives = 25/64 (39%), Gaps = 5/64 (7%)

Query: 32 GSSGKQLTGPE---GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
          GSSG   +GP+      L + +L    S   L  +F  +G V    +  +      + F 
Sbjct: 1  GSSGS--SGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFA 58

Query: 89 TIIF 92
           + F
Sbjct: 59 FVRF 62

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 44.6 bits (106), Expect = 3e-07
 Identities = 11/45 (24%), Positives = 26/45 (57%)

Query: 44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
           ++F+ ++P E ++  L  +F   G V+S ++  D++  + K +G
Sbjct: 9  RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYG 53

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 44.1 bits (105), Expect = 3e-07
 Identities = 16/47 (34%), Positives = 24/47 (51%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          +F+  L  + S  DL   F  FG V+   + +D    RS+ FG I+F
Sbjct: 14 MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILF 60

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 43.6 bits (104), Expect = 4e-07
 Identities = 14/47 (29%), Positives = 25/47 (53%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          +F+  L P+  +  +   FG FG V S ++ +D + N+ + F  I F
Sbjct: 2  IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITF 48

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 44.2 bits (105), Expect = 4e-07
 Identities = 15/60 (25%), Positives = 25/60 (41%), Gaps = 3/60 (5%)

Query: 29 AAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
           + GSSG          LF+  L  + ++  L   F      + A++  D++   SK FG
Sbjct: 1  GSSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFDG---SVRARIVTDRETGSSKGFG 57

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 44.2 bits (105), Expect = 5e-07
 Identities = 17/70 (24%), Positives = 31/70 (44%), Gaps = 6/70 (8%)

Query: 26 SSNAAVGSSGKQLTGPEGAN---LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNN 82
          SS ++  S G  + GP G N   +++ +LPP+    D+  +F  +G +    +   K   
Sbjct: 2  SSGSSGMSGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL---KNRR 58

Query: 83 RSKCFGTIIF 92
              F  + F
Sbjct: 59 GGPPFAFVEF 68

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 44.1 bits (104), Expect = 5e-07
 Identities = 16/69 (23%), Positives = 29/69 (42%), Gaps = 7/69 (10%)

Query: 16 MSPTA-----LSGLASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTV 70
          M  +       SGL    + +G S  +  G     + I  LP + ++ ++ S+  PFG V
Sbjct: 1  MGSSHHHHHHSSGLVPRGSHMGDS--RSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKV 58

Query: 71 LSAKVFIDK 79
           +  +   K
Sbjct: 59 TNLLMLKGK 67

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 43.1 bits (102), Expect = 8e-07
 Identities = 6/50 (12%), Positives = 20/50 (40%), Gaps = 2/50 (4%)

Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFI--DKQNNRSKCFG 88
               + + ++ P      + +   P+ ++    + +  DKQ  +++ F 
Sbjct: 7  HHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFA 56

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 43.6 bits (103), Expect = 8e-07
 Identities = 12/49 (24%), Positives = 18/49 (36%)

Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQ 80
          GSSG          + +  L     +ADL      FGT+    +   K+
Sbjct: 4  GSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR 52

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 43.5 bits (103), Expect = 8e-07
 Identities = 9/41 (21%), Positives = 20/41 (48%)

Query: 39 TGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDK 79
          + P+   ++   +    +D  +   F PFG ++  +VF +K
Sbjct: 21 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK 61

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 43.5 bits (103), Expect = 1e-06
 Identities = 8/48 (16%), Positives = 23/48 (47%), Gaps = 3/48 (6%)

Query: 45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
           L+I +LP + +  ++  +FG +G +   +V        ++    +++
Sbjct: 10 ILYIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVY 54

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 42.5 bits (101), Expect = 1e-06
 Identities = 15/47 (31%), Positives = 22/47 (46%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          +F+  L    +  D+   F  FG V  A +  DK  NR + FG + F
Sbjct: 2  IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTF 48

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 43.0 bits (102), Expect = 1e-06
 Identities = 14/47 (29%), Positives = 23/47 (48%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          LFI  L  E ++  L + +  +G +    V  D  + RS+ FG + F
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTF 76

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 42.6 bits (101), Expect = 1e-06
 Identities = 13/49 (26%), Positives = 21/49 (42%)

Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQ 80
          GSSG          L++  L    ++ DL + F  FG + +  V   +Q
Sbjct: 1  GSSGSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQ 49

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 42.7 bits (101), Expect = 1e-06
 Identities = 12/43 (27%), Positives = 22/43 (51%)

Query: 37 QLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDK 79
          +   P     +I ++P   ++ADL  +F  FG +L  K + +K
Sbjct: 21 RSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEK 63

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 42.1 bits (100), Expect = 2e-06
 Identities = 16/47 (34%), Positives = 21/47 (44%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          +FI  L  + +   L   FG FG V    V  D    RS+ FG + F
Sbjct: 3  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 49

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

 Score = 42.7 bits (101), Expect = 2e-06
 Identities = 10/35 (28%), Positives = 18/35 (51%)

Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKV 75
               LF+   P +  +++L  +FGPFG +   K+
Sbjct: 29 LSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKI 63

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 43.3 bits (102), Expect = 2e-06
 Identities = 7/52 (13%), Positives = 21/52 (40%)

Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
           +   L++ +L    ++  +  +F   G +    + +DK    +  F  + +
Sbjct: 37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEY 88

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 42.3 bits (100), Expect = 2e-06
 Identities = 13/60 (21%), Positives = 22/60 (36%), Gaps = 4/60 (6%)

Query: 29 AAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
           + GSSG      E   L + +L    ++  L  +F     +         QN +SK + 
Sbjct: 1  GSSGSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFI----KVPQNQNGKSKGYA 56

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 42.3 bits (100), Expect = 2e-06
 Identities = 10/73 (13%), Positives = 25/73 (34%), Gaps = 8/73 (10%)

Query: 31 VGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSA--------KVFIDKQNN 82
          +G      +  +   +F+  L    +   +A  F   G + +          ++ D++  
Sbjct: 1  MGHHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETG 60

Query: 83 RSKCFGTIIFMRK 95
          + K   T+ F   
Sbjct: 61 KLKGEATVSFDDP 73

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 42.4 bits (100), Expect = 2e-06
 Identities = 9/67 (13%), Positives = 23/67 (34%), Gaps = 8/67 (11%)

Query: 37 QLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSA--------KVFIDKQNNRSKCFG 88
          +    +   +F+  L    +   +A  F   G + +          ++ D++  + K   
Sbjct: 1  EQDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEA 60

Query: 89 TIIFMRK 95
          T+ F   
Sbjct: 61 TVSFDDP 67

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 42.4 bits (100), Expect = 3e-06
 Identities = 11/72 (15%), Positives = 29/72 (40%)

Query: 22 SGLASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQN 81
          +G  +       S ++    +  ++++ ++    +  DL + F   G++    +  DK +
Sbjct: 15 AGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFS 74

Query: 82 NRSKCFGTIIFM 93
             K +  I F 
Sbjct: 75 GHPKGYAYIEFA 86

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 41.8 bits (98), Expect = 4e-06
 Identities = 10/41 (24%), Positives = 20/41 (48%)

Query: 39 TGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDK 79
          +G     + I  LP + ++ ++ S+  PFG V +  +   K
Sbjct: 12 SGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK 52

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 43.1 bits (101), Expect = 4e-06
 Identities = 19/83 (22%), Positives = 31/83 (37%), Gaps = 7/83 (8%)

Query: 12 GAGTMSPTALSGLASSNAAVGSSGKQ-LTGPEGANLFIYHLPPE-FSDADLASMFGPFGT 69
          G+        SGL    + +G      L G   + L + +L PE  +   L  +FG +G 
Sbjct: 2  GSSHHHHHHSSGLVPRGSHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGD 61

Query: 70 VLSAKVFIDKQNNRSKCFGTIIF 92
          V   K+  +K     K    +  
Sbjct: 62 VQRVKILFNK-----KENALVQM 79

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 41.5 bits (97), Expect = 2e-05
 Identities = 17/56 (30%), Positives = 24/56 (42%), Gaps = 2/56 (3%)

Query: 32  GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCF 87
           GS   Q   P  A L + ++PP  S+ DL  +F   G V+    F   Q +R    
Sbjct: 140 GSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKF--FQKDRKMAL 193

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 41.7 bits (98), Expect = 6e-06
 Identities = 10/58 (17%), Positives = 18/58 (31%), Gaps = 5/58 (8%)

Query: 40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKV-----FIDKQNNRSKCFGTIIF 92
          G     +++ +L     + DL  +FG +    S            +  R K    I  
Sbjct: 42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGL 99

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 40.7 bits (96), Expect = 8e-06
 Identities = 9/61 (14%), Positives = 20/61 (32%)

Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTII 91
          GSSG     P    + + ++P   S  ++   F  +  +  +      +         + 
Sbjct: 4  GSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVA 63

Query: 92 F 92
          F
Sbjct: 64 F 64

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 40.2 bits (95), Expect = 9e-06
 Identities = 8/44 (18%), Positives = 20/44 (45%)

Query: 45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
          ++++ ++    +  +L + F   G+V    +  DK +   K F 
Sbjct: 8  SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFA 51

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 40.4 bits (95), Expect = 9e-06
 Identities = 9/64 (14%), Positives = 21/64 (32%)

Query: 29 AAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
           + GSSG     P    + + ++P   S  ++   F  +  +  +      +        
Sbjct: 1  GSSGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 60

Query: 89 TIIF 92
           + F
Sbjct: 61 MVAF 64

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 40.1 bits (94), Expect = 1e-05
 Identities = 8/48 (16%), Positives = 20/48 (41%), Gaps = 1/48 (2%)

Query: 45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          +++I   P + +  D+       G VL+ ++     +   K    ++F
Sbjct: 13 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVF 59

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 39.7 bits (93), Expect = 2e-05
 Identities = 10/40 (25%), Positives = 13/40 (32%)

Query: 40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDK 79
           P    + I  L     +ADL      FG +    V   K
Sbjct: 18 TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKK 57

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 39.6 bits (93), Expect = 2e-05
 Identities = 11/43 (25%), Positives = 16/43 (37%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
          +F   L       DL   F   G V   ++  D+ + RSK   
Sbjct: 28 VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIA 70

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 40.3 bits (94), Expect = 4e-05
 Identities = 17/61 (27%), Positives = 24/61 (39%), Gaps = 4/61 (6%)

Query: 32  GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTII 91
           GS   Q   P  A L + ++PP  S+ DL  +F   G V+    F  K     +    I 
Sbjct: 109 GSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----DRKMALIQ 164

Query: 92  F 92
            
Sbjct: 165 M 165

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 37.2 bits (86), Expect = 4e-04
 Identities = 12/50 (24%), Positives = 21/50 (42%), Gaps = 6/50 (12%)

Query: 44 ANLFIYHLPPE-FSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          + L + +L PE  +   L  +FG +G V   K+  +K     K    +  
Sbjct: 4  SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQM 48

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 38.8 bits (90), Expect = 6e-05
 Identities = 9/51 (17%), Positives = 23/51 (45%), Gaps = 2/51 (3%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNR--SKCFGTIIFMR 94
          +F+  LPP+  + ++ + F  FG ++       +  +    K +  ++F  
Sbjct: 11 VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQE 61

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 38.0 bits (89), Expect = 6e-05
 Identities = 11/44 (25%), Positives = 22/44 (50%), Gaps = 2/44 (4%)

Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKV 75
          GSSG   +G     L + ++ P  ++ +L + F  +G V+   +
Sbjct: 1  GSSGS--SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDI 42

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103

 Score = 38.0 bits (89), Expect = 8e-05
 Identities = 12/44 (27%), Positives = 18/44 (40%), Gaps = 1/44 (2%)

Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKV 75
          GSSG      +   LF+ +L    ++  L   F  FG +   K 
Sbjct: 1  GSSGSS-GMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKK 43

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 37.3 bits (87), Expect = 2e-04
 Identities = 11/61 (18%), Positives = 22/61 (36%), Gaps = 6/61 (9%)

Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTII 91
          GSSG + T      L++ +L    S+  +   F         +V       + + +  + 
Sbjct: 4  GSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV------KKIRDYAFVH 57

Query: 92 F 92
          F
Sbjct: 58 F 58

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 37.2 bits (87), Expect = 2e-04
 Identities = 11/44 (25%), Positives = 19/44 (43%), Gaps = 3/44 (6%)

Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKV 75
          GSSG          +F+ ++    +  +L S+F   G V+   V
Sbjct: 1  GSSGS---SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDV 41

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 37.4 bits (87), Expect = 2e-04
 Identities = 10/61 (16%), Positives = 19/61 (31%)

Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTII 91
          GSSG+           I ++P   +  D+           +A   +   N +      + 
Sbjct: 4  GSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQ 63

Query: 92 F 92
          F
Sbjct: 64 F 64

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 36.8 bits (86), Expect = 2e-04
 Identities = 15/44 (34%), Positives = 23/44 (52%), Gaps = 4/44 (9%)

Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKV 75
          GSSG          LFI +LP E ++ ++ S+F  +G VL   +
Sbjct: 1  GSSG----SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDI 40

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 38.3 bits (88), Expect = 3e-04
 Identities = 10/56 (17%), Positives = 22/56 (39%), Gaps = 7/56 (12%)

Query: 41 PEGANLFIYHLPPEFSDADLAS----MFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
               ++I +L  +    +L      +F  FG +L   V    ++ + +    +IF
Sbjct: 7  RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVS---RSLKMRGQAFVIF 59

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 36.6 bits (85), Expect = 3e-04
 Identities = 15/64 (23%), Positives = 22/64 (34%), Gaps = 3/64 (4%)

Query: 32 GSSGKQLTGPEGAN---LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFG 88
          GSSG     P+ AN   + +  LP   S  ++   F     V +          RS    
Sbjct: 1  GSSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEA 60

Query: 89 TIIF 92
           + F
Sbjct: 61 FVQF 64

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 36.1 bits (84), Expect = 4e-04
 Identities = 17/61 (27%), Positives = 23/61 (37%), Gaps = 9/61 (14%)

Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTII 91
          GSSG         ++F+   P     A L+  F  FG V  A V +DK       F  + 
Sbjct: 1  GSSGSSGLR----SVFVSGFPRGVDSAQLSEYFLAFGPV--ASVVMDKDKGV---FAIVE 51

Query: 92 F 92
           
Sbjct: 52 M 52

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 36.4 bits (84), Expect = 5e-04
 Identities = 7/81 (8%), Positives = 20/81 (24%)

Query: 12 GAGTMSPTALSGLASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVL 71
           +G +   +     +    +G             + +  LP   +  ++   F     V 
Sbjct: 11 SSGLVPRGSHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVP 70

Query: 72 SAKVFIDKQNNRSKCFGTIIF 92
          +          +      + F
Sbjct: 71 NGITLPVDPEGKITGEAFVQF 91

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

 Score = 35.6 bits (82), Expect = 8e-04
 Identities = 14/63 (22%), Positives = 27/63 (42%), Gaps = 3/63 (4%)

Query: 25 ASSNAAVGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRS 84
           SS ++   S      P  A++++ +LP +   +DL       G+V    + +  Q  R 
Sbjct: 1  GSSGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSV---PLRLTWQGPRR 57

Query: 85 KCF 87
          + F
Sbjct: 58 RAF 60

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	128
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.94
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.93
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.91
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.9
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.9
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.9
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.9
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.9
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.9
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.9
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.9
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.9
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.89
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.89
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.89
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.89
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.89
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.89
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.89
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.89
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.89
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.89
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.89
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.89
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.88
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.88
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.88
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.88
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.88
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.88
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.88
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.88
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.88
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.88
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.88
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.88
2div_A	99	TRNA selenocysteine associated protein; structural	99.88
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.88
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.88
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.88
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.88
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.88
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.88
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.88
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.88
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.88
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.88
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.88
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.88
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.88
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.88
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.87
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.87
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.87
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.87
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.87
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.87
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.87
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.87
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.87
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.87
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.87
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.87
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.87
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.87
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.87
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.87
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.86
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.86
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.86
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.86
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.86
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.86
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.86
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.86
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.86
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.86
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.86
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.86
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.86
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.86
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.86
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.85
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.85
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.85
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.85
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.85
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.85
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.85
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.85
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.85
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.85
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.85
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.85
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.85
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.85
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.84
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.84
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.84
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.84
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.84
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.84
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.83
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.83
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.83
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.83
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.83
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.83
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.83
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.83
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.83
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.83
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.83
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.72
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.83
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.82
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.82
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.82
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.82
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.82
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.82
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.82
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.82
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.82
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.82
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.82
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.82
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.82
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.82
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.81
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.81
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.81
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.81
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.81
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.81
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.81
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.81
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.8
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.8
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.8
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.8
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.8
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.8
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.8
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.8
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.8
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.8
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.8
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.79
1x5p_A	97	Negative elongation factor E; structure genomics,	99.79
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.79
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.79
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.79
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.79
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.79
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.79
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.78
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.78
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.78
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.78
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.78
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.77
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.77
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.77
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.77
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.77
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.77
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.76
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.76
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.76
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.76
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.75
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.75
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.75
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.75
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.75
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.74
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.74
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.73
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.73
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.73
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.73
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.72
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.72
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.71
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.71
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.69
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.68
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.68
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.68
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.67
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.66
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.66
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.65
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.65
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.64
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.64
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.63
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.63
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.63
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.57
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.54
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.52
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.43
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.42
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.31
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.29
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	99.27
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.38
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.88
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.62
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.43
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.37
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	96.56
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	96.44
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.29
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	95.75
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.42
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	95.37
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	90.32
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	87.47
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	83.85

>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=99.94  E-value=9.4e-27  Score=146.28  Aligned_cols=83  Identities=27%  Similarity=0.350  Sum_probs=78.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ..++++|||+|||+++++++|+++|++||.|.+++++.|+.||+++|||||+|.+.+ +|.+|++.|||. ++|+.|+|+
T Consensus        16 ~~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~-~A~~Ai~~lng~~~~gr~l~V~   94 (99)
T 4fxv_A           16 YFQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAK-DAERAINTLNGLRLQSKTIKVS   94 (99)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHH-HHHHHHHHHTTCEETTEECEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHH-HHHHHHHHhCCCEECCEEEEEE
Confidence            355899999999999999999999999999999999999999999999999997777 999999999999 999999999


Q ss_pred             ecccc
Q psy8615         119 FNTYV  123 (128)
Q Consensus       119 ~~~~~  123 (128)
                      |++|+
T Consensus        95 ~AkPS   99 (99)
T 4fxv_A           95 YARPS   99 (99)
T ss_dssp             ECCBC
T ss_pred             EeeCC
Confidence            99974

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

Probab=99.93  E-value=2.2e-25  Score=143.39  Aligned_cols=88  Identities=52%  Similarity=0.876  Sum_probs=80.5

Q ss_pred             CCCCCCCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CC
Q psy8615          33 SSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LG  111 (128)
Q Consensus        33 ~~~~~~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~  111 (128)
                      ....+.+..+.++|||+|||+++++++|+++|++||.|.+++++.++.+|+++|||||+|.+.+ +|++|++.|||. ++
T Consensus        30 ~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~-~A~~A~~~l~g~~~~  108 (118)
T 2khc_A           30 AAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPD-SAQVAIKAMNGFQVG  108 (118)
T ss_dssp             CCSSSCCCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSH-HHHHHHHHCCCCEET
T ss_pred             cCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHH-HHHHHHHHcCCCEEC
Confidence            3444556677899999999999999999999999999999999999999999999999998888 999999999999 99


Q ss_pred             CeEEEEEecc
Q psy8615         112 QSFLKPSFNT  121 (128)
Q Consensus       112 ~~~l~V~~~~  121 (128)
                      |+.|+|.|++
T Consensus       109 g~~l~V~~ak  118 (118)
T 2khc_A          109 TKRLKVQLKK  118 (118)
T ss_dssp             TEECCEEEC-
T ss_pred             CEEEEEEecC
Confidence            9999999975

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.91  E-value=3.8e-24  Score=136.76  Aligned_cols=81  Identities=7%  Similarity=0.104  Sum_probs=76.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      ++.++|||+|||+++++++|+++|++||.|.+++++.|+.||+++|||||+|++.+ +|.+|++.|||. ++|+.|+|.+
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~-~A~~Ai~~lng~~~~gr~i~V~~   82 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTR-GAKETVKNLHLTSVMGNIIHAQL   82 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHH-HHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHH-HHHHHHHHhCCCEECCeEEEEEE
Confidence            44679999999999999999999999999999999999999999999999997777 999999999999 9999999999


Q ss_pred             ccc
Q psy8615         120 NTY  122 (128)
Q Consensus       120 ~~~  122 (128)
                      +..
T Consensus        83 a~~   85 (110)
T 3s8s_A           83 DIK   85 (110)
T ss_dssp             CST
T ss_pred             CCC
Confidence            864

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.90  E-value=3.1e-23  Score=130.38  Aligned_cols=88  Identities=20%  Similarity=0.329  Sum_probs=80.9

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCe
Q psy8615          35 GKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQS  113 (128)
Q Consensus        35 ~~~~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~  113 (128)
                      .++.+..+.++|||+|||+++++++|+++|++||.|.+++++.++.+|+++|||||+|.+.+ +|..|++.||+. ++|+
T Consensus         7 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-~A~~A~~~l~g~~~~g~   85 (103)
T 2cq0_A            7 GPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRE-DAARAIAGVSGFGYDHL   85 (103)
T ss_dssp             CSCCCCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHH-HHHHHHHHTTTCEETTE
T ss_pred             CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHH-HHHHHHHHcCCCeeCCc
Confidence            33445666889999999999999999999999999999999999999999999999997777 999999999999 9999


Q ss_pred             EEEEEecccc
Q psy8615         114 FLKPSFNTYV  123 (128)
Q Consensus       114 ~l~V~~~~~~  123 (128)
                      .|+|.|.++.
T Consensus        86 ~l~v~~a~~~   95 (103)
T 2cq0_A           86 ILNVEWAKPS   95 (103)
T ss_dssp             ECEEEESSCC
T ss_pred             EEEEEECCCC
Confidence            9999999875

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.90  E-value=3e-23  Score=128.26  Aligned_cols=83  Identities=23%  Similarity=0.362  Sum_probs=77.3

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEE
Q psy8615          38 LTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLK  116 (128)
Q Consensus        38 ~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~  116 (128)
                      ...+..++|||+|||.++++++|+++|++||.|.++++..++.+|+++|||||+|.+.+ +|++|++.||+. ++|+.|+
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~-~A~~A~~~l~g~~~~g~~l~   89 (94)
T 2e5h_A           11 GLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKD-SAQNCTRAINNKQLFGRVIK   89 (94)
T ss_dssp             SCCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHH-HHHHHHHHTTTEEETTEEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHH-HHHHHHHHcCCCeeCCcEEE
Confidence            33456789999999999999999999999999999999999999999999999997777 999999999999 9999999


Q ss_pred             EEecc
Q psy8615         117 PSFNT  121 (128)
Q Consensus       117 V~~~~  121 (128)
                      |+|+|
T Consensus        90 v~~ak   94 (94)
T 2e5h_A           90 ASIAI   94 (94)
T ss_dssp             EEECC
T ss_pred             EEecC
Confidence            99985

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A

Probab=99.90  E-value=2.3e-23  Score=133.42  Aligned_cols=86  Identities=51%  Similarity=0.824  Sum_probs=79.7

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEE
Q psy8615          37 QLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFL  115 (128)
Q Consensus        37 ~~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l  115 (128)
                      +...++.++|||+|||+++++++|+++|++||.|.+++++.++.+|+++|||||+|.+.+ +|++|++.||+. ++|+.|
T Consensus        19 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~-~a~~A~~~l~g~~~~g~~l   97 (115)
T 2cpz_A           19 QKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPV-SAQAAIQSMNGFQIGMKRL   97 (115)
T ss_dssp             CCCCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHH-HHHHHHHHHTTCEETTEEC
T ss_pred             CcCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHH-HHHHHHHHcCCCEECCEEE
Confidence            444556789999999999999999999999999999999999989999999999997777 999999999999 999999


Q ss_pred             EEEecccc
Q psy8615         116 KPSFNTYV  123 (128)
Q Consensus       116 ~V~~~~~~  123 (128)
                      +|.|+++.
T Consensus        98 ~V~~a~~~  105 (115)
T 2cpz_A           98 KVQLKRSK  105 (115)
T ss_dssp             EEECCCCS
T ss_pred             EEEEcCCC
Confidence            99999864

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.90  E-value=4.4e-23  Score=127.64  Aligned_cols=84  Identities=19%  Similarity=0.225  Sum_probs=77.9

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEE
Q psy8615          38 LTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLK  116 (128)
Q Consensus        38 ~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~  116 (128)
                      ......++|||+|||+++++++|+++|++||.|.+++++.++.+|+++|||||+|.+.+ +|.+|++.||+. ++|+.|+
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~-~A~~A~~~l~g~~~~g~~l~   88 (95)
T 2cqc_A           10 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD-DAKEAKERANGMELDGRRIR   88 (95)
T ss_dssp             CSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHH-HHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHH-HHHHHHHHhCCCEECCEEEE
Confidence            33455789999999999999999999999999999999999999999999999997777 999999999999 9999999


Q ss_pred             EEeccc
Q psy8615         117 PSFNTY  122 (128)
Q Consensus       117 V~~~~~  122 (128)
                      |.|++.
T Consensus        89 v~~a~~   94 (95)
T 2cqc_A           89 VSGPSS   94 (95)
T ss_dssp             EECCSC
T ss_pred             EEecCC
Confidence            999874

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.90  E-value=1.2e-22  Score=127.08  Aligned_cols=83  Identities=16%  Similarity=0.242  Sum_probs=77.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEE
Q psy8615          39 TGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKP  117 (128)
Q Consensus        39 ~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V  117 (128)
                      ...+.++|||+|||+++++++|+++|++||.|.++++..++ +|+++|||||+|.+.+ +|.+|++.||+. ++|+.|+|
T Consensus        13 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~-~a~~A~~~l~g~~~~g~~l~v   90 (100)
T 2do4_A           13 TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENES-QASQAVMKMDGMTIKENIIKV   90 (100)
T ss_dssp             SCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHH-HHHHHHHHHTTEESSSCEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHH-HHHHHHHHhCCCEECCEEEEE
Confidence            34557899999999999999999999999999999999998 7999999999997777 999999999999 99999999


Q ss_pred             Eecccc
Q psy8615         118 SFNTYV  123 (128)
Q Consensus       118 ~~~~~~  123 (128)
                      .|+++.
T Consensus        91 ~~a~~~   96 (100)
T 2do4_A           91 AISNSG   96 (100)
T ss_dssp             EECCCC
T ss_pred             EECCCC
Confidence            999875

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.90  E-value=5.3e-23  Score=128.54  Aligned_cols=82  Identities=17%  Similarity=0.254  Sum_probs=76.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEE--------EEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-
Q psy8615          39 TGPEGANLFIYHLPPEFSDADLASMFGPFGTVLS--------AKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-  109 (128)
Q Consensus        39 ~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~--------~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-  109 (128)
                      ..+..++|||+|||+++++++|+++|++||.|.+        ++++.++.+|+++|||||+|.+.+ +|.+|++.|||. 
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~-~a~~Ai~~l~g~~   87 (99)
T 2la6_A            9 SHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP-SAKAAIDWFDGKE   87 (99)
T ss_dssp             SCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHH-HHHHHHHHHTTCB
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHH-HHHHHHHHhCCCE
Confidence            3455789999999999999999999999999999        999999999999999999997777 999999999999 


Q ss_pred             CCCeEEEEEecc
Q psy8615         110 LGQSFLKPSFNT  121 (128)
Q Consensus       110 ~~~~~l~V~~~~  121 (128)
                      ++|+.|+|.|++
T Consensus        88 ~~g~~l~V~~A~   99 (99)
T 2la6_A           88 FSGNPIKVSFAT   99 (99)
T ss_dssp             SSSSBCEEEECC
T ss_pred             eCCcEEEEEecC
Confidence            999999999975

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.90  E-value=1.5e-23  Score=130.76  Aligned_cols=80  Identities=10%  Similarity=0.230  Sum_probs=74.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCc--eEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-----CCCeEE
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGT--VLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-----LGQSFL  115 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~--i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-----~~~~~l  115 (128)
                      -.+|||+|||+++++++|+++|++||.  +.+|++++|+.||+++|||||+|.+.+ +|.+|++.||+.     ++||+|
T Consensus         9 m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~-~A~~Ai~~lng~~~~~~i~Gr~i   87 (95)
T 2lkz_A            9 MDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAM-DASQLLQILQSLHPPLKIDGKTI   87 (95)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSH-HHHHHHHHHHSSSSCEEETTEEE
T ss_pred             cCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHH-HHHHHHHHhcCCCCCceECCEEE
Confidence            458999999999999999999999995  678999999999999999999998888 999999999983     889999


Q ss_pred             EEEecccc
Q psy8615         116 KPSFNTYV  123 (128)
Q Consensus       116 ~V~~~~~~  123 (128)
                      +|+|++.+
T Consensus        88 ~V~~Akss   95 (95)
T 2lkz_A           88 GVDFAKSA   95 (95)
T ss_dssp             EEEECCCC
T ss_pred             EEEEccCC
Confidence            99999863

>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=99.90  E-value=5.2e-23  Score=124.41  Aligned_cols=79  Identities=24%  Similarity=0.314  Sum_probs=75.3

Q ss_pred             CeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEeccc
Q psy8615          44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNTY  122 (128)
Q Consensus        44 ~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~~  122 (128)
                      ++|||+|||.++++++|+++|++||.|.+++++.++.+|+++|||||+|.+.+ +|+.|++.|||. ++|+.|+|.|+++
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~-~a~~a~~~l~g~~~~g~~l~v~~a~~   80 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQD-DAQNAMDSMQGQDLNGRPLRINWAAK   80 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHH-HHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHH-HHHHHHHHhcCCeeCCcEEEEEecCc
Confidence            58999999999999999999999999999999999999999999999997777 999999999999 9999999999986


Q ss_pred             c
Q psy8615         123 V  123 (128)
Q Consensus       123 ~  123 (128)
                      .
T Consensus        81 ~   81 (83)
T 3md1_A           81 L   81 (83)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.90  E-value=6.6e-23  Score=131.21  Aligned_cols=87  Identities=23%  Similarity=0.433  Sum_probs=80.2

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeE
Q psy8615          36 KQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSF  114 (128)
Q Consensus        36 ~~~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~  114 (128)
                      ...+..+.++|||+|||+++++++|+++|++||.|.+++++.++.+|.++|||||+|.+.+ +|++|++.||+. ++|+.
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-~a~~A~~~l~g~~~~g~~   86 (115)
T 2dgo_A            8 QKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKW-DAENAIQQMGGQWLGGRQ   86 (115)
T ss_dssp             SCCCSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHH-HHHHHHHHTTTCEETTEE
T ss_pred             CCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHHhCCCEECCEE
Confidence            3445566889999999999999999999999999999999999989999999999997777 999999999999 99999


Q ss_pred             EEEEecccc
Q psy8615         115 LKPSFNTYV  123 (128)
Q Consensus       115 l~V~~~~~~  123 (128)
                      |+|.|+++.
T Consensus        87 l~V~~a~~~   95 (115)
T 2dgo_A           87 IRTNWATRK   95 (115)
T ss_dssp             CEEEESSCC
T ss_pred             EEEEEccCC
Confidence            999999864

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}

Probab=99.89  E-value=3.5e-23  Score=126.22  Aligned_cols=82  Identities=26%  Similarity=0.450  Sum_probs=75.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      .+.++|||+|||.++++++|+++|++||.|.+++++.++.+|+++|||||+|.+.+ +|+.|++.||+. ++|+.|+|.|
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-~A~~A~~~l~g~~~~g~~l~v~~   82 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKW-DAENAIQQMGGQWLGGRQIRTNW   82 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHH-HHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHH-HHHHHHHHcCCCEECCeEEEEEe
Confidence            34679999999999999999999999999999999999989999999999997777 999999999999 9999999999


Q ss_pred             cccc
Q psy8615         120 NTYV  123 (128)
Q Consensus       120 ~~~~  123 (128)
                      +++.
T Consensus        83 a~~k   86 (87)
T 3bs9_A           83 ATRK   86 (87)
T ss_dssp             EC--
T ss_pred             cCCC
Confidence            9864

>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=99.89  E-value=4.6e-23  Score=129.92  Aligned_cols=86  Identities=13%  Similarity=0.123  Sum_probs=79.5

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEE
Q psy8615          38 LTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLK  116 (128)
Q Consensus        38 ~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~  116 (128)
                      .+....++|||+|||+++++++|+++|++||.|.++++..++.+|+++|||||+|.+.+ +|.+|++.||+. ++|+.|+
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-~a~~A~~~l~g~~~~g~~l~   88 (105)
T 1x5u_A           10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEE-DADYAIKIMDMIKLYGKPIR   88 (105)
T ss_dssp             CCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHH-HHHHHHHHSSSCBCSSCBCE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHH-HHHHHHHHhCCCeECCeEEE
Confidence            34456789999999999999999999999999999999999989999999999997777 999999999999 9999999


Q ss_pred             EEeccccc
Q psy8615         117 PSFNTYVL  124 (128)
Q Consensus       117 V~~~~~~~  124 (128)
                      |.|+++.-
T Consensus        89 v~~a~~~~   96 (105)
T 1x5u_A           89 VNKASAHN   96 (105)
T ss_dssp             EEETTTTS
T ss_pred             EEECCCCC
Confidence            99998753

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ISO mRNA processing, mRNA splicing, nucleus; 1.85A {Homo sapiens} SCOP: d.58.7.1 PDB: 2kyx_A 3lpy_A*

Probab=99.89  E-value=3.3e-23  Score=125.81  Aligned_cols=81  Identities=19%  Similarity=0.267  Sum_probs=76.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ..+.++|||+|||+++++++|+++|++||.|.+++++.++.+|+++|||||+|.+.+ +|..|++.|||. ++|+.|+|+
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-~a~~A~~~l~g~~~~g~~l~v~   82 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE-DAAAAIDNMNESELFGRTIRVN   82 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHH-HHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHH-HHHHHHHHhCCCEECCcEEEEE
Confidence            345789999999999999999999999999999999999999999999999997777 999999999999 999999999


Q ss_pred             ecc
Q psy8615         119 FNT  121 (128)
Q Consensus       119 ~~~  121 (128)
                      |++
T Consensus        83 ~ak   85 (85)
T 3mdf_A           83 LAK   85 (85)
T ss_dssp             ECC
T ss_pred             EcC
Confidence            985

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C

Probab=99.89  E-value=8.2e-24  Score=130.27  Aligned_cols=81  Identities=20%  Similarity=0.140  Sum_probs=71.1

Q ss_pred             CeEEEcCCCCCCCHHHHHhhhcCCC--ceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          44 ANLFIYHLPPEFSDADLASMFGPFG--TVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        44 ~~l~V~nLp~~~~e~~l~~~f~~~G--~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      .+|||+|||+++++++|+++|++||  .|.+++++.|+.+|+++|||||+|.+.+ +|++|++.|||. ++|+.|+|.++
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~-~a~~Ai~~l~g~~~~gr~i~V~~~   80 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEA-SSKKLMDLLPKRELHGQNPVVTPS   80 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHH-HHHHHHHHGGGSCSSSCCCEECCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHH-HHHHHHHHcCCCeeCCEEEEEEEC
Confidence            4799999999999999999999999  9999999999999999999999997777 999999999999 99999999999


Q ss_pred             ccccc
Q psy8615         121 TYVLM  125 (128)
Q Consensus       121 ~~~~~  125 (128)
                      ++...
T Consensus        81 ~~~~~   85 (90)
T 3p5t_L           81 NKLEH   85 (90)
T ss_dssp             -----
T ss_pred             CCCcc
Confidence            87653

>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=99.89  E-value=9.7e-23  Score=129.64  Aligned_cols=86  Identities=23%  Similarity=0.339  Sum_probs=79.6

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEE
Q psy8615          37 QLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFL  115 (128)
Q Consensus        37 ~~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l  115 (128)
                      +...+..++|||+|||.++++++|+++|++||.|.+++++.++.+|+++|||||+|.+.+ +|..|++.|||. ++|+.|
T Consensus        20 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~-~A~~Ai~~l~g~~i~g~~l   98 (108)
T 2jrs_A           20 QKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSE-CAKKALEQLNGFELAGRPM   98 (108)
T ss_dssp             CCSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHH-HHHHHHHHHTTCCSSSSCC
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHH-HHHHHHHHcCCCEECCEEE
Confidence            344556789999999999999999999999999999999999999999999999997777 999999999999 999999


Q ss_pred             EEEecccc
Q psy8615         116 KPSFNTYV  123 (128)
Q Consensus       116 ~V~~~~~~  123 (128)
                      +|+|+++.
T Consensus        99 ~V~~a~~k  106 (108)
T 2jrs_A           99 KVGHVTER  106 (108)
T ss_dssp             EEECSCSS
T ss_pred             EEEEcccC
Confidence            99999864

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.89  E-value=8.8e-23  Score=128.30  Aligned_cols=84  Identities=14%  Similarity=0.087  Sum_probs=78.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEE
Q psy8615          39 TGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKP  117 (128)
Q Consensus        39 ~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V  117 (128)
                      +....++|||+|||+++++++|+++|++||.|.++++..++.||+++|||||+|.+.+ +|++|++.||+. ++|+.|+|
T Consensus         9 ~~~~~~~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            9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRR-DAQDAEAAMDGAELDGRELRV   87 (103)
T ss_dssp             CCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSS-HHHHHHHHHSSCCBTTBCCEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHH-HHHHHHHHcCCCEECCcEEEE
Confidence            4455789999999999999999999999999999999999999999999999998888 999999999999 99999999


Q ss_pred             Eecccc
Q psy8615         118 SFNTYV  123 (128)
Q Consensus       118 ~~~~~~  123 (128)
                      .|+++.
T Consensus        88 ~~a~~~   93 (103)
T 2dnm_A           88 QVARYG   93 (103)
T ss_dssp             EECSSC
T ss_pred             EECCcC
Confidence            999864

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.89  E-value=9.3e-23  Score=126.27  Aligned_cols=83  Identities=22%  Similarity=0.336  Sum_probs=77.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      +..++|||+|||.++++++|+++|++||.|.++++..++.+|+++|||||+|.+.+ +|.+|++.||+. ++|+.|+|.|
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~-~a~~A~~~l~g~~~~g~~l~V~~   81 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSE-CARRALEQLNGFELAGRPMRVGH   81 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHH-HHHHHHHHHTTCCSSSSCCEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHH-HHHHHHHHhCCCeeCCcEEEEEE
Confidence            45789999999999999999999999999999999999999999999999997777 999999999999 9999999999


Q ss_pred             ccccc
Q psy8615         120 NTYVL  124 (128)
Q Consensus       120 ~~~~~  124 (128)
                      .++..
T Consensus        82 a~~~~   86 (95)
T 2dnz_A           82 VTERL   86 (95)
T ss_dssp             SSCCC
T ss_pred             ccccc
Confidence            98753

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.89  E-value=1.1e-23  Score=132.29  Aligned_cols=80  Identities=15%  Similarity=0.062  Sum_probs=75.7

Q ss_pred             CCCeEEEcCCCC------CCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCC-e
Q psy8615          42 EGANLFIYHLPP------EFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQ-S  113 (128)
Q Consensus        42 ~~~~l~V~nLp~------~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~-~  113 (128)
                      ..++|||+|||.      ++++++|+++|++||.|.+++++.|+.||+++|||||+|.+.+ +|.+|++.|||. ++| +
T Consensus         5 ~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~-~A~~Ai~~lng~~~~g~r   83 (100)
T 3ns6_A            5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMN-DAKKIIKSFHGKRLDLKH   83 (100)
T ss_dssp             GGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHH-HHHHHHHHHTTCBSSSSC
T ss_pred             cCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHH-HHHHHHHHhCCcccCCCe
Confidence            367999999999      9999999999999999999999999999999999999997777 999999999999 998 9


Q ss_pred             EEEEEeccc
Q psy8615         114 FLKPSFNTY  122 (128)
Q Consensus       114 ~l~V~~~~~  122 (128)
                      .|+|.+.++
T Consensus        84 ~l~V~~a~~   92 (100)
T 3ns6_A           84 RLFLYTMKD   92 (100)
T ss_dssp             BCEEEESHH
T ss_pred             EEEEEECch
Confidence            999999875

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.89  E-value=6e-23  Score=138.57  Aligned_cols=82  Identities=13%  Similarity=0.127  Sum_probs=76.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCCC--ceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPFG--TVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~G--~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      +.++|||+|||+++++++|+++|++||  .|.+++++.|+.||+++|||||+|.+.+ +|.+|++.|||. ++|+.|+|.
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~-~A~~Ai~~lng~~~~Gr~l~V~  132 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASEN-SVHKLLELLPGKVLNGEKVDVR  132 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHH-HHHHHHHHSTTCEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHH-HHHHHHHHcCCCEECCeEeEEE
Confidence            468999999999999999999999999  9999999999999999999999997777 999999999999 999999999


Q ss_pred             eccccc
Q psy8615         119 FNTYVL  124 (128)
Q Consensus       119 ~~~~~~  124 (128)
                      ++++..
T Consensus       133 ~a~~~~  138 (156)
T 3n9u_C          133 PATRQN  138 (156)
T ss_dssp             ECCHHH
T ss_pred             EcCCCc
Confidence            998653

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A

Probab=99.89  E-value=3.4e-22  Score=125.93  Aligned_cols=83  Identities=20%  Similarity=0.235  Sum_probs=76.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCC---eE
Q psy8615          39 TGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQ---SF  114 (128)
Q Consensus        39 ~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~---~~  114 (128)
                      .....++|||+|||+++++++|+++|++||.|.++++..++ +|+++|||||+|.+.+ +|.+|++.||+. +.+   +.
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~-~A~~Ai~~l~g~~~~gg~~~~   88 (105)
T 2dnh_A           11 RGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHT-EAQAAIHALHGSQTMPGASSS   88 (105)
T ss_dssp             SCCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHH-HHHHHHHHHSSCCCCTTCSSC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHH-HHHHHHHHHcCCccCCCCCcc
Confidence            34558899999999999999999999999999999999998 6999999999997777 999999999998 776   99


Q ss_pred             EEEEecccc
Q psy8615         115 LKPSFNTYV  123 (128)
Q Consensus       115 l~V~~~~~~  123 (128)
                      |+|.|+++.
T Consensus        89 l~V~~a~~~   97 (105)
T 2dnh_A           89 LVVKFADTD   97 (105)
T ss_dssp             CEEEESCSS
T ss_pred             EEEEECccC
Confidence            999999764

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.89  E-value=1e-22  Score=128.56  Aligned_cols=83  Identities=14%  Similarity=0.191  Sum_probs=77.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ..+.++|||+|||.++++++|+++|++||.|.++++..++.+|+++|||||+|.+.+ +|..|++.|||. ++|+.|+|.
T Consensus        20 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-~a~~A~~~l~g~~~~g~~l~V~   98 (106)
T 1p27_B           20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK-EAQAAMEGLNGQDLMGQPISVD   98 (106)
T ss_dssp             BTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHH-HHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHH-HHHHHHHHhcCCEECCcEEEEE
Confidence            445789999999999999999999999999999999999999999999999997777 999999999999 999999999


Q ss_pred             ecccc
Q psy8615         119 FNTYV  123 (128)
Q Consensus       119 ~~~~~  123 (128)
                      |+++.
T Consensus        99 ~a~~~  103 (106)
T 1p27_B           99 WCFVR  103 (106)
T ss_dssp             ESEES
T ss_pred             eecCC
Confidence            98764

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.89  E-value=2.1e-22  Score=127.93  Aligned_cols=84  Identities=20%  Similarity=0.252  Sum_probs=78.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhc------Cc-CC
Q psy8615          39 TGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTAN------DY-LG  111 (128)
Q Consensus        39 ~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~------g~-~~  111 (128)
                      .....++|||+|||+++++++|+++|++||.|.+|+++.++.+|.++|||||+|.+.+ +|.+|++.||      +. ++
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~-~A~~A~~~~~~~~~~~~~~~~   89 (111)
T 1x4h_A           11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQE-AAQKCLAAASLEAEGGGLKLD   89 (111)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHH-HHHHHHHHHCTTTTTCCEESS
T ss_pred             cCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHH-HHHHHHHHhccccccCCcEEc
Confidence            3455789999999999999999999999999999999999999999999999997777 9999999999      98 99


Q ss_pred             CeEEEEEecccc
Q psy8615         112 QSFLKPSFNTYV  123 (128)
Q Consensus       112 ~~~l~V~~~~~~  123 (128)
                      |+.|+|.|+++.
T Consensus        90 g~~l~v~~a~~~  101 (111)
T 1x4h_A           90 GRQLKVDLAVTR  101 (111)
T ss_dssp             SCEEEEECCCCC
T ss_pred             CEEEEEEECCCC
Confidence            999999998764

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.88  E-value=8.1e-23  Score=128.17  Aligned_cols=84  Identities=18%  Similarity=0.243  Sum_probs=78.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ....++|||+|||+++++++|+++|++||.|.+++++.++.+|+++|||||+|.+.+ +|.+|++.||+. ++|+.|+|.
T Consensus         9 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-~A~~A~~~l~g~~~~g~~l~V~   87 (102)
T 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE-DAAAAIDNMNESELFGRTIRVN   87 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHH-HHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHH-HHHHHHHHhCCCEECCcEEEEE
Confidence            345789999999999999999999999999999999999999999999999997777 999999999999 999999999


Q ss_pred             eccccc
Q psy8615         119 FNTYVL  124 (128)
Q Consensus       119 ~~~~~~  124 (128)
                      |+++.-
T Consensus        88 ~a~~~~   93 (102)
T 2cqb_A           88 LAKPMR   93 (102)
T ss_dssp             ECCCCC
T ss_pred             eCCCCC
Confidence            998753

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.88  E-value=3.3e-22  Score=125.63  Aligned_cols=84  Identities=29%  Similarity=0.383  Sum_probs=77.1

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEE
Q psy8615          37 QLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFL  115 (128)
Q Consensus        37 ~~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l  115 (128)
                      .....+.++|||+|||+++++++|+++|++||.|.++++..+  +|.++|||||+|.+.+ +|..|++.||+. ++|+.|
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~-~A~~A~~~l~g~~~~g~~l   85 (103)
T 2d9p_A            9 RITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPE-EATKAVTEMNGRIVATKPL   85 (103)
T ss_dssp             CCCCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHH-HHHHHHHHHTTCBSSSSBC
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHH-HHHHHHHHhCCCEeCCcEE
Confidence            344556889999999999999999999999999999999998  6999999999997777 999999999999 999999


Q ss_pred             EEEecccc
Q psy8615         116 KPSFNTYV  123 (128)
Q Consensus       116 ~V~~~~~~  123 (128)
                      +|.|+++.
T Consensus        86 ~V~~a~~~   93 (103)
T 2d9p_A           86 YVALAQRK   93 (103)
T ss_dssp             EEEECSSC
T ss_pred             EEEEeccc
Confidence            99998764

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.88  E-value=1.6e-22  Score=127.75  Aligned_cols=85  Identities=13%  Similarity=0.228  Sum_probs=78.4

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEec-CCCCCcceEEEEEEecCHHHHHHHHHHh-cCc-CCCeE
Q psy8615          38 LTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFID-KQNNRSKCFGTIIFMRKFFILTIRFDTA-NDY-LGQSF  114 (128)
Q Consensus        38 ~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~-~~tg~~~g~~fv~f~~~~~~a~~Ai~~l-~g~-~~~~~  114 (128)
                      ......++|||+|||+++++++|+++|++||.|.+++++.+ +.+|+++|||||+|.+.+ +|.+|++.| |+. ++|+.
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~-~a~~A~~~l~~~~~~~g~~   88 (107)
T 2cph_A           10 PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQ-DAKKAFNALCHSTHLYGRR   88 (107)
T ss_dssp             CCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHH-HHHHHHHHHHTCCBSSSCB
T ss_pred             ccCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHH-HHHHHHHHhccCCeECCCE
Confidence            34556789999999999999999999999999999999999 788999999999997777 999999999 899 99999


Q ss_pred             EEEEecccc
Q psy8615         115 LKPSFNTYV  123 (128)
Q Consensus       115 l~V~~~~~~  123 (128)
                      |+|.|+++.
T Consensus        89 l~v~~a~~~   97 (107)
T 2cph_A           89 LVLEWADSE   97 (107)
T ss_dssp             CEEEECCCC
T ss_pred             EEEEeCCCC
Confidence            999999875

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.88  E-value=1.8e-22  Score=126.04  Aligned_cols=82  Identities=17%  Similarity=0.286  Sum_probs=76.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ....++|||+|||+++++++|+++|++||.|.+++++.++.+|+++|||||+|.+.+ +|.+|++ +|+. ++|+.|+|.
T Consensus         7 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-~a~~A~~-~~~~~~~g~~l~V~   84 (99)
T 2dgs_A            7 GSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQ-SVDQAVN-MHFHDIMGKKVEVK   84 (99)
T ss_dssp             CSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHH-HHHHHHH-HCCCBSSSCBCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHH-HHHHHHH-hCCCEECCeEEEEE
Confidence            345789999999999999999999999999999999999999999999999997777 9999999 9999 999999999


Q ss_pred             ecccc
Q psy8615         119 FNTYV  123 (128)
Q Consensus       119 ~~~~~  123 (128)
                      |.++.
T Consensus        85 ~a~~~   89 (99)
T 2dgs_A           85 RAEPR   89 (99)
T ss_dssp             ECCCC
T ss_pred             ECCCC
Confidence            99865

>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=99.88  E-value=1.3e-22  Score=126.52  Aligned_cols=82  Identities=20%  Similarity=0.269  Sum_probs=77.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      .+.++|||+|||+++++++|+++|++||.|.+++++.++.+|+++|||||+|.+.+ +|.+|++.||+. ++|+.|+|.|
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-~a~~A~~~l~g~~~~g~~l~V~~   84 (99)
T 1whw_A            6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPE-HAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHH-HHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHH-HHHHHHHHhCCCEECCcEEEEEE
Confidence            45789999999999999999999999999999999999988999999999997777 999999999999 9999999999


Q ss_pred             cccc
Q psy8615         120 NTYV  123 (128)
Q Consensus       120 ~~~~  123 (128)
                      +++.
T Consensus        85 a~~~   88 (99)
T 1whw_A           85 STIK   88 (99)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9875

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B

Probab=99.88  E-value=1.1e-22  Score=126.49  Aligned_cols=81  Identities=22%  Similarity=0.360  Sum_probs=76.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecc
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNT  121 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~  121 (128)
                      .++|||+|||.++++++|+++|++||.|.++++..++.+|+++|||||+|.+.+ +|..|++.|||. ++|+.|+|.|++
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~-~A~~Ai~~l~g~~~~g~~l~V~~a~   80 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLE-SSASAVRNLNGYQLGSRFLKCGYSS   80 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHH-HHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHH-HHHHHHHHhCCCeECCeEEEEEEcC
Confidence            579999999999999999999999999999999999999999999999997777 999999999999 999999999998


Q ss_pred             ccc
Q psy8615         122 YVL  124 (128)
Q Consensus       122 ~~~  124 (128)
                      +.-
T Consensus        81 ~~~   83 (96)
T 2x1f_A           81 NSD   83 (96)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            754

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.88  E-value=9.9e-24  Score=130.45  Aligned_cols=79  Identities=11%  Similarity=0.178  Sum_probs=73.4

Q ss_pred             CeEEEcCCCCCCCHHHHHhhhcCCC-ceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhc-Cc-CCCeEEEEEec
Q psy8615          44 ANLFIYHLPPEFSDADLASMFGPFG-TVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTAN-DY-LGQSFLKPSFN  120 (128)
Q Consensus        44 ~~l~V~nLp~~~~e~~l~~~f~~~G-~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~-g~-~~~~~l~V~~~  120 (128)
                      .+|||+|||++++|++|+++|++|| .|.++++++|+.||+++|||||+|.+.+ +|.+|++.++ +. ++|+.|+|.|+
T Consensus         2 ~~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            2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQ-DATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHH-HHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHH-HHHHHHHhcCCCeEECCEEEEEEEc
Confidence            5799999999999999999999999 8999999999999999999999997777 9999999885 55 99999999999


Q ss_pred             ccc
Q psy8615         121 TYV  123 (128)
Q Consensus       121 ~~~  123 (128)
                      ++.
T Consensus        81 ~~~   83 (91)
T 2lxi_A           81 DPK   83 (91)
T ss_dssp             CSC
T ss_pred             CCC
Confidence            875

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.88  E-value=4e-22  Score=125.36  Aligned_cols=82  Identities=18%  Similarity=0.220  Sum_probs=75.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEE
Q psy8615          39 TGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKP  117 (128)
Q Consensus        39 ~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V  117 (128)
                      .....++|||+|||+++++++|+++|++|| |.+++++.++.||+++|||||+|.+.+ +|.+|+ .||+. ++|+.|+|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~-~a~~A~-~l~g~~~~g~~l~V   87 (103)
T 2dng_A           11 PTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVD-SLKEAL-TYDGALLGDRSLRV   87 (103)
T ss_dssp             CSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHH-HHHHHG-GGTTCEETTEECEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHH-HHHHHH-hhCCCeECCeEEEE
Confidence            344578999999999999999999999997 999999999999999999999997777 999999 89999 99999999


Q ss_pred             Eecccc
Q psy8615         118 SFNTYV  123 (128)
Q Consensus       118 ~~~~~~  123 (128)
                      .|+++.
T Consensus        88 ~~a~~~   93 (103)
T 2dng_A           88 DIAEGR   93 (103)
T ss_dssp             EECCCC
T ss_pred             EEecCC
Confidence            999864

>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=99.88  E-value=2e-22  Score=124.81  Aligned_cols=82  Identities=16%  Similarity=0.199  Sum_probs=76.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEE
Q psy8615          39 TGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKP  117 (128)
Q Consensus        39 ~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V  117 (128)
                      .....++|||+|||+++++++|+++|++||.|.++++..++. |+++|||||+|.+.+ +|.+|++.||+. ++|+.|+|
T Consensus        12 ~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~-~a~~A~~~l~g~~~~g~~l~V   89 (95)
T 2ywk_A           12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPE-SVSYAIALLNGIRLYGRPINV   89 (95)
T ss_dssp             CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTH-HHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHH-HHHHHHHHhCCCEECCCEEEE
Confidence            344578999999999999999999999999999999999987 999999999998888 999999999999 99999999


Q ss_pred             Eeccc
Q psy8615         118 SFNTY  122 (128)
Q Consensus       118 ~~~~~  122 (128)
                      .|++.
T Consensus        90 ~~a~~   94 (95)
T 2ywk_A           90 SGPSS   94 (95)
T ss_dssp             ECCCC
T ss_pred             EEcCC
Confidence            99863

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.88  E-value=1.8e-22  Score=128.82  Aligned_cols=85  Identities=18%  Similarity=0.217  Sum_probs=78.8

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceE--------EEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc
Q psy8615          38 LTGPEGANLFIYHLPPEFSDADLASMFGPFGTVL--------SAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY  109 (128)
Q Consensus        38 ~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~--------~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~  109 (128)
                      .+....++|||+|||+++++++|+++|++||.|.        .+++..++.+|+++|||||+|.+.+ +|.+|++.||+.
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~-~A~~Ai~~l~g~   88 (113)
T 2cpe_A           10 DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPP-TAKAAVEWFDGK   88 (113)
T ss_dssp             CCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHH-HHHHHHHHHTTC
T ss_pred             ccCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHH-HHHHHHHHcCCC
Confidence            4456688999999999999999999999999999        6999999999999999999997777 999999999999


Q ss_pred             -CCCeEEEEEecccc
Q psy8615         110 -LGQSFLKPSFNTYV  123 (128)
Q Consensus       110 -~~~~~l~V~~~~~~  123 (128)
                       ++|+.|+|.|+++.
T Consensus        89 ~~~g~~l~V~~a~~~  103 (113)
T 2cpe_A           89 DFQGSKLKVSLARKK  103 (113)
T ss_dssp             EETTEECEEECSSCC
T ss_pred             ccCCCEEEEEECCCC
Confidence             99999999999864

>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=99.88  E-value=1.5e-22  Score=132.64  Aligned_cols=85  Identities=19%  Similarity=0.256  Sum_probs=78.7

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEE
Q psy8615          38 LTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLK  116 (128)
Q Consensus        38 ~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~  116 (128)
                      ......++|||+|||+++++++|+++|++||.|.+++++.++.+|+++|||||+|.+.+ +|++|++.|||. ++|+.|+
T Consensus        41 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~-~A~~Ai~~lng~~i~g~~l~  119 (129)
T 2kxn_B           41 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD-DAKEAKERANGMELDGRRIR  119 (129)
T ss_dssp             SCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHH-HHHHHHHHHTTCCSSSSCCE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHH-HHHHHHHHhCCCEECCEEEE
Confidence            34455789999999999999999999999999999999999999999999999997777 999999999999 9999999


Q ss_pred             EEecccc
Q psy8615         117 PSFNTYV  123 (128)
Q Consensus       117 V~~~~~~  123 (128)
                      |.|+++.
T Consensus       120 V~~a~~~  126 (129)
T 2kxn_B          120 VDFSITK  126 (129)
T ss_dssp             ESCCSSS
T ss_pred             EEEecCC
Confidence            9998763

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.88  E-value=6.5e-22  Score=130.43  Aligned_cols=85  Identities=18%  Similarity=0.282  Sum_probs=78.8

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEE
Q psy8615          38 LTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLK  116 (128)
Q Consensus        38 ~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~  116 (128)
                      .+....++|||+|||+++++++|+++|++||.|.+++++.++.+|+++|||||+|.+.+ +|.+|++.||+. ++|+.|+
T Consensus        37 ~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-~a~~A~~~l~g~~~~g~~l~  115 (139)
T 1u6f_A           37 PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGS-SAQQAIAGLNGFNILNKRLK  115 (139)
T ss_dssp             CCTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHH-HHHHHHHHTTTEECSSCEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHHhCCCEECCeEEE
Confidence            34455789999999999999999999999999999999999999999999999997777 999999999999 9999999


Q ss_pred             EEecccc
Q psy8615         117 PSFNTYV  123 (128)
Q Consensus       117 V~~~~~~  123 (128)
                      |.|+++.
T Consensus       116 v~~a~~~  122 (139)
T 1u6f_A          116 VALAASG  122 (139)
T ss_dssp             EEESSCC
T ss_pred             EEECCCC
Confidence            9999864

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.88  E-value=9.8e-23  Score=127.15  Aligned_cols=82  Identities=17%  Similarity=0.250  Sum_probs=77.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceE-EEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeE----
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVL-SAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSF----  114 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~-~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~----  114 (128)
                      ...++|||+|||+++++++|+++|++||.|. +++++.++.+|+++|||||+|.+.+ +|++|++.|||. ++|+.    
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~-~a~~A~~~l~g~~~~g~~~~~~   85 (99)
T 2div_A            7 GMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLA-TAEKCLHKINGKPLPGATPAKR   85 (99)
T ss_dssp             SSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHH-HHHHHHHTTTTSEESSCSSCEE
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHH-HHHHHHHHHcCCccCCCCccee
Confidence            4478999999999999999999999999999 9999999999999999999997777 999999999999 99988    


Q ss_pred             EEEEecccc
Q psy8615         115 LKPSFNTYV  123 (128)
Q Consensus       115 l~V~~~~~~  123 (128)
                      |+|+|+++.
T Consensus        86 l~v~~a~~~   94 (99)
T 2div_A           86 FKLNYATYS   94 (99)
T ss_dssp             CCEEETTCC
T ss_pred             EEEeecCCC
Confidence            999999875

>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=99.88  E-value=1.5e-22  Score=126.06  Aligned_cols=84  Identities=12%  Similarity=0.093  Sum_probs=77.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      .+..++|||+|||+++++++|+++|++||.|.++.++.++.+|+++|||||+|.+.+ +|++|++.||+. ++|+.|+|.
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~-~a~~Ai~~l~g~~~~g~~l~V~   90 (98)
T 2cqp_A           12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRD-EATAAVIDLNDRPIGSRKVKLV   90 (98)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHH-HHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHH-HHHHHHHHhCCCeeCCeEEEEE
Confidence            344689999999999999999999999999999999999999999999999997777 999999999999 999999999


Q ss_pred             eccccc
Q psy8615         119 FNTYVL  124 (128)
Q Consensus       119 ~~~~~~  124 (128)
                      |++...
T Consensus        91 ~a~~~~   96 (98)
T 2cqp_A           91 LGSGPS   96 (98)
T ss_dssp             ESSCSS
T ss_pred             EcCCCC
Confidence            998653

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A

Probab=99.88  E-value=7.4e-22  Score=120.43  Aligned_cols=81  Identities=23%  Similarity=0.395  Sum_probs=73.5

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEE
Q psy8615          38 LTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLK  116 (128)
Q Consensus        38 ~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~  116 (128)
                      ....+.++|||+|||+++++++|+++|++||.|.+++++.++.+|+++|||||+|.+.+ +|.+|++. ++. ++|+.|+
T Consensus         6 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~-~a~~A~~~-~~~~~~g~~i~   83 (87)
T 3s7r_A            6 KNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAA-SVEKVLDQ-KEHRLDGRVID   83 (87)
T ss_dssp             -CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTH-HHHHHHHS-SCEEETTEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHH-HHHHHHHh-CCCEECCEEEE
Confidence            34456789999999999999999999999999999999999999999999999998888 99999965 677 9999999


Q ss_pred             EEec
Q psy8615         117 PSFN  120 (128)
Q Consensus       117 V~~~  120 (128)
                      |.++
T Consensus        84 v~~A   87 (87)
T 3s7r_A           84 PKKA   87 (87)
T ss_dssp             EEEC
T ss_pred             EEeC
Confidence            9874

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A

Probab=99.88  E-value=1.9e-22  Score=129.47  Aligned_cols=77  Identities=26%  Similarity=0.347  Sum_probs=71.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecc
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNT  121 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~  121 (128)
                      .++|||+|||+++++++|+++|++||.|.+|+++.|+  +.++|||||+|.+.+ +|++|++.||+. ++|+.|+|.+.+
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~-~A~~Ai~~l~~~~~~g~~i~V~~a~   81 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQE-AAERAIEKMNGMLLNDRKVFVGRFK   81 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHH-HHHHHHHHHTTCEETTEECEEEESS
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHH-HHHHHHHHcCCCEECCEEEEEEECC
Confidence            4689999999999999999999999999999999996  458999999997777 999999999999 999999999976


Q ss_pred             c
Q psy8615         122 Y  122 (128)
Q Consensus       122 ~  122 (128)
                      +
T Consensus        82 ~   82 (115)
T 4f25_A           82 S   82 (115)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.88  E-value=4.8e-22  Score=130.80  Aligned_cols=84  Identities=18%  Similarity=0.242  Sum_probs=76.9

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeE
Q psy8615          36 KQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSF  114 (128)
Q Consensus        36 ~~~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~  114 (128)
                      ........++|||+|||.++++++|+++|++||.|.+++++.++.+|+++|||||+|.+.+ +|++|++.||+. ++|+.
T Consensus        56 ~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-~a~~A~~~l~g~~~~g~~  134 (140)
T 2ku7_A           56 SGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE-DAAAAIDNMNESELFGRT  134 (140)
T ss_dssp             SCSSCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHH-HHHHHHHHSTEEEETTEE
T ss_pred             CCCCCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHH-HHHHHHHHhCCCEECCEE
Confidence            3444556889999999999999999999999999999999999999999999999997777 999999999999 99999


Q ss_pred             EEEEec
Q psy8615         115 LKPSFN  120 (128)
Q Consensus       115 l~V~~~  120 (128)
                      |+|.|+
T Consensus       135 l~v~~A  140 (140)
T 2ku7_A          135 IRVNLA  140 (140)
T ss_dssp             EEEEC-
T ss_pred             EEEEeC
Confidence            999984

>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=99.88  E-value=1.4e-21  Score=124.87  Aligned_cols=84  Identities=21%  Similarity=0.305  Sum_probs=76.8

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-C------
Q psy8615          38 LTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-L------  110 (128)
Q Consensus        38 ~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~------  110 (128)
                      ....+.++|||+|||+++++++|+++|++||.|.+++++.++ +|.++|||||+|.+.+ +|..|++.|||. +      
T Consensus        20 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~-~a~~A~~~l~g~~~~~~~~~   97 (114)
T 1x5o_A           20 QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTE-KCEAVIGHFNGKFIKTPPGV   97 (114)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHH-HHHHHHHHHBTCCCCCCTTS
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHH-HHHHHHHHhCCCEEcCCccc
Confidence            344567899999999999999999999999999999999998 7999999999997777 999999999998 7      


Q ss_pred             --CCeEEEEEecccc
Q psy8615         111 --GQSFLKPSFNTYV  123 (128)
Q Consensus       111 --~~~~l~V~~~~~~  123 (128)
                        .+++|+|.|.++.
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              5788999999864

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D*

Probab=99.88  E-value=1.6e-22  Score=128.45  Aligned_cols=84  Identities=13%  Similarity=0.193  Sum_probs=78.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEE
Q psy8615          39 TGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKP  117 (128)
Q Consensus        39 ~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V  117 (128)
                      ...+.++|||+|||+++++++|+++|++||.|.+++++.++.+|+++|||||+|.+.+ +|..|++.|||. ++|+.|+|
T Consensus        22 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-~A~~Ai~~l~g~~~~g~~l~V  100 (110)
T 1oo0_B           22 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHK-QALAAKEALNGAEIMGQTIQV  100 (110)
T ss_dssp             CBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHH-HHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHH-HHHHHHHHcCCCEECCcEEEE
Confidence            3455789999999999999999999999999999999999999999999999997777 999999999999 99999999


Q ss_pred             Eecccc
Q psy8615         118 SFNTYV  123 (128)
Q Consensus       118 ~~~~~~  123 (128)
                      .|+++.
T Consensus       101 ~~a~~~  106 (110)
T 1oo0_B          101 DWCFVK  106 (110)
T ss_dssp             EESEES
T ss_pred             EEcccC
Confidence            998764

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.88  E-value=3.7e-22  Score=127.99  Aligned_cols=86  Identities=19%  Similarity=0.255  Sum_probs=78.7

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCcCCCeEEE
Q psy8615          37 QLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDYLGQSFLK  116 (128)
Q Consensus        37 ~~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~~~~~~l~  116 (128)
                      ...+...++|||+|||+++++++|+++|++||.|.+++++.++.+++++|||||+|.+.+ +|++|++.+++.+.|+.|+
T Consensus        11 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-~a~~Ai~~~~~~~~g~~l~   89 (116)
T 2cqd_A           11 SQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRA-AAERACKDPNPIIDGRKAN   89 (116)
T ss_dssp             CCCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHH-HHHHHHTCSSCEETTEECE
T ss_pred             CcCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHH-HHHHHHHhCCCcCCCEEEE
Confidence            344556789999999999999999999999999999999999999999999999997777 9999999999889999999


Q ss_pred             EEecccc
Q psy8615         117 PSFNTYV  123 (128)
Q Consensus       117 V~~~~~~  123 (128)
                      |.|+++.
T Consensus        90 V~~a~~~   96 (116)
T 2cqd_A           90 VNLAYLG   96 (116)
T ss_dssp             EEESTTT
T ss_pred             EEEcccC
Confidence            9998653

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.88  E-value=2.2e-22  Score=128.05  Aligned_cols=86  Identities=22%  Similarity=0.347  Sum_probs=78.2

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEE
Q psy8615          37 QLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFL  115 (128)
Q Consensus        37 ~~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l  115 (128)
                      .......++|||+|||.++++++|+++|++||.|.++++..++  +.++|||||+|.+.+ +|++|++.|||. ++|+.|
T Consensus        23 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~-~A~~Ai~~l~g~~~~g~~l   99 (109)
T 2err_A           23 TENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSA-DADRAREKLHGTVVEGRKI   99 (109)
T ss_dssp             CSCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSH-HHHHHHHHHTTCEETTEEC
T ss_pred             ccCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHH-HHHHHHHHcCCCEECCEEE
Confidence            3445568899999999999999999999999999999999886  458999999998888 999999999999 999999


Q ss_pred             EEEecccccc
Q psy8615         116 KPSFNTYVLM  125 (128)
Q Consensus       116 ~V~~~~~~~~  125 (128)
                      +|.|+++..|
T Consensus       100 ~V~~a~~~~l  109 (109)
T 2err_A          100 EVNNATARVM  109 (109)
T ss_dssp             EEEECCCSCC
T ss_pred             EEEECCCCcC
Confidence            9999998765

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.88  E-value=3.7e-22  Score=125.81  Aligned_cols=85  Identities=22%  Similarity=0.245  Sum_probs=78.7

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEE
Q psy8615          38 LTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLK  116 (128)
Q Consensus        38 ~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~  116 (128)
                      ....+.++|||+|||+++++++|+++|++||.|.+++++.++.+|+++|||||+|.+.+ +|.+|++. ++. ++|+.|+
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~-~a~~a~~~-~~~~~~g~~l~   88 (105)
T 2dh8_A           11 SGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPN-CVGTVLAS-RPHTLDGRNID   88 (105)
T ss_dssp             CCSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTT-HHHHHHHH-CSEEETTEEEB
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHH-HHHHHHHh-CCCeECCEEEE
Confidence            34556789999999999999999999999999999999999999999999999998887 99999999 999 9999999


Q ss_pred             EEeccccc
Q psy8615         117 PSFNTYVL  124 (128)
Q Consensus       117 V~~~~~~~  124 (128)
                      |.|.++.-
T Consensus        89 V~~a~~~~   96 (105)
T 2dh8_A           89 PKPCTPRG   96 (105)
T ss_dssp             CCCSCCSS
T ss_pred             EEEccCCC
Confidence            99998754

>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=99.88  E-value=1.9e-22  Score=129.02  Aligned_cols=81  Identities=16%  Similarity=0.224  Sum_probs=75.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      ...++|||+|||+++++++|+++|++||.|.+++++.++.+|+++|||||+|.+.+ +|.+|+ .||+. ++|+.|+|.|
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~-~a~~A~-~l~g~~~~g~~l~V~~  100 (114)
T 2cq4_A           23 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQ-SVPLAI-GLTGQRLLGVPIIVQA  100 (114)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGG-GHHHHH-HHTTEEETTEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHH-HHHHHH-HcCCCEeCCeEEEEEe
Confidence            44679999999999999999999999999999999999999999999999998877 999999 99999 9999999999


Q ss_pred             cccc
Q psy8615         120 NTYV  123 (128)
Q Consensus       120 ~~~~  123 (128)
                      +++.
T Consensus       101 a~~~  104 (114)
T 2cq4_A          101 SQAE  104 (114)
T ss_dssp             HHHH
T ss_pred             cCCC
Confidence            8753

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.88  E-value=1.1e-22  Score=126.20  Aligned_cols=82  Identities=23%  Similarity=0.318  Sum_probs=77.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEE-EEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSA-KVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~-~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ...++|||+|||+++++++|+++|++||.|.++ +++.++.+|.++|||||+|.+.+ +|+.|++.||+. ++|+.|+|.
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~-~A~~A~~~l~g~~~~g~~l~v~   81 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFD-ASDAAIEAMNGQYLCNRPITVS   81 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHH-HHHHHHHTTTTCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHH-HHHHHHHHcCCCEECCEEEEEE
Confidence            347899999999999999999999999999999 99999889999999999997777 999999999999 999999999


Q ss_pred             ecccc
Q psy8615         119 FNTYV  123 (128)
Q Consensus       119 ~~~~~  123 (128)
                      |+++.
T Consensus        82 ~a~~~   86 (96)
T 1x5t_A           82 YAFKK   86 (96)
T ss_dssp             ESCCC
T ss_pred             Eeccc
Confidence            98764

>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=99.88  E-value=1.3e-22  Score=128.01  Aligned_cols=85  Identities=14%  Similarity=0.222  Sum_probs=78.2

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-C---CCe
Q psy8615          38 LTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-L---GQS  113 (128)
Q Consensus        38 ~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~---~~~  113 (128)
                      ......++|||+|||.++++++|+++|++||.|.+++++.++.+|+++|||||+|.+.+ +|..|++.||+. +   +++
T Consensus         8 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~-~A~~A~~~l~g~~~~~~~g~   86 (106)
T 2dgp_A            8 MKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERE-SALKAQSALHEQKTLPGMNR   86 (106)
T ss_dssp             CCCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHH-HHHHHHHHHTTTCCCTTCSS
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHH-HHHHHHHHhcCCcccCCCCc
Confidence            34556789999999999999999999999999999999999999999999999997777 999999999998 6   889


Q ss_pred             EEEEEecccc
Q psy8615         114 FLKPSFNTYV  123 (128)
Q Consensus       114 ~l~V~~~~~~  123 (128)
                      .|+|.|.++.
T Consensus        87 ~l~v~~a~~~   96 (106)
T 2dgp_A           87 PIQVKPADSE   96 (106)
T ss_dssp             CCEEEECCCC
T ss_pred             eEEEEECCcc
Confidence            9999998764

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.88  E-value=1.6e-22  Score=126.79  Aligned_cols=84  Identities=17%  Similarity=0.231  Sum_probs=78.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ..+.++|||+|||+++++++|+++|++||.|.+++++.++.+++++|||||+|.+.+ +|..|++.||+. ++|+.|+|.
T Consensus         9 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-~A~~A~~~l~g~~~~g~~l~v~   87 (102)
T 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENID-DAKDAMMAMNGKSVDGRQIRVD   87 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHH-HHHHHHHHHTTCCTTSCCCEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHH-HHHHHHHHhCCCEECCeEEEEE
Confidence            345789999999999999999999999999999999999999999999999997777 999999999999 999999999


Q ss_pred             eccccc
Q psy8615         119 FNTYVL  124 (128)
Q Consensus       119 ~~~~~~  124 (128)
                      |+++..
T Consensus        88 ~a~~~~   93 (102)
T 1x5s_A           88 QAGKSS   93 (102)
T ss_dssp             EEECCC
T ss_pred             ECCCCC
Confidence            998754

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.88  E-value=2.2e-22  Score=125.30  Aligned_cols=83  Identities=16%  Similarity=0.170  Sum_probs=76.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCC---CCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEE
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQ---NNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLK  116 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~---tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~  116 (128)
                      .+.++|||+|||+++++++|+++|++||.|.++++..++.   |++++|||||+|.+.+ +|..|++.||+. ++|+.|+
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~-~a~~A~~~l~g~~~~g~~l~   81 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPE-QAQKALKQLQGHTVDGHKLE   81 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHH-HHHHHHHHSTTCEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHH-HHHHHHHHhCCCeeCCeEEE
Confidence            4578999999999999999999999999999999999886   6799999999997777 999999999999 9999999


Q ss_pred             EEeccccc
Q psy8615         117 PSFNTYVL  124 (128)
Q Consensus       117 V~~~~~~~  124 (128)
                      |.|+++..
T Consensus        82 V~~a~~~~   89 (98)
T 2cpf_A           82 VRISERAT   89 (98)
T ss_dssp             EECSSCSS
T ss_pred             EEEccCCC
Confidence            99998753

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens}

Probab=99.87  E-value=1.8e-22  Score=123.20  Aligned_cols=82  Identities=9%  Similarity=0.127  Sum_probs=76.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCC-cceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNR-SKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~-~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ...++|||+|||.++++++|+++|++||.|.+++++.++.++. ++|||||+|.+.+ +|.+|++.|||. ++|+.|+|+
T Consensus         2 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~-~a~~A~~~l~g~~~~g~~l~v~   80 (88)
T 4a8x_A            2 MKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPD-EAEKALKHMDGGQIDGQEITAT   80 (88)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHH-HHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHH-HHHHHHHHcCCCeECCeEEEEE
Confidence            3578999999999999999999999999999999999988776 8999999997777 999999999999 999999999


Q ss_pred             ecccc
Q psy8615         119 FNTYV  123 (128)
Q Consensus       119 ~~~~~  123 (128)
                      +.++.
T Consensus        81 ~a~~~   85 (88)
T 4a8x_A           81 AVLAP   85 (88)
T ss_dssp             EECCC
T ss_pred             ECCCC
Confidence            98765

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.87  E-value=8.3e-23  Score=124.18  Aligned_cols=80  Identities=24%  Similarity=0.378  Sum_probs=75.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      ...++|||+|||+++++++|+++|++||.|.+++++.++.+|+++|||||+|.+.+ +|..|++.|||. ++|+.|++++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~-~a~~A~~~l~g~~~~g~~~~~~~   81 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPS-AAQKAVTALKASGVQAQMAKQSG   81 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHH-HHHHHHHHHHHHTCCEESCCSSC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHH-HHHHHHHHhcCCeEeeEEEeecC
Confidence            35789999999999999999999999999999999999999999999999997777 999999999999 9999999988


Q ss_pred             cc
Q psy8615         120 NT  121 (128)
Q Consensus       120 ~~  121 (128)
                      .+
T Consensus        82 ~~   83 (85)
T 1x4e_A           82 PS   83 (85)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=99.87  E-value=5.9e-22  Score=125.19  Aligned_cols=80  Identities=28%  Similarity=0.318  Sum_probs=75.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ....++|||+|||+++++++|+++|++||.|.+++++.++ +|+++|||||+|.+.+ +|.+|++.||+. ++|+.|+|+
T Consensus        26 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~-~a~~A~~~l~g~~~~g~~l~V~  103 (107)
T 3ulh_A           26 VETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKA-DALKAMKQYNGVPLDGRPMNIQ  103 (107)
T ss_dssp             CCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHH-HHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHH-HHHHHHHHhCCCEeCCcEEEEE
Confidence            3557899999999999999999999999999999999999 7999999999997777 999999999999 999999999


Q ss_pred             ecc
Q psy8615         119 FNT  121 (128)
Q Consensus       119 ~~~  121 (128)
                      |++
T Consensus       104 ~a~  106 (107)
T 3ulh_A          104 LVT  106 (107)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            986

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.87  E-value=1.7e-21  Score=124.36  Aligned_cols=83  Identities=20%  Similarity=0.289  Sum_probs=76.3

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEE
Q psy8615          38 LTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLK  116 (128)
Q Consensus        38 ~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~  116 (128)
                      ......++|||+|||+++++++|+++|++||.|.+++++.++. |+++|||||+|.+.+ +|+.|++.||+. ++|+.|+
T Consensus        10 ~~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~-g~~~g~afV~f~~~~-~a~~A~~~l~g~~~~g~~l~   87 (114)
T 2do0_A           10 QAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD-GKSRGIGTVTFEQSI-EAVQAISMFNGQLLFDRPMH   87 (114)
T ss_dssp             CCCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTT-CSEEEEEEEEESSHH-HHHHHHHHHTTCEETTEECE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCC-CCeeeEEEEEECCHH-HHHHHHHHhCCCEeCCCEEE
Confidence            3445578999999999999999999999999999999999984 999999999997777 999999999999 9999999


Q ss_pred             EEeccc
Q psy8615         117 PSFNTY  122 (128)
Q Consensus       117 V~~~~~  122 (128)
                      |.|++.
T Consensus        88 v~~a~~   93 (114)
T 2do0_A           88 VKMDER   93 (114)
T ss_dssp             EEECSC
T ss_pred             EEEccc
Confidence            999874

>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=99.87  E-value=5.7e-22  Score=121.23  Aligned_cols=80  Identities=15%  Similarity=0.173  Sum_probs=75.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecc
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNT  121 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~  121 (128)
                      .++|||+|||+++++++|+++|++||.|.++++..++.+|+++|||||+|.+.+ +|.+|+ .+|+. ++|+.|+|.+++
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-~a~~a~-~~~g~~~~g~~l~V~~a~   83 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKE-SVRTSL-ALDESLFRGRQIKVIPKR   83 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTH-HHHHHG-GGTTCEETTEECEEEETT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHH-HHHHHH-hcCCCEECCcEEEEEEcc
Confidence            579999999999999999999999999999999999989999999999998887 999999 99999 999999999998


Q ss_pred             ccc
Q psy8615         122 YVL  124 (128)
Q Consensus       122 ~~~  124 (128)
                      +..
T Consensus        84 ~~~   86 (89)
T 3ucg_A           84 TNR   86 (89)
T ss_dssp             TTS
T ss_pred             CCC
Confidence            753

>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=99.87  E-value=3.7e-22  Score=128.41  Aligned_cols=83  Identities=20%  Similarity=0.205  Sum_probs=77.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ..+.++|||+|||.++++++|+++|++||.|.++++..++ +|+++|||||+|.+.+ +|+.|++.|||. ++|+.|+|.
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~-~A~~Ai~~l~g~~~~g~~l~V~   81 (116)
T 2fy1_A            4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPA-DAKNAAKDMNGKSLHGKAIKVE   81 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHH-HHHHHHHHCSSCBCSSSBCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHH-HHHHHHHHhCCCEECCEEEEEE
Confidence            4557899999999999999999999999999999999998 7999999999997777 999999999999 999999999


Q ss_pred             eccccc
Q psy8615         119 FNTYVL  124 (128)
Q Consensus       119 ~~~~~~  124 (128)
                      |+++..
T Consensus        82 ~a~~~~   87 (116)
T 2fy1_A           82 QAKKPS   87 (116)
T ss_dssp             ECCCSS
T ss_pred             ECCCCC
Confidence            998754

>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=99.87  E-value=6.6e-22  Score=124.54  Aligned_cols=81  Identities=17%  Similarity=0.253  Sum_probs=75.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCC-CCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQN-NRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKP  117 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~t-g~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V  117 (128)
                      ....++|||+|||+++++++|+++|++|| |.+++++.++.+ |+++|||||+|.+.+ +|++|+ .||+. ++|+.|+|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~-~a~~A~-~l~g~~~~g~~l~V   88 (104)
T 1wi8_A           12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLD-SLLSAL-SLNEESLGNKRIRV   88 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHH-HHHHHH-GGGTCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHH-HHHHHH-hcCCCEeCCcEEEE
Confidence            34568999999999999999999999999 999999999988 999999999997777 999999 99999 99999999


Q ss_pred             Eecccc
Q psy8615         118 SFNTYV  123 (128)
Q Consensus       118 ~~~~~~  123 (128)
                      .|+++.
T Consensus        89 ~~a~~~   94 (104)
T 1wi8_A           89 DVADQA   94 (104)
T ss_dssp             EECCCC
T ss_pred             EEccCC
Confidence            998864

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.87  E-value=1.7e-21  Score=122.36  Aligned_cols=85  Identities=20%  Similarity=0.255  Sum_probs=76.6

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeE
Q psy8615          36 KQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSF  114 (128)
Q Consensus        36 ~~~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~  114 (128)
                      ......+.++|||+|||+++++++|+++|++||.|.+++++.++.+|+++|||||+|.+.+ +|.+|++  ++. ++|+.
T Consensus         8 ~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~-~a~~A~~--~~~~~~g~~   84 (103)
T 2cqg_A            8 VKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYE-TQVKVMS--QRHMIDGRW   84 (103)
T ss_dssp             CSCCCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHH-HHHHHHH--SCEEETTEE
T ss_pred             CCCccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHH-HHHHHHH--cCCeeCCeE
Confidence            3444566789999999999999999999999999999999999999999999999997777 9999998  467 99999


Q ss_pred             EEEEecccc
Q psy8615         115 LKPSFNTYV  123 (128)
Q Consensus       115 l~V~~~~~~  123 (128)
                      |+|.|.++.
T Consensus        85 l~v~~a~~~   93 (103)
T 2cqg_A           85 CDCKLPNSK   93 (103)
T ss_dssp             EEEECCCTT
T ss_pred             EEEEecCCC
Confidence            999999764

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.87  E-value=8.6e-22  Score=125.63  Aligned_cols=86  Identities=15%  Similarity=0.216  Sum_probs=76.9

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHH---hhhcCCCceEEEEEEecCCCC---CcceEEEEEEecCHHHHHHHHHHhcCc-C
Q psy8615          38 LTGPEGANLFIYHLPPEFSDADLA---SMFGPFGTVLSAKVFIDKQNN---RSKCFGTIIFMRKFFILTIRFDTANDY-L  110 (128)
Q Consensus        38 ~~~~~~~~l~V~nLp~~~~e~~l~---~~f~~~G~i~~~~~~~~~~tg---~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~  110 (128)
                      ......++|||+|||+++++++|+   ++|++||.|.++++..++.++   +++|||||+|++.+ +|++|++.||+. +
T Consensus        10 ~r~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~-~A~~Ai~~lng~~~   88 (111)
T 2cpi_A           10 VRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSE-DALRAIQCVNNVVV   88 (111)
T ss_dssp             CCCCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHH-HHHHHHHHHTTEEE
T ss_pred             ccccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHH-HHHHHHHHhCCCEE
Confidence            344557899999999999999999   999999999999999988754   55699999997777 999999999999 9


Q ss_pred             CCeEEEEEeccccc
Q psy8615         111 GQSFLKPSFNTYVL  124 (128)
Q Consensus       111 ~~~~l~V~~~~~~~  124 (128)
                      +|+.|+|.|+++..
T Consensus        89 ~gr~l~V~~a~~k~  102 (111)
T 2cpi_A           89 DGRTLKASLGTTKY  102 (111)
T ss_dssp             TTEEEEEESCCCCS
T ss_pred             CCEEEEEEeccccc
Confidence            99999999998764

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.87  E-value=1.1e-22  Score=131.76  Aligned_cols=81  Identities=12%  Similarity=0.200  Sum_probs=75.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      +.++|||+|||+++++++|+++|++||.|.+++++.++.+|+++|||||+|.+.+ +|..|+ .|||. ++|+.|+|.|+
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-~a~~A~-~l~g~~~~g~~l~V~~a  112 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERN-SVDAAV-AMDETVFRGRTIKVLPK  112 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHH-HHHHHH-TTTTCEETTEECEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHH-HHHHHH-hcCCCeECCeEEEEEEC
Confidence            4689999999999999999999999999999999999999999999999997777 999999 89999 99999999999


Q ss_pred             cccc
Q psy8615         121 TYVL  124 (128)
Q Consensus       121 ~~~~  124 (128)
                      +...
T Consensus       113 ~~~~  116 (124)
T 2jwn_A          113 RTNM  116 (124)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            8643

>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=99.87  E-value=2.1e-21  Score=121.98  Aligned_cols=85  Identities=22%  Similarity=0.353  Sum_probs=77.0

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEE
Q psy8615          38 LTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLK  116 (128)
Q Consensus        38 ~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~  116 (128)
                      ......++|||+|||+++++++|+++|++||.|.+++++.++.  .++|||||+|.+.+ +|.+|++.||+. ++|+.|+
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~-~a~~A~~~l~g~~~~g~~l~   86 (103)
T 2cq3_A           10 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSA-DADRAREKLHGTVVEGRKIE   86 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHH-HHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHH-HHHHHHHHhCCCEECCEEEE
Confidence            3445578999999999999999999999999999999999875  38999999997777 999999999999 9999999


Q ss_pred             EEecccccc
Q psy8615         117 PSFNTYVLM  125 (128)
Q Consensus       117 V~~~~~~~~  125 (128)
                      |.|+++..+
T Consensus        87 v~~a~~~~~   95 (103)
T 2cq3_A           87 VNNATARVM   95 (103)
T ss_dssp             EEECCSSCC
T ss_pred             EEEcccCCC
Confidence            999988654

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A

Probab=99.87  E-value=2.2e-22  Score=124.60  Aligned_cols=81  Identities=14%  Similarity=0.106  Sum_probs=74.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      +..++|||+|||+++++++|+++|++||.|.+++++.++.+|+++|||||+|.+.+ +|++|++.||+. ++|+.|+|.+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~-~a~~Ai~~l~g~~~~gr~l~v~~   91 (95)
T 2ek1_A           13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRD-EATAAVIDLNDRPIGSRKVKLSG   91 (95)
T ss_dssp             --CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHH-HHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHH-HHHHHHHHhCCCeECCcEEEEEe
Confidence            34589999999999999999999999999999999999999999999999997777 999999999999 9999999999


Q ss_pred             ccc
Q psy8615         120 NTY  122 (128)
Q Consensus       120 ~~~  122 (128)
                      .+.
T Consensus        92 a~s   94 (95)
T 2ek1_A           92 PSS   94 (95)
T ss_dssp             CC-
T ss_pred             ccC
Confidence            864

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.87  E-value=3.7e-21  Score=124.68  Aligned_cols=85  Identities=24%  Similarity=0.249  Sum_probs=78.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEE
Q psy8615          39 TGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKP  117 (128)
Q Consensus        39 ~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V  117 (128)
                      .....++|||+|||.++++++|+++|++||.|.++++..++ +|+++|||||+|.+.+ +|..|++.|||. ++|+.|+|
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~-~A~~Ai~~l~g~~~~g~~l~V  108 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRA-DALKAMKQYKGVPLDGRPMDI  108 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHH-HHHHHHHHHTTEESSSCEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHH-HHHHHHHHcCCCEECCcEEEE
Confidence            34557899999999999999999999999999999999998 7999999999997777 999999999999 99999999


Q ss_pred             Eecccccc
Q psy8615         118 SFNTYVLM  125 (128)
Q Consensus       118 ~~~~~~~~  125 (128)
                      .|+++...
T Consensus       109 ~~a~~~~~  116 (124)
T 2kt5_A          109 QLVASQID  116 (124)
T ss_dssp             EEECCTTC
T ss_pred             EEeCCCCC
Confidence            99987654

>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=99.87  E-value=1.4e-21  Score=122.73  Aligned_cols=84  Identities=12%  Similarity=0.160  Sum_probs=75.9

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEE
Q psy8615          38 LTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLK  116 (128)
Q Consensus        38 ~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~  116 (128)
                      .+....++|||+|||+++++++|+++|++||.|.+|+++.++.  .++|||||+|.+.+ +|.+|++.||+. ++|+.|+
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~~~g~afV~f~~~~-~a~~A~~~l~g~~~~g~~l~   86 (103)
T 2cqi_A           10 EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT--SNDPYCFVEFYEHR-DAAAALAAMNGRKILGKEVK   86 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCC--SSCCEEEEEESSHH-HHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCC--CCCCEEEEEECCHH-HHHHHHHHhCCCCcCCCeEE
Confidence            3445678999999999999999999999999999999999865  36999999997777 999999999999 9999999


Q ss_pred             EEeccccc
Q psy8615         117 PSFNTYVL  124 (128)
Q Consensus       117 V~~~~~~~  124 (128)
                      |.|+++..
T Consensus        87 V~~a~~~~   94 (103)
T 2cqi_A           87 VNWATTPS   94 (103)
T ss_dssp             EEECCCTT
T ss_pred             EEECCCCc
Confidence            99998753

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.87  E-value=2.7e-22  Score=126.74  Aligned_cols=81  Identities=12%  Similarity=0.065  Sum_probs=74.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEE
Q psy8615          39 TGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKP  117 (128)
Q Consensus        39 ~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V  117 (128)
                      .+...++|||+|||+++++++|+++|++||.|.+++++.|+. |+++|||||+|.+.+ +|..|+. +++. ++|+.|+|
T Consensus         7 ~~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e-~a~~Ai~-~~~~~~~gr~l~V   83 (103)
T 1s79_A            7 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIE-SAKKFVE-TPGQKYKETDLLI   83 (103)
T ss_dssp             SCSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHH-HHHHHHT-SSCCCCTTTTCEE
T ss_pred             ccCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHH-HHHHHHH-cCCCEECCEEEEE
Confidence            344568999999999999999999999999999999999988 999999999997766 9999999 8998 99999999


Q ss_pred             Eeccc
Q psy8615         118 SFNTY  122 (128)
Q Consensus       118 ~~~~~  122 (128)
                      .|++.
T Consensus        84 ~~~~~   88 (103)
T 1s79_A           84 LFKDD   88 (103)
T ss_dssp             EEHHH
T ss_pred             EEchH
Confidence            99764

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.87  E-value=4.6e-22  Score=124.99  Aligned_cols=81  Identities=16%  Similarity=0.267  Sum_probs=76.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      ..++|||+|||+++++++|+++|++||.|.++++..++.+|+++|||||+|.+.+ +|..|++.|||. ++|+.|+|.|+
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~-~a~~A~~~l~g~~~~g~~l~v~~a   85 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE-TALSAMRNLNGREFSGRALRVDNA   85 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHH-HHHHHHHHSSSBSCSSSCBEEEET
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHH-HHHHHHHHhCCCeeCCcEEEEEeC
Confidence            3579999999999999999999999999999999999999999999999997777 999999999999 99999999999


Q ss_pred             ccc
Q psy8615         121 TYV  123 (128)
Q Consensus       121 ~~~  123 (128)
                      ++.
T Consensus        86 ~~~   88 (104)
T 1p1t_A           86 ASE   88 (104)
T ss_dssp             TCT
T ss_pred             CCc
Confidence            864

>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=99.86  E-value=6.2e-22  Score=128.53  Aligned_cols=84  Identities=14%  Similarity=0.188  Sum_probs=78.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEE
Q psy8615          39 TGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKP  117 (128)
Q Consensus        39 ~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V  117 (128)
                      ...+.++|||+|||+++++++|+++|++||.|.+++++.++.+|.++|||||+|.+.+ +|+.|++.||+. ++|+.|+|
T Consensus        18 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-~a~~A~~~l~g~~~~g~~l~v   96 (126)
T 3ex7_B           18 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK-EAQAAMEGLNGQDLMGQPISV   96 (126)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHH-HHHHHHHHHTTCBSSSSBCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHH-HHHHHHHHhCCCeeCCeEEEE
Confidence            3455789999999999999999999999999999999999989999999999997777 999999999999 99999999


Q ss_pred             Eecccc
Q psy8615         118 SFNTYV  123 (128)
Q Consensus       118 ~~~~~~  123 (128)
                      .|+++.
T Consensus        97 ~~a~~~  102 (126)
T 3ex7_B           97 DWCFVR  102 (126)
T ss_dssp             EESEES
T ss_pred             EEecCC
Confidence            998764

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}

Probab=99.86  E-value=2e-22  Score=126.36  Aligned_cols=83  Identities=17%  Similarity=0.245  Sum_probs=72.8

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecC-CCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEE
Q psy8615          38 LTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDK-QNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFL  115 (128)
Q Consensus        38 ~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~-~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l  115 (128)
                      ......++|||+|||+++++++|+++|++|| |.+++++.++ .+|+++|||||+|.+.+ +|.+|+ .|||. ++|+.|
T Consensus        14 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~-~a~~Ai-~l~g~~~~g~~l   90 (100)
T 2j76_E           14 LPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLD-SLLSAL-SLNEESLGNRRI   90 (100)
T ss_dssp             ------CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHH-HHHHHH-HTTTCCBTTBCC
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHH-HHHHHH-hcCCCEECCeEE
Confidence            3445578999999999999999999999999 9999999998 68999999999997777 999999 99999 999999


Q ss_pred             EEEecccc
Q psy8615         116 KPSFNTYV  123 (128)
Q Consensus       116 ~V~~~~~~  123 (128)
                      +|.|+++.
T Consensus        91 ~V~~a~~~   98 (100)
T 2j76_E           91 RVDVADQA   98 (100)
T ss_dssp             CCEECCCS
T ss_pred             EEEeccCC
Confidence            99998864

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.86  E-value=9e-22  Score=125.29  Aligned_cols=84  Identities=25%  Similarity=0.360  Sum_probs=73.6

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEE
Q psy8615          38 LTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLK  116 (128)
Q Consensus        38 ~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~  116 (128)
                      ....+.++|||+|||+++++++|+++|++||.|.+++++.++.+|+++|||||+|.+.+ +|.+|++.++ . ++|+.|+
T Consensus        20 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~-~A~~Ai~~~~-~~l~g~~l~   97 (109)
T 2rs2_A           20 HMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQA-GVDKVLAQSR-HELDSKTID   97 (109)
T ss_dssp             ------CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHH-HHHHHHHSSC-EEETTEEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHH-HHHHHHHHCC-CcCCCEEEE
Confidence            34455789999999999999999999999999999999999999999999999997776 9999999886 7 9999999


Q ss_pred             EEecccc
Q psy8615         117 PSFNTYV  123 (128)
Q Consensus       117 V~~~~~~  123 (128)
                      |.+.++.
T Consensus        98 V~~a~~~  104 (109)
T 2rs2_A           98 PKVAFPR  104 (109)
T ss_dssp             EEECCCC
T ss_pred             EEEccCC
Confidence            9998764

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.86  E-value=9.7e-22  Score=126.81  Aligned_cols=83  Identities=12%  Similarity=0.135  Sum_probs=75.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHhhhcCCCc---eEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeE
Q psy8615          39 TGPEGANLFIYHLPPEFSDADLASMFGPFGT---VLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSF  114 (128)
Q Consensus        39 ~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~---i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~  114 (128)
                      .....++|||+|||+++++++|+++|++||.   |.+++++.++. |+++|||||+|.+.+ +|++|++ +|+. ++|+.
T Consensus        13 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~-~a~~Al~-~~g~~~~gr~   89 (118)
T 2db1_A           13 EGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESED-DVKLALK-KDRESMGHRY   89 (118)
T ss_dssp             CBCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHH-HHHHHGG-GTTEEETTEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHH-HHHHHHh-cCCCeECCeE
Confidence            3455789999999999999999999999999   89999999988 999999999997766 9999999 9999 99999


Q ss_pred             EEEEeccccc
Q psy8615         115 LKPSFNTYVL  124 (128)
Q Consensus       115 l~V~~~~~~~  124 (128)
                      |+|.+++..-
T Consensus        90 i~V~~a~~~~   99 (118)
T 2db1_A           90 IEVFKSHRTE   99 (118)
T ss_dssp             EEEEEECHHH
T ss_pred             EEEEECCHHH
Confidence            9999987653

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.86  E-value=1.4e-21  Score=123.51  Aligned_cols=82  Identities=11%  Similarity=0.149  Sum_probs=73.8

Q ss_pred             CCCCCCCeEEEcCCCCCC------CHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-C
Q psy8615          38 LTGPEGANLFIYHLPPEF------SDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-L  110 (128)
Q Consensus        38 ~~~~~~~~l~V~nLp~~~------~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~  110 (128)
                      ......++|||+|||+.+      ++++|+.+|++||.|.+++++  +.+|+++|||||+|.+.+ +|..|++.|||. +
T Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~-~A~~Ai~~l~g~~~   86 (105)
T 2nlw_A           10 EADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPA-HAVDAVKNADGYKL   86 (105)
T ss_dssp             SCCSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSS-HHHHHHHHCSSEEC
T ss_pred             CCCCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHH-HHHHHHHHhCCccc
Confidence            344457899999999999      789999999999999999887  467999999999998888 999999999999 9


Q ss_pred             CCe-EEEEEeccc
Q psy8615         111 GQS-FLKPSFNTY  122 (128)
Q Consensus       111 ~~~-~l~V~~~~~  122 (128)
                      +|+ .|+|.|.+.
T Consensus        87 ~g~~~l~V~~a~~   99 (105)
T 2nlw_A           87 DKQHTFRVNLFTD   99 (105)
T ss_dssp             STTCEEEEECSCC
T ss_pred             CCCceEEEEEcch
Confidence            998 999999875

>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=99.86  E-value=8.5e-22  Score=122.58  Aligned_cols=80  Identities=15%  Similarity=0.149  Sum_probs=74.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHH----hhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEE
Q psy8615          41 PEGANLFIYHLPPEFSDADLA----SMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFL  115 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~----~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l  115 (128)
                      .+.++|||+|||+++++++|+    ++|++||.|.+++++.|+.+   +|||||+|.+.+ +|.+|++.|||. ++|+.|
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~-~A~~Ai~~l~g~~~~gr~l   82 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQ-DAIGAVNSLHRYKIGSKKI   82 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHH-HHHHHHHHHTTEEETTEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHH-HHHHHHHHhCCCEECCeEE
Confidence            347899999999999999999    99999999999999999875   899999997777 999999999999 999999


Q ss_pred             EEEeccccc
Q psy8615         116 KPSFNTYVL  124 (128)
Q Consensus       116 ~V~~~~~~~  124 (128)
                      +|+|+++..
T Consensus        83 ~V~~a~~~~   91 (96)
T 2dgx_A           83 LVSLATGAS   91 (96)
T ss_dssp             EEEECCCSS
T ss_pred             EEEEcCCCC
Confidence            999998764

>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=99.86  E-value=2e-21  Score=130.54  Aligned_cols=83  Identities=11%  Similarity=0.158  Sum_probs=77.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ....++|||+|||+++++++|+++|++||.|.+|+++.++.++.++|||||+|.+.+ +|+.|++.||+. ++|+.|+|.
T Consensus        36 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-~A~~Ai~~l~g~~~~g~~l~V~  114 (156)
T 1h2v_Z           36 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRA-DAENAMRYINGTRLDDRIIRTD  114 (156)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHH-HHHHHHHHTTTSEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHH-HHHHHHHHhCCCEECCeEEEEE
Confidence            345789999999999999999999999999999999999999999999999997777 999999999999 999999999


Q ss_pred             ecccc
Q psy8615         119 FNTYV  123 (128)
Q Consensus       119 ~~~~~  123 (128)
                      |+++.
T Consensus       115 ~a~~~  119 (156)
T 1h2v_Z          115 WDAGF  119 (156)
T ss_dssp             EESCC
T ss_pred             ECCCC
Confidence            99763

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.86  E-value=1.5e-21  Score=120.09  Aligned_cols=81  Identities=21%  Similarity=0.290  Sum_probs=74.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      ...++|||+|||+++++++|+++|++||.|.++++..+  +|+++|||||+|.+.+ +|+.|++.||+. ++|+.|+|.|
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~-~a~~a~~~l~g~~~~g~~l~v~~   82 (92)
T 2dgv_A            6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPE-VAERACRMMNGMKLSGREIDVRI   82 (92)
T ss_dssp             SSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHH-HHHHHHHHHTTCCBTTBCCCCEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHH-HHHHHHHHhCCCEECCcEEEEEE
Confidence            45789999999999999999999999999999999874  6999999999997777 999999999999 9999999999


Q ss_pred             ccccc
Q psy8615         120 NTYVL  124 (128)
Q Consensus       120 ~~~~~  124 (128)
                      +++..
T Consensus        83 a~~~~   87 (92)
T 2dgv_A           83 DRNAS   87 (92)
T ss_dssp             CSCCS
T ss_pred             cCCCC
Confidence            98754

>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=99.86  E-value=1.2e-21  Score=131.62  Aligned_cols=83  Identities=19%  Similarity=0.165  Sum_probs=77.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ....++|||+|||+++++++|+++|++||.|.+++++.|+.+|+++|||||+|.+.+ +|..|++.|||. ++|+.|+|.
T Consensus        67 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~-~a~~A~~~l~g~~~~g~~l~v~  145 (158)
T 2kn4_A           67 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKR-DAEDAMDAMDGAVLDGRELRVQ  145 (158)
T ss_dssp             CCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHH-HHHHHHHHSTTEESSSSEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHH-HHHHHHHHhCCCEECCeEEEEE
Confidence            345789999999999999999999999999999999999999999999999997777 999999999999 999999999


Q ss_pred             ecccc
Q psy8615         119 FNTYV  123 (128)
Q Consensus       119 ~~~~~  123 (128)
                      |+++.
T Consensus       146 ~a~~~  150 (158)
T 2kn4_A          146 MARYG  150 (158)
T ss_dssp             EECCS
T ss_pred             ECCCC
Confidence            99864

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.86  E-value=1e-21  Score=123.51  Aligned_cols=83  Identities=20%  Similarity=0.296  Sum_probs=76.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHhhhcC-CCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc--CCCeEE
Q psy8615          39 TGPEGANLFIYHLPPEFSDADLASMFGP-FGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY--LGQSFL  115 (128)
Q Consensus        39 ~~~~~~~l~V~nLp~~~~e~~l~~~f~~-~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~--~~~~~l  115 (128)
                      +....++|||+|||+++++++|+++|++ ||.|.+++++.++ +|+++|||||+|.+.+ +|..|++.||+.  ++|+.|
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~-~a~~A~~~l~g~~~~~g~~l   82 (104)
T 2dhg_A            5 SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDEL-EQKRALTECQGAVGLGSKPV   82 (104)
T ss_dssp             CSSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHH-HHHHHHHHTTTCCSSSSSCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHH-HHHHHHHHccCCcccCCEeE
Confidence            4455789999999999999999999999 9999999999999 8999999999997777 999999999995  899999


Q ss_pred             EEEecccc
Q psy8615         116 KPSFNTYV  123 (128)
Q Consensus       116 ~V~~~~~~  123 (128)
                      +|.|+++.
T Consensus        83 ~v~~a~~~   90 (104)
T 2dhg_A           83 RLSVAIPK   90 (104)
T ss_dssp             CCCBCCCC
T ss_pred             EEEEccCC
Confidence            99998754

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.86  E-value=3.6e-21  Score=118.37  Aligned_cols=80  Identities=8%  Similarity=0.167  Sum_probs=74.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ....++|||+|||+++++++|+++|++| .|.+++++.+ .+|+++|||||+|.+.+ +|.+|++ +|+. ++|+.|+|.
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~-~a~~A~~-~~g~~~~gr~i~v~   82 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEE-EVKQALK-CNREYMGGRYIEVF   82 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHH-HHHHHHH-SCSEEETTEEEEEE
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHH-HHHHHHH-hCCceeCCcEEEEE
Confidence            3457899999999999999999999999 9999999999 67999999999997777 9999999 9999 999999999


Q ss_pred             ecccc
Q psy8615         119 FNTYV  123 (128)
Q Consensus       119 ~~~~~  123 (128)
                      ++++.
T Consensus        83 ~a~~~   87 (91)
T 2dgw_A           83 REKSG   87 (91)
T ss_dssp             EESSC
T ss_pred             ECCcC
Confidence            98865

>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=99.86  E-value=4.5e-21  Score=120.82  Aligned_cols=80  Identities=13%  Similarity=0.242  Sum_probs=72.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ....++|||+|||+++++++|+++|++||. .+++++.|+ +|+++|||||+|.+.+ +|++|++ +|+. ++++.|+|.
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~i~~d~-~g~~~G~afV~F~~~~-~a~~Al~-~~~~~~~gr~i~V~   87 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHE-DAVAAMA-KDKANMQHRYVELF   87 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSH-HHHHHHT-TSSCCSSSSCCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEECC-CCCEeeEEEEEECCHH-HHHHHHH-hCCCeECCcEEEEE
Confidence            345689999999999999999999999995 599999998 7999999999998888 9999994 7998 999999999


Q ss_pred             ecccc
Q psy8615         119 FNTYV  123 (128)
Q Consensus       119 ~~~~~  123 (128)
                      +++..
T Consensus        88 ~~~~~   92 (102)
T 1wez_A           88 LNSTA   92 (102)
T ss_dssp             EECCC
T ss_pred             ECCCC
Confidence            88764

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.86  E-value=5.9e-22  Score=118.13  Aligned_cols=75  Identities=25%  Similarity=0.386  Sum_probs=71.5

Q ss_pred             CeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        44 ~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      ++|||+|||+++++++|+++|++||.|.+++++.++.+|+++|||||+|.+.+ +|++|++.++ . ++|+.|+|.++
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 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQA-GVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTT-HHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHH-HHHHHHHhCC-CccCCEEEEEEec
Confidence            57999999999999999999999999999999999999999999999998888 9999999999 7 99999999885

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=1.1e-21  Score=125.68  Aligned_cols=81  Identities=19%  Similarity=0.265  Sum_probs=75.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      ...++|||+|||+++++++|+++|++||.|.+++++.++.+|+++|||||+|.+.+ +|.+|++. ++. ++|+.|+|.|
T Consensus        25 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~-~a~~Ai~~-~~~~~~g~~l~V~~  102 (116)
T 1x4b_A           25 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMA-EVDAAMAA-RPHSIDGRVVEPKR  102 (116)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHH-HHHHHHTS-CSEEETTEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHH-HHHHHHHh-CCcEECCEEEEEEE
Confidence            34689999999999999999999999999999999999999999999999997777 99999998 998 9999999999


Q ss_pred             cccc
Q psy8615         120 NTYV  123 (128)
Q Consensus       120 ~~~~  123 (128)
                      .++.
T Consensus       103 a~~~  106 (116)
T 1x4b_A          103 AVAR  106 (116)
T ss_dssp             CSSC
T ss_pred             CCCC
Confidence            8764

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=3.2e-21  Score=121.66  Aligned_cols=83  Identities=13%  Similarity=0.164  Sum_probs=74.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEE-EEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLS-AKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKP  117 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~-~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V  117 (128)
                      ....++|||+|||+++++++|+++|++||.|.+ ++++.+ .+|+++|||||+|.+.+ +|++|++. |+. ++|+.|+|
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~-~a~~A~~~-~~~~~~gr~i~v   88 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQE-IAEKALKK-HKERIGHRYIEI   88 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHH-HHHHHHTT-TTCCSSSSCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHH-HHHHHHHh-CcchhCCcEEEE
Confidence            345789999999999999999999999999987 888888 67999999999997777 99999998 888 99999999


Q ss_pred             Eecccccc
Q psy8615         118 SFNTYVLM  125 (128)
Q Consensus       118 ~~~~~~~~  125 (128)
                      .+.+..-|
T Consensus        89 ~~~~~~~~   96 (104)
T 1wg5_A           89 FKSSRAEV   96 (104)
T ss_dssp             EEECTTTS
T ss_pred             EECCHHHH
Confidence            99887654

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=2.1e-21  Score=126.03  Aligned_cols=82  Identities=15%  Similarity=0.161  Sum_probs=75.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ....++|||+|||+++++++|+++|++||.|.++.++.+..+|+++|||||+|.+.+ +|..|++ +|+. ++|+.|+|.
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~-~a~~Al~-~~g~~~~gr~i~V~   99 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEA-DYKAALC-RHKQYMGNRFIQVH   99 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSH-HHHHHHT-SCSBCSTTSCBEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHH-HHHHHHH-hCCCeECCcEEEEE
Confidence            345689999999999999999999999999998777777788999999999998888 9999999 9999 999999999


Q ss_pred             ecccc
Q psy8615         119 FNTYV  123 (128)
Q Consensus       119 ~~~~~  123 (128)
                      +.++.
T Consensus       100 ~a~~~  104 (124)
T 1wel_A          100 PITKK  104 (124)
T ss_dssp             EECHH
T ss_pred             ECCHH
Confidence            98764

>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=99.85  E-value=7.2e-21  Score=119.85  Aligned_cols=82  Identities=15%  Similarity=0.173  Sum_probs=71.4

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhc--Cc-CCCe
Q psy8615          37 QLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTAN--DY-LGQS  113 (128)
Q Consensus        37 ~~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~--g~-~~~~  113 (128)
                      ....++.++|||+|||+++++++|+++|++||.|.++.++.+      +|||||+|++.+ +|..|++.|+  +. +.|+
T Consensus         9 ~~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~-~A~~Ai~~l~~~~~~~~Gr   81 (101)
T 2cq1_A            9 KMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEE-AAITMVNYYSAVTPHLRNQ   81 (101)
T ss_dssp             CCCSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHH-HHHHHHHHHHHSCCEETTE
T ss_pred             CccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHH-HHHHHHHHhccCCceECCc
Confidence            344456789999999999999999999999999999988754      789999997777 9999999875  56 9999


Q ss_pred             EEEEEecccccc
Q psy8615         114 FLKPSFNTYVLM  125 (128)
Q Consensus       114 ~l~V~~~~~~~~  125 (128)
                      +|+|+|+++.-+
T Consensus        82 ~l~V~~a~~~~~   93 (101)
T 2cq1_A           82 PIYIQYSNHKEL   93 (101)
T ss_dssp             ECEEEECSCSSC
T ss_pred             EEEEEEcCcccC
Confidence            999999987654

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=1.4e-21  Score=125.12  Aligned_cols=83  Identities=12%  Similarity=0.022  Sum_probs=75.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCce-EEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTV-LSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKP  117 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i-~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V  117 (128)
                      ..+.++|||+|||+++++++|+++|++||.| .+++++.|+ +|+++|||||+|.+.+ +|.+|++. |+. ++|+.|+|
T Consensus        12 ~~~~~~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           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNED-DARKSERL-HRKKLNGREAFV   88 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHH-HHHHHGGG-CSEEETTEEEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHH-HHHHHHHh-CCCccCCeEEEE
Confidence            3457899999999999999999999999999 889999998 7999999999997766 99999988 998 99999999


Q ss_pred             Eecccccc
Q psy8615         118 SFNTYVLM  125 (128)
Q Consensus       118 ~~~~~~~~  125 (128)
                      .+.++.-+
T Consensus        89 ~~a~~~~~   96 (114)
T 2cpy_A           89 HVVTLEDM   96 (114)
T ss_dssp             EEECHHHH
T ss_pred             EECCHHHH
Confidence            99887543

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.85  E-value=5e-22  Score=118.06  Aligned_cols=74  Identities=22%  Similarity=0.321  Sum_probs=69.7

Q ss_pred             eEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        45 ~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      +|||+|||+++++++|+++|++||.|.+++++.++.+|+++|||||+|.+.+ +|++|++ +|+. ++|+.|+|.|+
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 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESED-IVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHH-HHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHH-HHHHHHH-CCCCEECCEEEEEEeC
Confidence            5899999999999999999999999999999999989999999999997776 9999998 9999 99999999874

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C

Probab=99.85  E-value=1.6e-21  Score=138.89  Aligned_cols=81  Identities=20%  Similarity=0.132  Sum_probs=75.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCCC--ceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPFG--TVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~G--~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ..++|||+|||+++++++|+++|++||  .|.+|+++.|+.||+++|||||+|.+.+ +|.+||+.||+. |.|+.|+|.
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~-~a~~Ai~~lng~~~~Gr~l~V~  145 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEA-SSKKLMDLLPKRELHGQNPVVT  145 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTT-HHHHHHTTSTTSCBTTBCCEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHH-HHHHHHHHcCCCeECCEEeEEE
Confidence            567999999999999999999999999  9999999999999999999999998887 999999999999 999999999


Q ss_pred             ecccc
Q psy8615         119 FNTYV  123 (128)
Q Consensus       119 ~~~~~  123 (128)
                      |+++.
T Consensus       146 ~a~~~  150 (229)
T 3q2s_C          146 PVNKQ  150 (229)
T ss_dssp             ECCHH
T ss_pred             ECCCC
Confidence            98764

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.85  E-value=3.9e-22  Score=131.55  Aligned_cols=86  Identities=19%  Similarity=0.142  Sum_probs=79.1

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEE
Q psy8615          38 LTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLK  116 (128)
Q Consensus        38 ~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~  116 (128)
                      ......++|||+|||+++++++|+++|++||.|.+++++.++.+|+++|||||+|.+.+ +|++|++.||+. ++|+.|+
T Consensus        42 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~-~A~~Ai~~l~g~~i~g~~l~  120 (135)
T 2lea_A           42 PDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKR-DAEDAMDAMDGAVLDGRELR  120 (135)
T ss_dssp             SSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHH-HHHHHHTTTTTCCSSSSCCE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHH-HHHHHHHHcCCCEECCEEEE
Confidence            34455789999999999999999999999999999999999989999999999997777 999999999999 9999999


Q ss_pred             EEeccccc
Q psy8615         117 PSFNTYVL  124 (128)
Q Consensus       117 V~~~~~~~  124 (128)
                      |.|+++..
T Consensus       121 V~~a~~~~  128 (135)
T 2lea_A          121 VQMARYGR  128 (135)
T ss_dssp             EEECCCCC
T ss_pred             EEECCCCC
Confidence            99998653

>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=99.85  E-value=8.1e-21  Score=120.44  Aligned_cols=81  Identities=15%  Similarity=0.240  Sum_probs=72.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEE
Q psy8615          39 TGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKP  117 (128)
Q Consensus        39 ~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V  117 (128)
                      .....++|||+|||+++++++|+++|++||.|.++++..+   +.++|||||+|.+.+ +|.+|++.||+. +.|+.|+|
T Consensus        18 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~-~A~~A~~~l~g~~~~g~~l~V   93 (109)
T 1x4a_A           18 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPR-DAEDAVYGRDGYDYDGYRLRV   93 (109)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHH-HHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHH-HHHHHHHHcCCCEECCeEEEE
Confidence            3455789999999999999999999999999999998554   568999999997777 999999999999 99999999


Q ss_pred             Eecccc
Q psy8615         118 SFNTYV  123 (128)
Q Consensus       118 ~~~~~~  123 (128)
                      .|+++.
T Consensus        94 ~~a~~~   99 (109)
T 1x4a_A           94 EFPRSG   99 (109)
T ss_dssp             ECCCCC
T ss_pred             EEcccC
Confidence            999864

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.85  E-value=1.1e-20  Score=118.42  Aligned_cols=83  Identities=16%  Similarity=0.189  Sum_probs=74.3

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEE
Q psy8615          37 QLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFL  115 (128)
Q Consensus        37 ~~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l  115 (128)
                      .......++|||+|||+++++++|+++|+.|+   +++++.++.+++++|||||+|.+.+ +|.+|++.||+. ++|+.|
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~-~A~~A~~~l~g~~~~g~~l   84 (102)
T 2fc8_A            9 NARSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEE-DAKAAKEAMEDGEIDGNKV   84 (102)
T ss_dssp             SSSSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHH-HHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHH-HHHHHHHHhCCCeECCeEE
Confidence            34455678999999999999999999999874   6778899889999999999997777 999999999999 999999


Q ss_pred             EEEecccc
Q psy8615         116 KPSFNTYV  123 (128)
Q Consensus       116 ~V~~~~~~  123 (128)
                      +|.|+++.
T Consensus        85 ~V~~a~~~   92 (102)
T 2fc8_A           85 TLDWAKPK   92 (102)
T ss_dssp             EEEECCCC
T ss_pred             EEEEecCC
Confidence            99999864

>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=99.85  E-value=4.6e-21  Score=130.00  Aligned_cols=83  Identities=13%  Similarity=0.196  Sum_probs=76.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ....++|||+|||+++++++|+.+|++||.|..|.++.++.+|.++|||||+|.+.+ +|..|++.|||. ++|+.|+|.
T Consensus        69 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~-~A~~Ai~~l~g~~~~g~~l~V~  147 (165)
T 1rk8_A           69 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHK-QALAAKEALNGAEIMGQTIQVD  147 (165)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHH-HHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHH-HHHHHHHHhCCCEECCEEEEEE
Confidence            445779999999999999999999999999999999999999999999999997777 999999999999 999999999


Q ss_pred             ecccc
Q psy8615         119 FNTYV  123 (128)
Q Consensus       119 ~~~~~  123 (128)
                      |+++.
T Consensus       148 ~a~~~  152 (165)
T 1rk8_A          148 WCFVK  152 (165)
T ss_dssp             ESEEC
T ss_pred             EecCC
Confidence            98754

>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=99.85  E-value=2.5e-21  Score=127.97  Aligned_cols=84  Identities=12%  Similarity=0.134  Sum_probs=76.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHhhhcCCCc---eEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeE
Q psy8615          39 TGPEGANLFIYHLPPEFSDADLASMFGPFGT---VLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSF  114 (128)
Q Consensus        39 ~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~---i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~  114 (128)
                      +..+.++|||+|||+++++++|+++|++||.   |.+++++.|+. |+++|||||+|.+.+ +|++|++ +|+. ++|+.
T Consensus        40 ~~~~~~~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           40 EGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSED-DVKMALK-KDRESMGHRY  116 (136)
T ss_dssp             SCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHH-HHHHHHT-TTEEESSSSE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHH-HHHHHHh-cCCCEECCEE
Confidence            3455789999999999999999999999999   89999999998 999999999997776 9999999 9999 99999


Q ss_pred             EEEEecccccc
Q psy8615         115 LKPSFNTYVLM  125 (128)
Q Consensus       115 l~V~~~~~~~~  125 (128)
                      |+|.++++.-|
T Consensus       117 i~V~~a~~~e~  127 (136)
T 2hgl_A          117 IEVFKSHRTEM  127 (136)
T ss_dssp             EEEEECCHHHH
T ss_pred             EEEEECChHHH
Confidence            99999876543

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.85  E-value=9.1e-21  Score=118.61  Aligned_cols=80  Identities=18%  Similarity=0.153  Sum_probs=71.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEE
Q psy8615          39 TGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKP  117 (128)
Q Consensus        39 ~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V  117 (128)
                      .....++|||+|||+++++++|+++|++||.|   +++.+ .+|+++|||||+|.+.+ +|++|++.||+. ++|+.|+|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~-~A~~A~~~l~g~~~~g~~l~v   85 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFE-DAKEALNSCNKREIEGRAIRL   85 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHH-HHHHHHHHTSSEEETTEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHH-HHHHHHHHhCCCEeCCeEEEE
Confidence            44557899999999999999999999999987   45666 56999999999997777 999999999999 99999999


Q ss_pred             Eecccc
Q psy8615         118 SFNTYV  123 (128)
Q Consensus       118 ~~~~~~  123 (128)
                      .|+++.
T Consensus        86 ~~a~~~   91 (101)
T 2fc9_A           86 ELQGPR   91 (101)
T ss_dssp             EECSSC
T ss_pred             EEcCCC
Confidence            999875

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.85  E-value=1e-21  Score=128.65  Aligned_cols=84  Identities=13%  Similarity=0.212  Sum_probs=75.5

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEE--EEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-----C
Q psy8615          38 LTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLS--AKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-----L  110 (128)
Q Consensus        38 ~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~--~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-----~  110 (128)
                      ..+...++|||+|||+++++++|+++|++||.|..  |+++.|+.||+++|||||+|.+ . +|.+|++.|||.     +
T Consensus        18 ~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~-~-~a~~Ai~~l~g~~~~~~~   95 (131)
T 2m2b_A           18 SSENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLST-I-EAAQLLQILQALHPPLTI   95 (131)
T ss_dssp             CCSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCH-H-HHHHHHHHHTTCCCSCCG
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECC-H-HHHHHHHHhcCCCCCccC
Confidence            34455789999999999999999999999999977  9999999999999999999954 4 899999999993     8


Q ss_pred             CCeEEEEEecccc
Q psy8615         111 GQSFLKPSFNTYV  123 (128)
Q Consensus       111 ~~~~l~V~~~~~~  123 (128)
                      +|+.|+|.|.++.
T Consensus        96 ~gr~l~V~~a~~~  108 (131)
T 2m2b_A           96 DGKTINVEFAKGS  108 (131)
T ss_dssp             GGCCCCCEECCCS
T ss_pred             CCEEEEEEECCCC
Confidence            9999999999864

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=1.5e-21  Score=123.75  Aligned_cols=82  Identities=11%  Similarity=0.111  Sum_probs=75.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCc-eEEEEEE-ecCCCCCcceEEEEEEecCHHHHHHHHHHhc--Cc-CCCeEE
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGT-VLSAKVF-IDKQNNRSKCFGTIIFMRKFFILTIRFDTAN--DY-LGQSFL  115 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~-i~~~~~~-~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~--g~-~~~~~l  115 (128)
                      .+.++|||+|||+++++++|+++|++||. |.++.++ .++.+|+++|||||+|.+.+ +|..|++.||  +. ++|+.|
T Consensus         6 ~~~~~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            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHR-AAAMARRKLMPGRIQLWGHQI   84 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHH-HHHHHHTTTTTCCSCBTTBCC
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHH-HHHHHHHHhhCCCceecCCeE
Confidence            45789999999999999999999999998 9999998 88889999999999997777 9999999996  57 999999


Q ss_pred             EEEecccc
Q psy8615         116 KPSFNTYV  123 (128)
Q Consensus       116 ~V~~~~~~  123 (128)
                      +|.|+++.
T Consensus        85 ~V~~a~~~   92 (109)
T 2dis_A           85 AVDWAEPE   92 (109)
T ss_dssp             EEEESCSS
T ss_pred             EEEEcCCC
Confidence            99999865

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=1.3e-21  Score=123.92  Aligned_cols=79  Identities=16%  Similarity=0.145  Sum_probs=70.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcC--c-CCCeEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTAND--Y-LGQSFLK  116 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g--~-~~~~~l~  116 (128)
                      ....++|||+|||++++|++|+++|++||.|.+++++.+      +|||||+|++.+ +|+.|++.+++  . +.|++|+
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~-~A~~Ai~~l~~~~~~l~Gr~l~   85 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEE-AANTMVNYYTSVTPVLRGQPIY   85 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHH-HHHHHHHHHTTSCCEETTEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHH-HHHHHHHHhccCCceECCEEEE
Confidence            345789999999999999999999999999999998865      789999997777 99999999874  5 9999999


Q ss_pred             EEecccccc
Q psy8615         117 PSFNTYVLM  125 (128)
Q Consensus       117 V~~~~~~~~  125 (128)
                      |+|+++.-+
T Consensus        86 V~~A~~~~~   94 (105)
T 1sjq_A           86 IQFSNHKEL   94 (105)
T ss_dssp             BCCCSSSSC
T ss_pred             EEEcCCCCC
Confidence            999987643

>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=99.84  E-value=5.5e-22  Score=121.71  Aligned_cols=79  Identities=14%  Similarity=0.280  Sum_probs=71.2

Q ss_pred             CeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEeccc
Q psy8615          44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNTY  122 (128)
Q Consensus        44 ~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~~  122 (128)
                      ++|||+|||.++++++|+++|++||.|.++++..++.+|+++|||||+|.+.+  |..|++.|||. ++|+.|+|.|+++
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~--a~~a~~~l~g~~~~g~~l~V~~a~~   79 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES--VSEAIAKLDNTDFMGRTIRVTEANP   79 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH--HHHHHHTSCSSCCSSSSCSEEEC--
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH--HHHHHHHhCCCEECCeEEEEEEcCC
Confidence            58999999999999999999999999999999999999999999999995544  99999999999 9999999999987


Q ss_pred             cc
Q psy8615         123 VL  124 (128)
Q Consensus       123 ~~  124 (128)
                      ..
T Consensus        80 ~~   81 (90)
T 2ki2_A           80 KK   81 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            54

>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=99.84  E-value=1.5e-21  Score=123.78  Aligned_cols=83  Identities=8%  Similarity=0.039  Sum_probs=75.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHhhhcCCCc---eEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeE
Q psy8615          39 TGPEGANLFIYHLPPEFSDADLASMFGPFGT---VLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSF  114 (128)
Q Consensus        39 ~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~---i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~  114 (128)
                      +....++|||+|||+++++++|+++|++||.   |.+++++.++. |+++|||||+|.+.+ +|.+|++ +|+. ++|+.
T Consensus         7 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~-~a~~Al~-~~~~~~~gr~   83 (107)
T 2lmi_A            7 EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQ-DVQKALE-KHRMYMGQRY   83 (107)
T ss_dssp             CCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHH-HHHHHHT-TTTCCSSSSC
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHH-HHHHHHH-hCcceeCCeE
Confidence            3456789999999999999999999999998   89999999988 999999999997766 9999999 9999 99999


Q ss_pred             EEEEeccccc
Q psy8615         115 LKPSFNTYVL  124 (128)
Q Consensus       115 l~V~~~~~~~  124 (128)
                      |+|.++++.-
T Consensus        84 i~V~~a~~~~   93 (107)
T 2lmi_A           84 VEVYEINNED   93 (107)
T ss_dssp             CCCEECCHHH
T ss_pred             EEEEECCHHH
Confidence            9999988643

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.84  E-value=1.1e-20  Score=132.63  Aligned_cols=81  Identities=23%  Similarity=0.265  Sum_probs=75.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      +.++|||+|||++++|++|+++|++||.|.+|+++.|+.||+++|||||+|.+.+ +|.+|++.+|+. +.|+.|++.+.
T Consensus        14 p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~-~A~~Ai~~~~~~~~~g~~i~~~~~   92 (213)
T 4f02_A           14 PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPA-DAERALDTMNFDVIKGKPVRIMWS   92 (213)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHH-HHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHH-HHHHHHHHhhhhhcCCcccccccc
Confidence            3579999999999999999999999999999999999999999999999997777 999999999999 99999999998


Q ss_pred             ccc
Q psy8615         121 TYV  123 (128)
Q Consensus       121 ~~~  123 (128)
                      ...
T Consensus        93 ~~~   95 (213)
T 4f02_A           93 QRD   95 (213)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            653

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.84  E-value=1.1e-20  Score=118.70  Aligned_cols=76  Identities=18%  Similarity=0.144  Sum_probs=68.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc---CCCeEEEE
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY---LGQSFLKP  117 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~---~~~~~l~V  117 (128)
                      ++..+|||+|||+++++++|+++|++||.|.+++++.      .||||||+|++.+ +|..|++.|++.   ++|++|+|
T Consensus        19 ~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~------~kg~AFVef~~~~-~A~~Av~~ln~~~~~i~Gr~i~V   91 (100)
T 3r27_A           19 PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEFEDVL-GACNAVNYAADNQIYIAGHPAFV   91 (100)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET------TTTEEEEEESSHH-HHHHHHHHHHHSCEEETTEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc------CCCEEEEEECCHH-HHHHHHHHhcCCCceeCCcEEEE
Confidence            4567999999999999999999999999999999874      3789999997777 999999999985   78999999


Q ss_pred             Eecccc
Q psy8615         118 SFNTYV  123 (128)
Q Consensus       118 ~~~~~~  123 (128)
                      +|++..
T Consensus        92 ~~S~~k   97 (100)
T 3r27_A           92 NYSTSQ   97 (100)
T ss_dssp             EECSCS
T ss_pred             Eecccc
Confidence            999874

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.84  E-value=6.7e-21  Score=116.61  Aligned_cols=74  Identities=9%  Similarity=0.114  Sum_probs=68.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecc
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNT  121 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~  121 (128)
                      ...|||+||+++++|++|+++|.+||+|.++++..      ++|||||+|.+.+ +|..|++.||+. ++|++|+|.+++
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------NQGIALCKYTTRE-EANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHH-HHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHH-HHHHHHHHhcCCEECCcEEEEEECC
Confidence            56899999999999999999999999999999865      5899999997766 999999999999 999999999987


Q ss_pred             cc
Q psy8615         122 YV  123 (128)
Q Consensus       122 ~~  123 (128)
                      ..
T Consensus        80 e~   81 (89)
T 2wbr_A           80 EN   81 (89)
T ss_dssp             HH
T ss_pred             HH
Confidence            53

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.84  E-value=6.9e-21  Score=124.00  Aligned_cols=82  Identities=10%  Similarity=0.113  Sum_probs=73.1

Q ss_pred             CCeEEEcCC----CCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEec----CHHH---HHHHHH--HhcCc
Q psy8615          43 GANLFIYHL----PPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMR----KFFI---LTIRFD--TANDY  109 (128)
Q Consensus        43 ~~~l~V~nL----p~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~----~~~~---a~~Ai~--~l~g~  109 (128)
                      +++|||+||    |+.+++.+|+.+|++||+|.+++++.|+.||+++|||||+|.+    +++.   |.+|+.  .+||.
T Consensus         2 p~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~   81 (136)
T 2j8a_A            2 SCEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGC   81 (136)
T ss_dssp             CCEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCE
T ss_pred             CcEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCC
Confidence            378999999    9999999999999999999999999999999999999999974    3312   889988  78999


Q ss_pred             -CCCeEEEEEeccccc
Q psy8615         110 -LGQSFLKPSFNTYVL  124 (128)
Q Consensus       110 -~~~~~l~V~~~~~~~  124 (128)
                       ++|+.|+|.++..-.
T Consensus        82 ~I~Gr~irV~ln~~g~   97 (136)
T 2j8a_A           82 FIMGFKFEVILNKHSI   97 (136)
T ss_dssp             EETTEEEEEEECCTTH
T ss_pred             eecCcEEEEEECcccH
Confidence             999999999987643

>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=99.83  E-value=8.8e-21  Score=119.66  Aligned_cols=76  Identities=9%  Similarity=-0.006  Sum_probs=68.2

Q ss_pred             CCCCCeEEEcCCCC-CCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcC--c-CCCeEE
Q psy8615          40 GPEGANLFIYHLPP-EFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTAND--Y-LGQSFL  115 (128)
Q Consensus        40 ~~~~~~l~V~nLp~-~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g--~-~~~~~l  115 (128)
                      ..+.++|||+|||+ ++++++|+++|++||.|.++.++.+      +|||||+|++.+ +|..|++.||+  . +.|++|
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~-~A~~Ai~~l~~~~~~~~Gr~l   84 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTE-DAQAAVDYYTTTPALVFGKPV   84 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHH-HHHHHHHHHHHSCCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHH-HHHHHHHHHcCCCceECCcEE
Confidence            34578999999999 9999999999999999999998865      579999997777 99999999986  3 899999


Q ss_pred             EEEeccc
Q psy8615         116 KPSFNTY  122 (128)
Q Consensus       116 ~V~~~~~  122 (128)
                      +|+|++.
T Consensus        85 ~V~~a~~   91 (102)
T 1x4d_A           85 RVHLSQK   91 (102)
T ss_dssp             EEEEECC
T ss_pred             EEEECCC
Confidence            9999984

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.83  E-value=1.9e-21  Score=117.30  Aligned_cols=73  Identities=11%  Similarity=0.202  Sum_probs=66.1

Q ss_pred             CCeEEEcCCCCCC------CHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCe-E
Q psy8615          43 GANLFIYHLPPEF------SDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQS-F  114 (128)
Q Consensus        43 ~~~l~V~nLp~~~------~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~-~  114 (128)
                      .++|||+|||.++      ++++|+++|++||.|.++++.  +.+|+++|||||+|.+.+ +|..|++.|||. ++|+ +
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~-~A~~Ai~~lng~~~~g~~~   77 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPA-HAVDAVKNADGYKLDKQHT   77 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHH-HHHHHHTTSSSCCCSSSSC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHH-HHHHHHHHhcCcccCCcee
Confidence            3689999999999      779999999999999999877  467999999999997777 999999999999 9998 8


Q ss_pred             EEEE
Q psy8615         115 LKPS  118 (128)
Q Consensus       115 l~V~  118 (128)
                      |+|+
T Consensus        78 l~V~   81 (81)
T 2krb_A           78 FRVN   81 (81)
T ss_dssp             CCCC
T ss_pred             EEeC
Confidence            8874

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.83  E-value=4.7e-20  Score=123.32  Aligned_cols=83  Identities=23%  Similarity=0.303  Sum_probs=77.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEE
Q psy8615          39 TGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKP  117 (128)
Q Consensus        39 ~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V  117 (128)
                      .....++|||+|||.++++++|+++|++||.|.++++..++.+|.++|||||+|.+.+ +|.+|++.|||. ++|+.|+|
T Consensus        83 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~-~A~~A~~~l~g~~~~g~~i~v  161 (166)
T 3md3_A           83 SSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQD-DAQNAMDSMQGQDLNGRPLRI  161 (166)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHH-HHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHH-HHHHHHHHhCCCccCCcEEEE
Confidence            3455779999999999999999999999999999999999999999999999997777 999999999999 99999999


Q ss_pred             Eeccc
Q psy8615         118 SFNTY  122 (128)
Q Consensus       118 ~~~~~  122 (128)
                      +|+++
T Consensus       162 ~~a~~  166 (166)
T 3md3_A          162 NWAAK  166 (166)
T ss_dssp             EESCC
T ss_pred             EecCC
Confidence            99874

>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=99.83  E-value=3.4e-20  Score=115.68  Aligned_cols=80  Identities=21%  Similarity=0.340  Sum_probs=71.9

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEE
Q psy8615          38 LTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLK  116 (128)
Q Consensus        38 ~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~  116 (128)
                      ....+.++|||+|||+++++++|+++|++||.|.++++..+      +|||||+|.+.+ +|.+|++.||+. ++|+.|+
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~-~a~~a~~~l~g~~~~g~~l~   82 (99)
T 2cpj_A           10 KTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRT-LAEIAKVELDNMPLRGKQLR   82 (99)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSH-HHHHHHHHHTTCCBTTBCCE
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHH-HHHHHHHHhCCCEeCCceEE
Confidence            33455789999999999999999999999999999998744      789999998888 999999999999 9999999


Q ss_pred             EEeccccc
Q psy8615         117 PSFNTYVL  124 (128)
Q Consensus       117 V~~~~~~~  124 (128)
                      |.|.++.-
T Consensus        83 v~~a~~~~   90 (99)
T 2cpj_A           83 VRFACHSA   90 (99)
T ss_dssp             EEESSCCS
T ss_pred             EEEcCCCC
Confidence            99998753

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

Probab=99.83  E-value=8.3e-21  Score=124.13  Aligned_cols=80  Identities=15%  Similarity=0.182  Sum_probs=70.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHH----hhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLA----SMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSF  114 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~----~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~  114 (128)
                      ....++|||+|||+++++++|+    ++|++||.|.+|.+.   .+|+++|||||+|.+.+ +|..|++.|||. +.|++
T Consensus        26 ~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~---~~~~~rG~aFV~F~~~~-~A~~Ai~~lng~~l~gr~  101 (127)
T 2a3j_A           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVD---LSDDNSGKAYIVFATQE-SAQAFVEAFQGYPFQGNP  101 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEEC---CCCSSCCCEEEEESSHH-HHHHHHHHSTTCCCTTSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEec---cCCCcCCEEEEEECCHH-HHHHHHHHHCCCEeCCCE
Confidence            3447899999999999999876    699999999988764   35889999999997777 999999999999 99999


Q ss_pred             EEEEecccc
Q psy8615         115 LKPSFNTYV  123 (128)
Q Consensus       115 l~V~~~~~~  123 (128)
                      |+|.|++..
T Consensus       102 l~V~~a~~~  110 (127)
T 2a3j_A          102 LVITFSETP  110 (127)
T ss_dssp             CEEEECCCC
T ss_pred             EEEEEccCc
Confidence            999999864

>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=99.83  E-value=1.9e-20  Score=121.14  Aligned_cols=79  Identities=16%  Similarity=0.145  Sum_probs=70.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcC--c-CCCeEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTAND--Y-LGQSFLK  116 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g--~-~~~~~l~  116 (128)
                      .++.++|||+|||++++|++|+++|++||.|.+++++.+      +|||||+|++.+ +|..|++.+++  . ++|++|+
T Consensus        28 ~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e-~A~~Ai~~l~~~~~~l~Gr~l~  100 (119)
T 2ad9_A           28 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEE-AANTMVNYYTSVTPVLRGQPIY  100 (119)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHH-HHHHHHHHHHHHCCCBTTBCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHH-HHHHHHHHhccCCceECCeEEE
Confidence            345789999999999999999999999999999998865      789999997777 99999999985  5 9999999


Q ss_pred             EEecccccc
Q psy8615         117 PSFNTYVLM  125 (128)
Q Consensus       117 V~~~~~~~~  125 (128)
                      |+|+++.-+
T Consensus       101 V~~a~~k~~  109 (119)
T 2ad9_A          101 IQFSNHKEL  109 (119)
T ss_dssp             EEECSSSSC
T ss_pred             EEEccCCCC
Confidence            999987543

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.83  E-value=1.2e-20  Score=120.32  Aligned_cols=78  Identities=15%  Similarity=0.157  Sum_probs=71.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      +.++|||+|||+++++++|+++|++| .|.+++++.|+. |+++|||||+|.+.+ +|.+|+ .+|+. ++|+.|+|...
T Consensus        15 ~~~~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           15 DDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQ-DTFEAL-KRNRMLMIQRYVEVSPA   90 (109)
T ss_dssp             HHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHH-HHHHHH-HTTTEEETTEEEEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHH-HHHHHH-hcCCCeECCeEEEEEEC
Confidence            35799999999999999999999999 899999999987 999999999997777 999999 79999 99999999887


Q ss_pred             ccc
Q psy8615         121 TYV  123 (128)
Q Consensus       121 ~~~  123 (128)
                      ++.
T Consensus        91 ~~~   93 (109)
T 2dnn_A           91 TER   93 (109)
T ss_dssp             CHH
T ss_pred             Ccc
Confidence            653

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.83  E-value=8.7e-22  Score=123.30  Aligned_cols=81  Identities=19%  Similarity=0.098  Sum_probs=73.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      ...++|||+|||+++++++|+++|++||.|.. .++.++.+|+++|||||+|.+.+ +|.+|++ ||+. ++|+.|+|.|
T Consensus        15 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~-~a~~A~~-l~g~~~~g~~l~V~~   91 (101)
T 1fj7_A           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAE-DLEKALE-LTGLKVFGNEIKLEK   91 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHH-HHHHHHH-GGGCCBTTBCCEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHH-HHHHHHh-cCCcEECCcEEEEEE
Confidence            34779999999999999999999999999988 77788888999999999997777 9999999 9999 9999999999


Q ss_pred             ccccc
Q psy8615         120 NTYVL  124 (128)
Q Consensus       120 ~~~~~  124 (128)
                      +++.-
T Consensus        92 a~~~~   96 (101)
T 1fj7_A           92 PKGRD   96 (101)
T ss_dssp             CSCCC
T ss_pred             cCCCC
Confidence            98653

>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=99.83  E-value=3.7e-20  Score=117.13  Aligned_cols=78  Identities=15%  Similarity=0.034  Sum_probs=68.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcC--c-CCCeEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTAND--Y-LGQSFLK  116 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g--~-~~~~~l~  116 (128)
                      .++.++|||+|||+++++++|+++|++||.|.++.++.+      ||||||+|++.+ +|..|++.|++  . ++|++|+
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~-~A~~Ai~~l~~~~~~i~Gr~l~   84 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENID-SAKECVTFAADVPVYIAGQQAF   84 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHH-HHHHHHHHHHHSCCBSSSSBCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHH-HHHHHHHHhccCCceECCEEEE
Confidence            344679999999999999999999999999999988753      789999997777 99999999875  3 8999999


Q ss_pred             EEeccccc
Q psy8615         117 PSFNTYVL  124 (128)
Q Consensus       117 V~~~~~~~  124 (128)
                      |+|++..-
T Consensus        85 V~~a~~~~   92 (104)
T 1wex_A           85 FNYSTSKR   92 (104)
T ss_dssp             EEECSSSS
T ss_pred             EEEccCcc
Confidence            99998653

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} SCOP: d.58.7.1 PDB: 2f9d_A 2f9j_A 2fho_B

Probab=99.83  E-value=2.6e-20  Score=119.08  Aligned_cols=79  Identities=14%  Similarity=0.287  Sum_probs=72.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      ...++|||+|||+++++++|+++|++||.|.+++++.+   +.++|||||+|.+.+ +|..|++.|||. ++|+.|+|.|
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~-~A~~A~~~l~g~~~~g~~l~v~~   81 (115)
T 3lqv_A            6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIF-DAKNAVDHLSGFNVSNRYLVVLY   81 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHH-HHHHHHHHHTTCBSSSCBCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHH-HHHHHHHHcCCCEECCeEEEEEE
Confidence            34679999999999999999999999999999999876   556999999997777 999999999999 9999999999


Q ss_pred             cccc
Q psy8615         120 NTYV  123 (128)
Q Consensus       120 ~~~~  123 (128)
                      .++.
T Consensus        82 a~~~   85 (115)
T 3lqv_A           82 YNAN   85 (115)
T ss_dssp             CCHH
T ss_pred             ecCC
Confidence            9864

>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=99.83  E-value=3.5e-20  Score=112.38  Aligned_cols=76  Identities=16%  Similarity=0.234  Sum_probs=68.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHh-cCc-CCCeEEE
Q psy8615          39 TGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTA-NDY-LGQSFLK  116 (128)
Q Consensus        39 ~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l-~g~-~~~~~l~  116 (128)
                      .+...++|||+|||.++++++|+++|++||.|.++++..+      +|||||+|.+.+ +|..|++.| ++. ++|+.|+
T Consensus         8 ~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~-~A~~a~~~l~~~~~~~g~~l~   80 (85)
T 2ytc_A            8 EDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQ-AAEVAAEKSFNKLIVNGRRLN   80 (85)
T ss_dssp             SCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHH-HHHHHHHTTTTTCEETTEECC
T ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHH-HHHHHHHHhcCCeeECCCEEE
Confidence            3455789999999999999999999999999999998864      789999997777 999999999 988 9999999


Q ss_pred             EEecc
Q psy8615         117 PSFNT  121 (128)
Q Consensus       117 V~~~~  121 (128)
                      |.|++
T Consensus        81 v~~ak   85 (85)
T 2ytc_A           81 VKWGR   85 (85)
T ss_dssp             EEECC
T ss_pred             EEecC
Confidence            99975

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.72  E-value=3.8e-22  Score=128.02  Aligned_cols=83  Identities=17%  Similarity=0.237  Sum_probs=77.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEE--------EEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-C
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLS--------AKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-L  110 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~--------~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~  110 (128)
                      ..+.++|||+|||.++++++|+++|++||.|.+        ++++.++.+|+++|||||+|.+.+ +|..|++.||+. +
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~-~A~~Ai~~l~g~~~   82 (116)
T 2lcw_A            4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP-SAKAAIDWFDGKEF   82 (116)
Confidence            455789999999999999999999999999999        899999999999999999998887 999999999999 9


Q ss_pred             CCeEEEEEecccc
Q psy8615         111 GQSFLKPSFNTYV  123 (128)
Q Consensus       111 ~~~~l~V~~~~~~  123 (128)
                      +|+.|+|.|+++.
T Consensus        83 ~g~~l~V~~a~~~   95 (116)
T 2lcw_A           83 SGNPIKVSFATRR   95 (116)
Confidence            9999999998764

>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=99.83  E-value=4.7e-21  Score=122.47  Aligned_cols=83  Identities=23%  Similarity=0.299  Sum_probs=71.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ....++|||+|||+++++++|+++|++||.|.++.+..+..+|+++|||||+|.+.+ +|..|++.||+. ++|+.|+|.
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~-~a~~Ai~~l~g~~~~g~~l~v~  100 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKE-IAWQALHLVNGYKLYGKILVIE  100 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHH-HHHHHHHHSTTCBCSSCBCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHH-HHHHHHHHhCCCEeCCcEEEEE
Confidence            345789999999999999999999999999944333333336899999999997777 999999999999 999999999


Q ss_pred             ecccc
Q psy8615         119 FNTYV  123 (128)
Q Consensus       119 ~~~~~  123 (128)
                      |+++.
T Consensus       101 ~a~~~  105 (115)
T 2cpx_A          101 FGKNK  105 (115)
T ss_dssp             ECCCC
T ss_pred             EccCC
Confidence            99864

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.82  E-value=6.6e-20  Score=113.95  Aligned_cols=76  Identities=21%  Similarity=0.249  Sum_probs=69.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CC--CeEEEE
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LG--QSFLKP  117 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~--~~~l~V  117 (128)
                      +..++|||+|||.++++++|+++|++||.|.++++..+      +|||||+|.+.+ +|++|++.||+. +.  |+.|+|
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~-~A~~A~~~l~g~~~~~~g~~l~V   87 (97)
T 1why_A           15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLD-AAQAACAKMRGFPLGGPDRRLRV   87 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHH-HHHHHHHHHTTCBCSSSSCBCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHH-HHHHHHHHHCCCEeCCCCcEEEE
Confidence            44689999999999999999999999999999987643      789999997777 999999999999 88  999999


Q ss_pred             Eecccc
Q psy8615         118 SFNTYV  123 (128)
Q Consensus       118 ~~~~~~  123 (128)
                      .|+++.
T Consensus        88 ~~a~~~   93 (97)
T 1why_A           88 DFAKSG   93 (97)
T ss_dssp             EECCCC
T ss_pred             EECCCC
Confidence            999875

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.82  E-value=7.2e-20  Score=116.06  Aligned_cols=75  Identities=21%  Similarity=0.272  Sum_probs=69.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCC-----eE
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQ-----SF  114 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~-----~~  114 (128)
                      ...++|||+|||+++++++|+++|++||.|.+++++.+       |||||+|.+.+ +|+.|++.||+. +.|     +.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~-~a~~Ai~~l~g~~~~g~~~~~~~   84 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKE-DMTYAVRKLDNTKFRSHEGETAY   84 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHH-HHHHHHHHSSSEEEECTTSCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHH-HHHHHHHHHCcCCccCCcCcceE
Confidence            34789999999999999999999999999999999876       89999997777 999999999999 988     99


Q ss_pred             EEEEecccc
Q psy8615         115 LKPSFNTYV  123 (128)
Q Consensus       115 l~V~~~~~~  123 (128)
                      |+|.++++.
T Consensus        85 i~V~~a~~~   93 (108)
T 1x4c_A           85 IRVKVDGPR   93 (108)
T ss_dssp             EEEEESSCC
T ss_pred             EEEEeCCCC
Confidence            999998864

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

Probab=99.82  E-value=3.5e-20  Score=117.78  Aligned_cols=77  Identities=17%  Similarity=0.355  Sum_probs=69.7

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEE
Q psy8615          38 LTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLK  116 (128)
Q Consensus        38 ~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~  116 (128)
                      ......++|||+|||+++++++|+++|++||.|.++++.        +|||||+|.+.+ +|+.|++.|||. ++|+.|+
T Consensus        26 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~-~A~~Ai~~l~g~~~~g~~l~   96 (108)
T 2jvo_A           26 EGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAE-SAAKAIEEVHGKSFANQPLE   96 (108)
T ss_dssp             --CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHH-HHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHH-HHHHHHHHcCCCEECCeEEE
Confidence            345567899999999999999999999999999999987        789999997777 999999999999 9999999


Q ss_pred             EEecccc
Q psy8615         117 PSFNTYV  123 (128)
Q Consensus       117 V~~~~~~  123 (128)
                      |.|+++.
T Consensus        97 V~~a~~~  103 (108)
T 2jvo_A           97 VVYSKLP  103 (108)
T ss_dssp             EESCSCC
T ss_pred             EEEecCC
Confidence            9999864

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.82  E-value=1.9e-20  Score=117.18  Aligned_cols=76  Identities=18%  Similarity=0.275  Sum_probs=69.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      .+..++|||+|||.++++++|+++|++||.|.++++.      +++|||||+|.+.+ +|..|++.|||. ++|+.|+|.
T Consensus        24 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~------~~~g~afV~f~~~~-~A~~Ai~~l~g~~~~g~~l~V~   96 (101)
T 2la4_A           24 PPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFIKYDTHE-QAAVCIVALANFPFQGRNLRTG   96 (101)
T ss_dssp             CSSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE------TTTTEEEEECSSHH-HHHHHHHHHTTCEETTEECCCC
T ss_pred             CCCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe------cCCCEEEEEECCHH-HHHHHHHHhCCCeECCeEEEEE
Confidence            3447899999999999999999999999999999987      35899999997777 999999999999 999999999


Q ss_pred             eccc
Q psy8615         119 FNTY  122 (128)
Q Consensus       119 ~~~~  122 (128)
                      |+++
T Consensus        97 ~a~~  100 (101)
T 2la4_A           97 WGKE  100 (101)
T ss_dssp             BCCC
T ss_pred             eccC
Confidence            9986

>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=99.82  E-value=4.3e-20  Score=118.25  Aligned_cols=76  Identities=14%  Similarity=0.182  Sum_probs=67.7

Q ss_pred             CCCCCeEEEcCCCCC-CCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcC--c-CCCeEE
Q psy8615          40 GPEGANLFIYHLPPE-FSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTAND--Y-LGQSFL  115 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~-~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g--~-~~~~~l  115 (128)
                      ....++|||+|||++ +++++|+++|++||.|.+++++.      ++|||||+|++.+ +|..|++.|++  . +.|++|
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~------~kg~aFVef~~~~-~A~~Ai~~l~~~~~~l~Gr~l   94 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETRE-DAMAMVDHCLKKALWFQGRCV   94 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET------TTTEEEEECSSHH-HHHHHHHHHHHSCCCSSSSCC
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec------CCCEEEEEECCHH-HHHHHHHHhccCCceECCEEE
Confidence            445789999999998 99999999999999999999863      3789999997777 99999999864  4 899999


Q ss_pred             EEEeccc
Q psy8615         116 KPSFNTY  122 (128)
Q Consensus       116 ~V~~~~~  122 (128)
                      +|+|++.
T Consensus        95 ~V~~a~~  101 (112)
T 1x4f_A           95 KVDLSEK  101 (112)
T ss_dssp             EEEEECS
T ss_pred             EEEECcc
Confidence            9999875

>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=99.82  E-value=1.1e-19  Score=122.53  Aligned_cols=80  Identities=20%  Similarity=0.281  Sum_probs=75.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      ...++|||+|||.++++++|+++|++||.|.++++..++.+|+++|||||+|.+.+ +|.+|++.|||. ++|+.|+|+|
T Consensus        92 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~-~A~~A~~~l~g~~~~g~~l~V~~  170 (172)
T 2g4b_A           92 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDIN-VTDQAIAGLNGMQLGDKKLLVQR  170 (172)
T ss_dssp             TTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTT-HHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHH-HHHHHHHHcCCCEECCeEEEEEe
Confidence            34789999999999999999999999999999999999988999999999998888 999999999999 9999999999


Q ss_pred             cc
Q psy8615         120 NT  121 (128)
Q Consensus       120 ~~  121 (128)
                      ++
T Consensus       171 As  172 (172)
T 2g4b_A          171 AS  172 (172)
T ss_dssp             CC
T ss_pred             CC
Confidence            74

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ...

Probab=99.82  E-value=8.1e-21  Score=117.88  Aligned_cols=80  Identities=14%  Similarity=0.228  Sum_probs=72.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHH----hhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLA----SMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSF  114 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~----~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~  114 (128)
                      .+..++|||+|||+++++++|+    ++|++||.|.++++..   +|.++|||||+|.+.+ +|..|++.|||. ++|+.
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~-~A~~A~~~l~g~~~~g~~   80 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVS-SATNALRSMQGFPFYDKP   80 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHH-HHHHHHHHHTTCEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHH-HHHHHHHHhCCCEECCcE
Confidence            4457899999999999999999    9999999999998763   4788999999997777 999999999999 99999


Q ss_pred             EEEEecccc
Q psy8615         115 LKPSFNTYV  123 (128)
Q Consensus       115 l~V~~~~~~  123 (128)
                      |+|+|+++.
T Consensus        81 l~v~~a~~~   89 (97)
T 1nu4_A           81 MRIQYAKTD   89 (97)
T ss_dssp             CEEEECSSC
T ss_pred             EEEEEccCC
Confidence            999999875

>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=99.82  E-value=8e-20  Score=122.27  Aligned_cols=80  Identities=24%  Similarity=0.370  Sum_probs=75.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecc
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNT  121 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~  121 (128)
                      .++|||+|||.++++++|+++|++||.|.+++++.++.+|+++|||||+|.+.+ +|..|++.+||. ++|+.|+|.|.+
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~-~A~~a~~~l~~~~~~g~~l~v~~~~   80 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPK-DAEKAINTLNGLRLQTKTIKVSYAR   80 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHH-HHHHHHHHHTTCEETTEECEEEECC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHH-HHHHHHHHcCCCccCCceEEEEecC
Confidence            579999999999999999999999999999999999989999999999997777 999999999999 999999999987


Q ss_pred             cc
Q psy8615         122 YV  123 (128)
Q Consensus       122 ~~  123 (128)
                      +.
T Consensus        81 ~~   82 (167)
T 1fxl_A           81 PS   82 (167)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.82  E-value=3e-20  Score=127.62  Aligned_cols=83  Identities=24%  Similarity=0.272  Sum_probs=77.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      ...++|||+|||+++++++|+++|++||.|.+|++..++ +|.++|||||+|.+.+ +|..|++.||+. ++|+.|+|.|
T Consensus        86 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~-~A~~Ai~~lng~~l~Gr~l~V~~  163 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRA-DALKAMKQYKGVPLDGRPMDIQL  163 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHH-HHHHHHHHSTTCBCSSSBCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHH-HHHHHHHHhCCCEECCEEEEEEE
Confidence            446899999999999999999999999999999999998 7999999999997777 999999999999 9999999999


Q ss_pred             cccccc
Q psy8615         120 NTYVLM  125 (128)
Q Consensus       120 ~~~~~~  125 (128)
                      ++....
T Consensus       164 a~~~~~  169 (177)
T 2f3j_A          164 VASQID  169 (177)
T ss_dssp             ESSGGG
T ss_pred             ecCCCC
Confidence            987654

>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=99.82  E-value=4.6e-21  Score=113.74  Aligned_cols=74  Identities=22%  Similarity=0.350  Sum_probs=69.4

Q ss_pred             eEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        45 ~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      +|||+|||+++++++|+++|++||.|.+++++.++.+|.++|||||+|.+.+ +|.+|++. ++. ++|+.|+|.++
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 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEE-PVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSH-HHHHHHTT-SSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHH-HHHHHHHh-CCCeECCEEEEEEEC
Confidence            5899999999999999999999999999999999999999999999998888 99999986 777 99999999874

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.82  E-value=1.4e-20  Score=117.98  Aligned_cols=78  Identities=17%  Similarity=0.276  Sum_probs=72.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      ...++|||+|||+++++++|+++|++||.|.+++++.++ +|+++|||||+|.+.+ +|..|++  ++. ++|+.|.|.+
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~-~a~~Ai~--~~~~~~g~~l~v~~   82 (102)
T 2xs2_A            7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDV-DVQKIVE--SQINFHGKKLKLGP   82 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCC-CHHHHTT--CCCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHH-HHHHHHh--CCCeECCEEEEEEE
Confidence            346799999999999999999999999999999999998 8999999999998888 9999999  888 9999999988


Q ss_pred             ccc
Q psy8615         120 NTY  122 (128)
Q Consensus       120 ~~~  122 (128)
                      ..+
T Consensus        83 a~~   85 (102)
T 2xs2_A           83 AIR   85 (102)
T ss_dssp             EEE
T ss_pred             CCc
Confidence            764

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A

Probab=99.82  E-value=6.8e-20  Score=114.27  Aligned_cols=78  Identities=21%  Similarity=0.244  Sum_probs=68.8

Q ss_pred             CCCCCCCCeEEEcCCCC-CCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeE
Q psy8615          37 QLTGPEGANLFIYHLPP-EFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSF  114 (128)
Q Consensus        37 ~~~~~~~~~l~V~nLp~-~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~  114 (128)
                      ....+..++|||+|||+ ++++++|+++|++||.|.++++.        +|||||+|.+.+ +|.+|++.|||. ++|+.
T Consensus        16 ~~~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~-~A~~Ai~~l~g~~~~g~~   86 (97)
T 2xnq_A           16 PRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQ-SVRDAIEXESQEMNFGKK   86 (97)
T ss_dssp             ---CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHH-HHHHHHHHHTTSEETTEE
T ss_pred             cCCCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHH-HHHHHHHHcCCCEECCEE
Confidence            34455688999999998 99999999999999999999872        789999997777 999999999999 99999


Q ss_pred             EEEEecccc
Q psy8615         115 LKPSFNTYV  123 (128)
Q Consensus       115 l~V~~~~~~  123 (128)
                      |+|.|++..
T Consensus        87 l~V~~a~~~   95 (97)
T 2xnq_A           87 LILEVSSSN   95 (97)
T ss_dssp             CEEEECCCC
T ss_pred             EEEEecCCC
Confidence            999998764

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

Probab=99.82  E-value=7e-20  Score=113.90  Aligned_cols=78  Identities=14%  Similarity=0.216  Sum_probs=69.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ....++|||+|||+++++++|+++|++||.|. ++++.+    +++|||||+|.+.+ +|+.|++.|||. ++|+.|+|.
T Consensus        16 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~----~~~g~afV~f~~~~-~a~~A~~~l~g~~~~g~~l~V~   89 (97)
T 2e5j_A           16 APLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ----GPRRRAFLHYPDSA-AAQQAVSCLQGLRLGTDTLRVA   89 (97)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE----TTTTEEEEECSSHH-HHHHHHHHHTTCCSSSSCCEEE
T ss_pred             CCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC----CCCcEEEEEECCHH-HHHHHHHHhCCCEECCcEEEEE
Confidence            34478999999999999999999999999996 666654    66999999997777 999999999999 999999999


Q ss_pred             ecccc
Q psy8615         119 FNTYV  123 (128)
Q Consensus       119 ~~~~~  123 (128)
                      |+++.
T Consensus        90 ~a~~~   94 (97)
T 2e5j_A           90 LARQQ   94 (97)
T ss_dssp             ECCCC
T ss_pred             EcCCC
Confidence            99874

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.82  E-value=7.7e-20  Score=112.21  Aligned_cols=75  Identities=21%  Similarity=0.326  Sum_probs=68.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      ...++|||+|||+++++++|+++|++||.|.++++.        +|||||+|.+.+ +|+.|++.||+. ++|+.|+|.|
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~-~A~~A~~~l~g~~~~g~~l~v~~   76 (90)
T 2dnq_A            6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKT-AAEDAIRNLHHYKLHGVNINVEA   76 (90)
T ss_dssp             SCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHH-HHHHHHHHHTTCBCSSCBCEEEC
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHH-HHHHHHHHhcCCccCCcEEEEEE
Confidence            457899999999999999999999999999999887        679999997777 999999999999 9999999999


Q ss_pred             ccccc
Q psy8615         120 NTYVL  124 (128)
Q Consensus       120 ~~~~~  124 (128)
                      +++..
T Consensus        77 a~~~~   81 (90)
T 2dnq_A           77 SKNKS   81 (90)
T ss_dssp             SSCCC
T ss_pred             CCCCC
Confidence            98653

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.81  E-value=2.8e-20  Score=115.28  Aligned_cols=78  Identities=12%  Similarity=0.096  Sum_probs=69.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ....++|||+|||+++++++|+++|++||.|..+     ..+|+++|||||+|.+.+ +|..|++.|||. ++|+.|+|.
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~-~a~~A~~~l~g~~~~g~~l~v~   86 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEA-DAEKNLEEKQGAEIDGRSVSLY   86 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHH-HHHHHHHHTTEEEETTEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHH-HHHHHHHHhCCCEECCeEEEEE
Confidence            4457899999999999999999999999988765     345899999999997777 999999999999 999999999


Q ss_pred             ecccc
Q psy8615         119 FNTYV  123 (128)
Q Consensus       119 ~~~~~  123 (128)
                      |+++.
T Consensus        87 ~a~~~   91 (96)
T 1fjc_A           87 YTGEK   91 (96)
T ss_dssp             ECSSS
T ss_pred             EcCCC
Confidence            98764

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.81  E-value=1.2e-19  Score=126.35  Aligned_cols=85  Identities=21%  Similarity=0.325  Sum_probs=79.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      ...++|||+|||.++++++|+++|++||.|.++++..++.+|+++|||||+|.+.+ +|.+|++.|||. ++|+.|+|.|
T Consensus       123 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~-~A~~A~~~l~g~~~~g~~i~V~~  201 (216)
T 2qfj_A          123 RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQ-SSQDAVSSMNLFDLGGQYLRVGK  201 (216)
T ss_dssp             TTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHH-HHHHHHHHHTTCBCSSSBCEEEE
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHH-HHHHHHHHccCCEeCCcEEEEEE
Confidence            44679999999999999999999999999999999999999999999999997776 999999999999 9999999999


Q ss_pred             ccccccc
Q psy8615         120 NTYVLMN  126 (128)
Q Consensus       120 ~~~~~~~  126 (128)
                      +++...+
T Consensus       202 a~~~~~~  208 (216)
T 2qfj_A          202 AVTPPMP  208 (216)
T ss_dssp             CSSCSST
T ss_pred             ecCCCCC
Confidence            9987654

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.81  E-value=2.7e-19  Score=123.07  Aligned_cols=83  Identities=18%  Similarity=0.219  Sum_probs=78.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      ...++|||+|||+++++++|+++|++||.|.++++..++.+|.++|||||+|.+.+ +|.+|++.|||. ++|+.|+|+|
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~-~a~~A~~~l~g~~~~g~~l~v~~  190 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDIN-VTDQAIAGLNGMQLGDKKLLVQR  190 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSS-HHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHH-HHHHHHHHcCCCEECCEEEEEEE
Confidence            55789999999999999999999999999999999999988999999999998888 999999999999 9999999999


Q ss_pred             ccccc
Q psy8615         120 NTYVL  124 (128)
Q Consensus       120 ~~~~~  124 (128)
                      +++..
T Consensus       191 a~~~~  195 (198)
T 2yh0_A          191 ASVGA  195 (198)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            98753

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A

Probab=99.81  E-value=2e-19  Score=114.20  Aligned_cols=74  Identities=16%  Similarity=0.225  Sum_probs=68.4

Q ss_pred             CCCCeEEEcCCCCC-CCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          41 PEGANLFIYHLPPE-FSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        41 ~~~~~l~V~nLp~~-~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ...++|||+|||++ +++++|+++|++||.|.++++        ++|||||+|.+.+ +|..|++.||+. ++|+.|+|.
T Consensus        25 ~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~-~A~~A~~~l~g~~~~g~~l~V~   95 (110)
T 1wf1_A           25 SINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNER-HARAAVLGENGRVLAGQTLDIN   95 (110)
T ss_dssp             TCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSH-HHHHHHHHHTTCEETTEECCEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHH-HHHHHHHHcCCCEECCeEEEEE
Confidence            34689999999999 999999999999999999987        4889999998888 999999999999 999999999


Q ss_pred             ecccc
Q psy8615         119 FNTYV  123 (128)
Q Consensus       119 ~~~~~  123 (128)
                      |+++.
T Consensus        96 ~a~~~  100 (110)
T 1wf1_A           96 MAGEP  100 (110)
T ss_dssp             ESCCC
T ss_pred             ECCCC
Confidence            99753

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=4.7e-20  Score=116.96  Aligned_cols=78  Identities=15%  Similarity=0.298  Sum_probs=71.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ....++|||+|||.++++++|+.+|++||.|.++++..+      +|||||+|.+.+ +|..|++.|||. ++|+.|+|.
T Consensus        22 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~-~a~~A~~~l~g~~~~g~~l~v~   94 (109)
T 1x4g_A           22 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHE-SAAHAIVSVNGTTIEGHVVKCY   94 (109)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHH-HHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHH-HHHHHHHHcCCCEECCcEEEEE
Confidence            455789999999999999999999999999999998866      789999997777 999999999999 999999999


Q ss_pred             eccccc
Q psy8615         119 FNTYVL  124 (128)
Q Consensus       119 ~~~~~~  124 (128)
                      |+++..
T Consensus        95 ~a~~~~  100 (109)
T 1x4g_A           95 WGKESP  100 (109)
T ss_dssp             CCCCCC
T ss_pred             ecCCCC
Confidence            998753

>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=99.81  E-value=6.5e-20  Score=123.11  Aligned_cols=81  Identities=19%  Similarity=0.298  Sum_probs=76.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      ..++|||+|||+++++++|+++|++||.|.++++..++.+|+++|||||+|.+.+ +|..|++.+++. ++|+.|+|.|.
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-~A~~a~~~l~~~~~~g~~l~v~~~   80 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEM-DSQRAIKVLNGITVRNKRLKVSYA   80 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHH-HHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHH-HHHHHHHhcCCCEeCCcEEEEEec
Confidence            3689999999999999999999999999999999999989999999999997776 999999999999 99999999998


Q ss_pred             ccc
Q psy8615         121 TYV  123 (128)
Q Consensus       121 ~~~  123 (128)
                      ++.
T Consensus        81 ~~~   83 (168)
T 1b7f_A           81 RPG   83 (168)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            764

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.81  E-value=2.5e-20  Score=119.20  Aligned_cols=78  Identities=15%  Similarity=0.105  Sum_probs=69.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCC-ceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFG-TVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G-~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ...++|||+|||+++++++|+++|++|| .|..+++..    ++++|||||+|.+.+ +|+.|++.|||. ++|+.|+|.
T Consensus        26 ~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~----~~~rGfaFV~F~~~e-~A~~Ai~~lng~~l~Gr~i~V~  100 (111)
T 2jvr_A           26 AKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT----RDFDGTGALEFPSEE-ILVEALERLNNIEFRGSVITVE  100 (111)
T ss_dssp             CCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS----CSSSCCEEEEESSHH-HHHHHHHHTTTEEETTEEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc----CCCCCEEEEEECCHH-HHHHHHHHcCCCEECCeEEEEE
Confidence            3468999999999999999999999999 899988753    357999999997776 999999999999 999999999


Q ss_pred             ecccc
Q psy8615         119 FNTYV  123 (128)
Q Consensus       119 ~~~~~  123 (128)
                      +++..
T Consensus       101 ~a~~~  105 (111)
T 2jvr_A          101 RDDNP  105 (111)
T ss_dssp             ESCC-
T ss_pred             ECCCC
Confidence            98754

>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=99.81  E-value=4.7e-20  Score=120.36  Aligned_cols=81  Identities=7%  Similarity=0.165  Sum_probs=72.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceE--EEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEE
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVL--SAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKP  117 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~--~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V  117 (128)
                      ...++|||+|||++++|++|+++|++| .|.  +|+++.|+. |+++|||||+|.+.+ +|++|++. ++. ++|+.|+|
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e-~A~~Al~~-~~~~l~gR~I~V  115 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQE-LAEKALGK-HKERIGHRYIEV  115 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTT-HHHHHHTT-TTCCBTTBCCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHH-HHHHHHHH-CCCEECCEEEEE
Confidence            446789999999999999999999999 576  899999988 999999999998888 99999986 557 99999999


Q ss_pred             Eecccccc
Q psy8615         118 SFNTYVLM  125 (128)
Q Consensus       118 ~~~~~~~~  125 (128)
                      ..+++.-|
T Consensus       116 ~~a~~~e~  123 (126)
T 2hgm_A          116 FKSSQEEV  123 (126)
T ss_dssp             EEECHHHH
T ss_pred             EECCHHHh
Confidence            98876543

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=99.80  E-value=7.9e-20  Score=121.93  Aligned_cols=80  Identities=14%  Similarity=0.120  Sum_probs=72.5

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEE
Q psy8615          38 LTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLK  116 (128)
Q Consensus        38 ~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~  116 (128)
                      ......++|||+|||+++++++|+++|++||.|.+++++.+     ++|||||+|.+.+ +|..|++.|||. ++|++|+
T Consensus        68 ~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~-~a~~A~~~l~g~~~~g~~l~  141 (150)
T 2i2y_A           68 DSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPR-DAADAVRELDGRTLCGCRVR  141 (150)
T ss_dssp             SSSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHH-HHHHHHHHHSSSCSSSSCCE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHH-HHHHHHHHcCCCEECCeEEE
Confidence            33455789999999999999999999999999999999876     5899999997777 999999999999 9999999


Q ss_pred             EEecccc
Q psy8615         117 PSFNTYV  123 (128)
Q Consensus       117 V~~~~~~  123 (128)
                      |+|+++.
T Consensus       142 v~~a~~~  148 (150)
T 2i2y_A          142 VELSNGE  148 (150)
T ss_dssp             EEECCCC
T ss_pred             EEEcCCC
Confidence            9999864

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.80  E-value=2.6e-19  Score=117.26  Aligned_cols=79  Identities=18%  Similarity=0.205  Sum_probs=70.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceE-EEEEEecCHHHHHHHHHHhcCc-CCC--eEEEEE
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCF-GTIIFMRKFFILTIRFDTANDY-LGQ--SFLKPS  118 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~-~fv~f~~~~~~a~~Ai~~l~g~-~~~--~~l~V~  118 (128)
                      -..|||+||++.+++++|+++|++||.|.++++..+.     +|| |||+|++.+ +|..|++.|||. +.|  +.|+|+
T Consensus        28 VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~-----~gfqAFVef~~~~-~A~~Ai~~LnG~~i~g~~~~LrI~  101 (130)
T 3zzy_A           28 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN-----NQFQALLQYADPV-SAQHAKLSLDGQNIYNACCTLRID  101 (130)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET-----TEEEEEEEESCHH-HHHHHHHHHTTCEEETTEEEEEEE
T ss_pred             eEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC-----CCcEEEEEECCHH-HHHHHHHHcCCCeecCCCcEEEEE
Confidence            4578999999999999999999999999999887542     678 999997777 999999999999 755  999999


Q ss_pred             ecccccccc
Q psy8615         119 FNTYVLMNV  127 (128)
Q Consensus       119 ~~~~~~~~~  127 (128)
                      |+++.-+|+
T Consensus       102 ~ak~~~l~v  110 (130)
T 3zzy_A          102 FSKLTSLNV  110 (130)
T ss_dssp             ECSCSSCCC
T ss_pred             ecCCCceeE
Confidence            999987765

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=3.1e-20  Score=120.79  Aligned_cols=81  Identities=11%  Similarity=0.115  Sum_probs=72.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCce----EEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEE
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTV----LSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFL  115 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i----~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l  115 (128)
                      .+.++|||+|||+++++++|+++|++||.|    .+|+++.|+ +|+++|||||+|.+.+ +|.+|++. |+. ++++.|
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~-~gr~~G~aFV~F~~~~-~A~~Al~~-~~~~l~gR~i   97 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP-DGRPTGDAFVLFACEE-YAQNALRK-HKDLLGKRYI   97 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECT-TSCEEEEEEECCSSHH-HHHHHHTT-TTEESSSCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECC-CCCEeeEEEEEECCHH-HHHHHHHh-CCCeeCCeEE
Confidence            457899999999999999999999999875    689999995 7999999999997777 99999997 888 999999


Q ss_pred             EEEeccccc
Q psy8615         116 KPSFNTYVL  124 (128)
Q Consensus       116 ~V~~~~~~~  124 (128)
                      +|..+++.-
T Consensus        98 ~V~~a~~~e  106 (123)
T 2dha_A           98 ELFRSTAAE  106 (123)
T ss_dssp             CCEEECHHH
T ss_pred             EEEECCHHH
Confidence            998887643

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.80  E-value=3e-20  Score=116.21  Aligned_cols=74  Identities=11%  Similarity=0.117  Sum_probs=69.1

Q ss_pred             CeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEeccc
Q psy8615          44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNTY  122 (128)
Q Consensus        44 ~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~~  122 (128)
                      ++|||+|||+++++++|+++|++||.|.++++..+     ++|||||+|.+.+ +|.+|++.||+. ++|+.|+|.|+++
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~-~a~~A~~~l~g~~~~g~~l~V~~a~~   74 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPR-DAEDAVRGLDGKVICGSRVRVELSTG   74 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHH-HHHHHHHHHHHSCSSSCCCEEEESSS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHH-HHHHHHHHHCCCeECCcEEEEEEccC
Confidence            58999999999999999999999999999999877     6899999997777 999999999999 9999999999976


Q ss_pred             c
Q psy8615         123 V  123 (128)
Q Consensus       123 ~  123 (128)
                      .
T Consensus        75 ~   75 (101)
T 2hvz_A           75 M   75 (101)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=2.6e-19  Score=110.26  Aligned_cols=77  Identities=14%  Similarity=0.270  Sum_probs=69.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEE
Q psy8615          39 TGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKP  117 (128)
Q Consensus        39 ~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V  117 (128)
                      .....++|||+|||+++++++|+++|++||.|.++++.        ++||||+|.+.+ +|.+|++.||+. ++|+.|+|
T Consensus         6 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~--------~~~afV~f~~~~-~a~~A~~~l~g~~~~g~~l~V   76 (92)
T 2dgt_A            6 SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAE-DAVEAIRGLDNTEFQGKRMHV   76 (92)
T ss_dssp             CCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC--------SSEEEEEESCHH-HHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE--------CCEEEEEECCHH-HHHHHHHHhCCCeeCCcEEEE
Confidence            34557899999999999999999999999999999886        349999997777 999999999999 99999999


Q ss_pred             Eeccccc
Q psy8615         118 SFNTYVL  124 (128)
Q Consensus       118 ~~~~~~~  124 (128)
                      .|+++..
T Consensus        77 ~~a~~~~   83 (92)
T 2dgt_A           77 QLSTSRL   83 (92)
T ss_dssp             EESSCCC
T ss_pred             EEccCCC
Confidence            9998753

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

Probab=99.80  E-value=9.7e-20  Score=112.84  Aligned_cols=78  Identities=22%  Similarity=0.236  Sum_probs=70.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEE-EEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAK-VFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~-~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ...++|||+|||+++++++|+++|++||.|.+++ ++.++.+|.    |||+|.+.+ +|..|++.|||. ++|+.|+|.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~----afV~f~~~~-~a~~Ai~~l~g~~~~g~~l~V~   87 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAV----VNVTYSSKD-QARQALDKLNGFQLENFTLKVA   87 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEE----EEEEESSHH-HHHHHHHHHTTCBCSSCBCEEE
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCE----EEEEECCHH-HHHHHHHHhCCCEECCcEEEEE
Confidence            3468999999999999999999999999999994 888876443    999997777 999999999999 999999999


Q ss_pred             ecccc
Q psy8615         119 FNTYV  123 (128)
Q Consensus       119 ~~~~~  123 (128)
                      |.++.
T Consensus        88 ~a~~~   92 (96)
T 2e44_A           88 YIPDE   92 (96)
T ss_dssp             ECCCC
T ss_pred             EcCcc
Confidence            99875

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=6.9e-19  Score=109.70  Aligned_cols=75  Identities=16%  Similarity=0.139  Sum_probs=67.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCC--CceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPF--GTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLK  116 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~--G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~  116 (128)
                      ....++|||+|||+++++++|+++|++|  |.|.++++.        +|||||+|.+.+ +|..|++.||+. ++|+.|+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~-~A~~A~~~l~g~~~~g~~l~   82 (99)
T 2cpd_A           12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNRE-DAVEAMKALNGKVLDGSPIE   82 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHH-HHHHHHHHHSSEEETTEEEE
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHH-HHHHHHHHhCCCEeCCcEEE
Confidence            3456899999999999999999999999  899988753        679999997777 999999999999 9999999


Q ss_pred             EEecccc
Q psy8615         117 PSFNTYV  123 (128)
Q Consensus       117 V~~~~~~  123 (128)
                      |.|+++.
T Consensus        83 v~~a~~~   89 (99)
T 2cpd_A           83 VTLAKPV   89 (99)
T ss_dssp             EECCCCC
T ss_pred             EEECCCC
Confidence            9999874

>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=99.80  E-value=2.4e-19  Score=138.08  Aligned_cols=83  Identities=10%  Similarity=0.167  Sum_probs=77.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      ...++|||+|||+.+++++|+.+|++||.|..|.|+.++.||+++|||||+|.+.+ +|..||+.|||. |+|+.|+|.|
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e-~A~~Ai~~lng~~i~gr~i~V~~  178 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHER-DMHSAYKHADGKKIDGRRVLVDV  178 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHH-HHHHHHHHcCCCEECCEEEEEEE
Confidence            34579999999999999999999999999999999999999999999999997777 999999999999 9999999999


Q ss_pred             ccccc
Q psy8615         120 NTYVL  124 (128)
Q Consensus       120 ~~~~~  124 (128)
                      +++..
T Consensus       179 a~~~~  183 (437)
T 3pgw_S          179 ERGRT  183 (437)
T ss_pred             eCCCC
Confidence            98654

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.80  E-value=8.4e-20  Score=116.51  Aligned_cols=76  Identities=12%  Similarity=0.115  Sum_probs=68.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      ..++|||+|||+++++++|+++|++||.|.++.++.      ++|||||+|.+.+ +|..|++.|||. ++|+.|+|.|+
T Consensus         9 ~~~~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            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPL-EARKAFRHLAYSKFHHVPLYLEWA   81 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHH-HHHHHHHHHTTCBSSSSBCEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHH-HHHHHHHHhCCCEECCeEEEEEEC
Confidence            367999999999999999999999999999988763      4789999997777 999999999999 99999999998


Q ss_pred             cccc
Q psy8615         121 TYVL  124 (128)
Q Consensus       121 ~~~~  124 (128)
                      +..+
T Consensus        82 ~~~~   85 (111)
T 1whx_A           82 PIGV   85 (111)
T ss_dssp             ETTT
T ss_pred             CCCc
Confidence            7654

>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=99.80  E-value=2.2e-20  Score=123.82  Aligned_cols=82  Identities=12%  Similarity=0.214  Sum_probs=73.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ....++|||+|||++++|++|+++|++|| +.+|+++.|+. |+++|||||+|++.+ +|++|+ .+|+. ++++.|+|.
T Consensus        43 ~~~~~~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           43 STTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHE-EAVAAM-SKDRANMQHRYIELF  118 (139)
T ss_dssp             --CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHH-HHHHHT-TCCSCSSSSCCCCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHH-HHHHHH-hhCCCEECCEEEEEE
Confidence            34567999999999999999999999999 77999999987 999999999997777 999999 88998 999999999


Q ss_pred             ecccccc
Q psy8615         119 FNTYVLM  125 (128)
Q Consensus       119 ~~~~~~~  125 (128)
                      ++++.-+
T Consensus       119 ~a~~~~~  125 (139)
T 2hgn_A          119 LNSTTGA  125 (139)
T ss_dssp             ECCCSCC
T ss_pred             ECCCCCC
Confidence            9887543

>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=99.80  E-value=2.5e-19  Score=109.58  Aligned_cols=76  Identities=9%  Similarity=0.123  Sum_probs=69.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      ..++|||+|||+++++++|+++|++| .|.++++.      +++|||||+|.+.+ +|++|++.|||. ++|+.|+|.|+
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~-~a~~Ai~~l~g~~~~g~~l~V~~a   75 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGE-QAQNAIQMFHQYSFRGKDLIVQLQ   75 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHH-HHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHH-HHHHHHHHhCCCeECCcEEEEEEc
Confidence            46799999999999999999999999 99999874      56899999997777 999999999999 99999999998


Q ss_pred             ccccc
Q psy8615         121 TYVLM  125 (128)
Q Consensus       121 ~~~~~  125 (128)
                      +...+
T Consensus        76 ~~~~~   80 (88)
T 1wg1_A           76 PTDAL   80 (88)
T ss_dssp             CCCCC
T ss_pred             CCCce
Confidence            76554

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.79  E-value=2.6e-19  Score=122.95  Aligned_cols=83  Identities=22%  Similarity=0.278  Sum_probs=75.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEE
Q psy8615          39 TGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKP  117 (128)
Q Consensus        39 ~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V  117 (128)
                      +....++|||+|||+++++++|+++|++||.|.+++++.++.+|.++|||||+|.+.+ +|..|++. ++. ++|+.|+|
T Consensus         9 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~-~A~~A~~~-~~~~~~g~~l~v   86 (196)
T 1l3k_A            9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE-EVDAAMNA-RPHKVDGRVVEP   86 (196)
T ss_dssp             CCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHH-HHHHHHHT-CSCEETTEECEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHH-HHHHHHhc-CCCEECCEEeee
Confidence            3445789999999999999999999999999999999999999999999999997776 99999987 777 99999999


Q ss_pred             Eecccc
Q psy8615         118 SFNTYV  123 (128)
Q Consensus       118 ~~~~~~  123 (128)
                      .+....
T Consensus        87 ~~~~~~   92 (196)
T 1l3k_A           87 KRAVSR   92 (196)
T ss_dssp             EECCC-
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=99.79  E-value=9.6e-19  Score=108.72  Aligned_cols=76  Identities=14%  Similarity=0.230  Sum_probs=68.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ....++|||+|+  ++++++|+++|++||.|.++++.      +++|||||+|.+.+ +|.+|++.||+. ++|+.|+|.
T Consensus        12 ~~~~~~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           12 PRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKME-SADQAVAELNGTQVESVQLKVN   82 (97)
T ss_dssp             CCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHH-HHHHHHHHTTTEEETTEEEEEE
T ss_pred             CCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHH-HHHHHHHHhCCCeECCeEEEEE
Confidence            345789999995  99999999999999999999873      56899999997777 999999999999 999999999


Q ss_pred             eccccc
Q psy8615         119 FNTYVL  124 (128)
Q Consensus       119 ~~~~~~  124 (128)
                      |+++..
T Consensus        83 ~a~~~~   88 (97)
T 1x5p_A           83 IARKQP   88 (97)
T ss_dssp             CCSSCC
T ss_pred             ECCCCC
Confidence            998753

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.79  E-value=1.4e-19  Score=112.35  Aligned_cols=75  Identities=23%  Similarity=0.306  Sum_probs=67.5

Q ss_pred             CCCCCeEEEcCCCC-CCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEE
Q psy8615          40 GPEGANLFIYHLPP-EFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKP  117 (128)
Q Consensus        40 ~~~~~~l~V~nLp~-~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V  117 (128)
                      .++.++|||+|||+ ++++++|+++|++||.|.++++.        +|||||+|.+.+ +|..|++.||+. ++|+.|+|
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~-~A~~A~~~l~g~~~~g~~l~V   77 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQ-SVRDAIECESQEMNFGKKLIL   77 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHH-HHHHHHHHHTCSSCBTTTBCE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHH-HHHHHHHHcCCCeeCCcEEEE
Confidence            45578999999999 99999999999999999999873        789999997777 999999999999 99999999


Q ss_pred             Eecccc
Q psy8615         118 SFNTYV  123 (128)
Q Consensus       118 ~~~~~~  123 (128)
                      .|+++.
T Consensus        78 ~~a~~~   83 (96)
T 2kvi_A           78 EVSSSN   83 (96)
T ss_dssp             EEEECC
T ss_pred             EEcCcC
Confidence            998754

>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=99.79  E-value=2.5e-20  Score=123.51  Aligned_cols=83  Identities=18%  Similarity=0.221  Sum_probs=70.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEE--E---EecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCe
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAK--V---FIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQS  113 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~--~---~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~  113 (128)
                      ....++|||+|||+++++++|+.+|++||.|.++.  +   +....+|+++|||||+|.+.+ +|..|++.|||. ++|+
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~-~A~~Ai~~lng~~~~g~  120 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEK-AAAKALKEANGYVLFGK  120 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHH-HHHHHHHHHTTBEETTE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHH-HHHHHHHHhCCCEeCCc
Confidence            34568999999999999999999999999987641  1   111246999999999997777 999999999999 9999


Q ss_pred             EEEEEecccc
Q psy8615         114 FLKPSFNTYV  123 (128)
Q Consensus       114 ~l~V~~~~~~  123 (128)
                      .|+|.|+++.
T Consensus       121 ~l~V~~a~~~  130 (143)
T 3egn_A          121 PMVVQFARSA  130 (143)
T ss_dssp             ECEEEECCCS
T ss_pred             EEEEEECCCC
Confidence            9999999753

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A

Probab=99.79  E-value=3.3e-19  Score=111.97  Aligned_cols=74  Identities=19%  Similarity=0.209  Sum_probs=67.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      ...++|||+|||+++++++|+++|++||.|.++++.        +|||||+|.+.+ +|.+|++.||+. +.|+.|+|.|
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~-~a~~A~~~l~g~~~~g~~l~v~~   79 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERD-GAVKAMEEMNGKDLEGENIEIVF   79 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHH-HHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHH-HHHHHHHHHCCCccCCCEEEEEE
Confidence            346899999999999999999999999999999876        559999997777 999999999999 9999999999


Q ss_pred             cccc
Q psy8615         120 NTYV  123 (128)
Q Consensus       120 ~~~~  123 (128)
                      +++.
T Consensus        80 a~~~   83 (103)
T 2dgu_A           80 AKPP   83 (103)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9764

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=2.4e-19  Score=109.98  Aligned_cols=75  Identities=13%  Similarity=0.175  Sum_probs=68.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ....++|||+|||+++++++|+++|++||.|.++++.        ++||||+|.+.+ +|..|++.||+. ++|+.|+|.
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~--------~~~afV~f~~~~-~a~~A~~~l~g~~~~g~~l~v~   76 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEA-DAKAAIAQLNGKEVKGKRINVE   76 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESCHH-HHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE--------CCEEEEEECCHH-HHHHHHHHhCCCEECCcEEEEE
Confidence            4557899999999999999999999999999999887        349999997777 999999999999 999999999


Q ss_pred             ecccc
Q psy8615         119 FNTYV  123 (128)
Q Consensus       119 ~~~~~  123 (128)
                      |+++.
T Consensus        77 ~a~~~   81 (90)
T 2dnp_A           77 LSTKG   81 (90)
T ss_dssp             ESCCC
T ss_pred             ECCCC
Confidence            99865

>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=99.79  E-value=1.2e-18  Score=116.91  Aligned_cols=80  Identities=18%  Similarity=0.363  Sum_probs=74.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCC--eEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQ--SFLK  116 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~--~~l~  116 (128)
                      ....++|||+|||.++++++|+++|++||.|.++++..++.+|+++|||||+|.+.+ +|.+|++.|||. +.|  ++|+
T Consensus        86 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~-~A~~A~~~l~g~~~~g~~~~l~  164 (168)
T 1b7f_A           86 SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKRE-EAQEAISALNNVIPEGGSQPLS  164 (168)
T ss_dssp             TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHH-HHHHHHHHHTTCCCTTCSSCCE
T ss_pred             cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHHhcCCEecCCCeEEE
Confidence            445789999999999999999999999999999999999988999999999997777 999999999999 866  9999


Q ss_pred             EEec
Q psy8615         117 PSFN  120 (128)
Q Consensus       117 V~~~  120 (128)
                      |+|+
T Consensus       165 V~~A  168 (168)
T 1b7f_A          165 VRLA  168 (168)
T ss_dssp             EEEC
T ss_pred             EEeC
Confidence            9985

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=99.79  E-value=3.8e-19  Score=120.57  Aligned_cols=80  Identities=16%  Similarity=0.163  Sum_probs=70.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CC--CeEEEEEe
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LG--QSFLKPSF  119 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~--~~~l~V~~  119 (128)
                      ..+|||+||++.+++++|+++|++||.|.++.+..++    ++|||||+|++.+ +|+.|++.|||. +.  ++.|+|+|
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~----~rgfAFVeF~d~~-~A~~Ai~~LnG~~i~g~g~~L~V~~  120 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPV-SAQHAKLSLDGQNIYNACCTLRIDF  120 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS----SCEEEEEEESCHH-HHHHHHHHSTTBCSSSSCSCEEEEE
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC----CCCEEEEEECCHH-HHHHHHHHhCCCEecCCCcEEEEEE
Confidence            4579999999999999999999999999999986442    5899999997777 999999999999 74  49999999


Q ss_pred             cccccccc
Q psy8615         120 NTYVLMNV  127 (128)
Q Consensus       120 ~~~~~~~~  127 (128)
                      +++.-.|+
T Consensus       121 Ak~~~l~v  128 (164)
T 1sjr_A          121 SKLTSLNV  128 (164)
T ss_dssp             CSSSSCCC
T ss_pred             ecCCcccc
Confidence            99876554

>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=99.78  E-value=1.7e-19  Score=121.12  Aligned_cols=80  Identities=14%  Similarity=0.294  Sum_probs=74.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      ..++|||+|||.++++++|+++|++||.|.++++..++.+|.++|||||+|.+.+ +|.+|++ +++. ++|+.|+|.|+
T Consensus        86 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~-~a~~A~~-~~~~~~~g~~i~V~~a  163 (167)
T 2cjk_A           86 KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSAD-AVDRVCQ-NKFIDFKDRKIEIKRA  163 (167)
T ss_dssp             HCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHH-HHHHHHH-CSEECSSSSCEEEEEC
T ss_pred             CCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHH-HHHHHHh-CCCEEeCCeEEEEeec
Confidence            3568999999999999999999999999999999999989999999999997776 9999998 8998 99999999999


Q ss_pred             ccc
Q psy8615         121 TYV  123 (128)
Q Consensus       121 ~~~  123 (128)
                      ++.
T Consensus       164 ~pk  166 (167)
T 2cjk_A          164 EPR  166 (167)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            863

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.78  E-value=4.8e-19  Score=124.07  Aligned_cols=76  Identities=11%  Similarity=0.169  Sum_probs=69.9

Q ss_pred             CCCCeEEEcCCC-CCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          41 PEGANLFIYHLP-PEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        41 ~~~~~l~V~nLp-~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      +++++|||+||| +++++++|+++|++||.|.+++++.+     .+|||||+|++.+ +|+.|++.|||. +.|+.|+|.
T Consensus         2 ~~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~-----~~g~afV~f~~~~-~A~~Ai~~lng~~~~g~~l~v~   75 (205)
T 3tyt_A            2 ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGY-AVDRAITHLNNNFMFGQKMNVC   75 (205)
T ss_dssp             CCCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT-----STTCEEEEESSHH-HHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC-----CCCEEEEEECCHH-HHHHHHHHhCCCEECCceEEEE
Confidence            457899999999 89999999999999999999999865     3799999998777 999999999999 999999999


Q ss_pred             eccc
Q psy8615         119 FNTY  122 (128)
Q Consensus       119 ~~~~  122 (128)
                      |++.
T Consensus        76 ~s~~   79 (205)
T 3tyt_A           76 VSKQ   79 (205)
T ss_dssp             ECSC
T ss_pred             EccC
Confidence            9874

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.78  E-value=6.2e-19  Score=123.62  Aligned_cols=77  Identities=26%  Similarity=0.331  Sum_probs=71.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecc
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNT  121 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~  121 (128)
                      .++|||+|||+++++++|+++|++||.|.+++++.|+  +.++|||||+|.+.+ +|.+|++.|||. ++|+.|+|.|++
T Consensus       103 ~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f~~~~-~a~~Ai~~lng~~~~g~~i~V~~a~  179 (213)
T 4f02_A          103 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQE-AAERAIEKMNGMLLNDRKVFVGRFK  179 (213)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESSHH-HHHHHHHHHTTCEETTEECEEEECC
T ss_pred             cccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC--CCCceEEEEEeCCHH-HHHHHHHHhCCCEECCEEEEEEEcC
Confidence            5689999999999999999999999999999999986  458999999997777 999999999999 999999999987


Q ss_pred             c
Q psy8615         122 Y  122 (128)
Q Consensus       122 ~  122 (128)
                      +
T Consensus       180 ~  180 (213)
T 4f02_A          180 S  180 (213)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.78  E-value=5.5e-18  Score=110.25  Aligned_cols=76  Identities=17%  Similarity=0.120  Sum_probs=67.0

Q ss_pred             eEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceE-EEEEEecCHHHHHHHHHHhcCc-CCC--eEEEEEec
Q psy8615          45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCF-GTIIFMRKFFILTIRFDTANDY-LGQ--SFLKPSFN  120 (128)
Q Consensus        45 ~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~-~fv~f~~~~~~a~~Ai~~l~g~-~~~--~~l~V~~~  120 (128)
                      .|||+||++.+++++|+++|++||.|.++.+.. +     .|| |||+|++.+ +|..|++.|||. +.|  +.|+|.|+
T Consensus        27 ~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~-~-----~Gf~aFVef~~~~-~A~~A~~~LnG~~i~g~~~~l~V~~A   99 (124)
T 2e5i_A           27 LLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK-R-----NGIQAMVEFESVL-CAQKAKAALNGADIYAGCCTLKIEYA   99 (124)
T ss_dssp             EEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEE-S-----SSEEEEEEESSHH-HHHHHHHHHTTCCCBTTBSEEEEECC
T ss_pred             EEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEe-C-----CCCEEEEEECCHH-HHHHHHHHhCCCEecCCCeEEEEEEe
Confidence            578999999999999999999999999999864 2     276 999997777 999999999999 765  69999999


Q ss_pred             ccccccc
Q psy8615         121 TYVLMNV  127 (128)
Q Consensus       121 ~~~~~~~  127 (128)
                      ++.-.++
T Consensus       100 k~~~l~v  106 (124)
T 2e5i_A          100 RPTRLNV  106 (124)
T ss_dssp             SCSCCCC
T ss_pred             cCCccee
Confidence            9887654

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.78  E-value=1.4e-18  Score=119.24  Aligned_cols=81  Identities=9%  Similarity=0.108  Sum_probs=73.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      ...++|||+|||+++++++|+++|++||.|.+++++.++.+|.++|||||+|.+.+ +|.+|++. ++. ++|+.|+|.|
T Consensus       102 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~-~A~~A~~~-~~~~~~G~~i~v~~  179 (196)
T 1l3k_A          102 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD-SVDKIVIQ-KYHTVNGHNCEVRK  179 (196)
T ss_dssp             -CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHH-HHHHHHHC-SCCEETTEECEEEE
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHH-HHHHHHHh-CCcEECCEEEEEEe
Confidence            34579999999999999999999999999999999999989999999999997777 99999987 677 9999999999


Q ss_pred             cccc
Q psy8615         120 NTYV  123 (128)
Q Consensus       120 ~~~~  123 (128)
                      +.+.
T Consensus       180 a~~k  183 (196)
T 1l3k_A          180 ALSK  183 (196)
T ss_dssp             CC--
T ss_pred             cCCh
Confidence            8764

>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=99.77  E-value=2.4e-19  Score=110.51  Aligned_cols=75  Identities=13%  Similarity=0.201  Sum_probs=66.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCc-eEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcC-c-CCCeEEEE
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGT-VLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTAND-Y-LGQSFLKP  117 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~-i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g-~-~~~~~l~V  117 (128)
                      ...++|||+|||+++++++|+++|++||. |..+.+       .++|||||+|.+.+ +|.+|++.||+ . ++|+.|+|
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~-------~~~g~afV~f~~~~-~A~~A~~~l~g~~~~~g~~l~v   77 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL-------LKSGYAFVDYPDQN-WAIRAIETLSGKVELHGKIMEV   77 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEE-------EETTEEEECCSCHH-HHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEE-------cCCCEEEEEECCHH-HHHHHHHHccCCeeECCEEEEE
Confidence            34689999999999999999999999999 555554       24789999997777 99999999999 8 99999999


Q ss_pred             Eecccc
Q psy8615         118 SFNTYV  123 (128)
Q Consensus       118 ~~~~~~  123 (128)
                      .|+++.
T Consensus        78 ~~a~~~   83 (93)
T 2cqh_A           78 DYSVSK   83 (93)
T ss_dssp             EECCCC
T ss_pred             EEccCc
Confidence            999864

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=1e-18  Score=108.01  Aligned_cols=71  Identities=18%  Similarity=0.224  Sum_probs=62.6

Q ss_pred             CCCeEEEcCCCCCCCHHH----HHhhhcCC-CceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEE
Q psy8615          42 EGANLFIYHLPPEFSDAD----LASMFGPF-GTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFL  115 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~----l~~~f~~~-G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l  115 (128)
                      ..|.|||+|||+++++++    |+++|++| |+|.++       ||   |+|||+|.+.+ +|++|++.|||+ +.||+|
T Consensus         8 ~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~e-sA~~A~~~l~G~~l~gr~i   76 (96)
T 2diu_A            8 CHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQD-SAERAQKRMENEDVFGNRI   76 (96)
T ss_dssp             SSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHH-HHHHHHHHHTTCCSSSSCC
T ss_pred             cceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHH-HHHHHHHHhcCCccCCceE
Confidence            345599999999999988    55899999 599987       34   99999997776 999999999999 999999


Q ss_pred             EEEecccc
Q psy8615         116 KPSFNTYV  123 (128)
Q Consensus       116 ~V~~~~~~  123 (128)
                      +|+|++..
T Consensus        77 ~v~~A~~~   84 (96)
T 2diu_A           77 IVSFTPKN   84 (96)
T ss_dssp             EEESSCCS
T ss_pred             EEEecCCC
Confidence            99999864

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.77  E-value=1e-18  Score=107.96  Aligned_cols=74  Identities=20%  Similarity=0.235  Sum_probs=67.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecc
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNT  121 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~  121 (128)
                      .++|||+|||+++++++|+++|++||.|.+|  +.++.+|+   ||||+|.+.+ +|..|++ ||+. ++|+.|+|.+++
T Consensus         8 ~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~-~a~~ai~-l~g~~~~g~~l~V~~a~   80 (94)
T 2e5g_A            8 LRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVG-AREAVLS-QSQHSLGGHRLRVRPRE   80 (94)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHH-HHHHHHT-CSCCEETTEECCCBCSC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHH-HHHHHHh-cCCeEECCEEEEEEECC
Confidence            5699999999999999999999999999987  77777676   9999997766 9999999 9999 999999999886


Q ss_pred             cc
Q psy8615         122 YV  123 (128)
Q Consensus       122 ~~  123 (128)
                      +.
T Consensus        81 ~~   82 (94)
T 2e5g_A           81 QK   82 (94)
T ss_dssp             CS
T ss_pred             cC
Confidence            53

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.77  E-value=8.4e-19  Score=122.06  Aligned_cols=81  Identities=16%  Similarity=0.254  Sum_probs=72.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      ..++|||+|||.++++++|+++|++||.|.+++++.++.+|+++|||||+|.+.+ +|.+|++.||+. ++|+.|+|.+.
T Consensus        27 ~~~~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           27 IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPE-AAQLALEQMNSVMLGGRNIKVGRP  105 (216)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHH-HHHHHHHHHSSCCCC-CCCEEECC
T ss_pred             cCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHH-HHHHHHHHccCCeeCCeeEEEecC
Confidence            3679999999999999999999999999999999999989999999999997776 999999999999 99999999887


Q ss_pred             ccc
Q psy8615         121 TYV  123 (128)
Q Consensus       121 ~~~  123 (128)
                      +..
T Consensus       106 ~~~  108 (216)
T 2qfj_A          106 SNI  108 (216)
T ss_dssp             SCC
T ss_pred             CCc
Confidence            643

>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=99.77  E-value=1.9e-18  Score=115.50  Aligned_cols=79  Identities=19%  Similarity=0.401  Sum_probs=72.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCe--EEEE
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQS--FLKP  117 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~--~l~V  117 (128)
                      ...++|||+|||.++++++|+++|++||.|.++++..++.+|.++|||||+|.+.+ +|.+|++.|||. ++|+  +|+|
T Consensus        86 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~-~A~~A~~~l~g~~~~g~~~~i~v  164 (167)
T 1fxl_A           86 IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRI-EAEEAIKGLNGQKPSGATEPITV  164 (167)
T ss_dssp             GTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHH-HHHHHHHHHTTCCCTTCSSCCEE
T ss_pred             CCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHH-HHHHHHHHhcCCccCCCccceEE
Confidence            44678999999999999999999999999999999999988999999999997776 999999999999 8885  4888


Q ss_pred             Eec
Q psy8615         118 SFN  120 (128)
Q Consensus       118 ~~~  120 (128)
                      +|+
T Consensus       165 ~~A  167 (167)
T 1fxl_A          165 KFA  167 (167)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            885

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus}

Probab=99.77  E-value=1.5e-18  Score=106.60  Aligned_cols=75  Identities=12%  Similarity=0.184  Sum_probs=60.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc---CCCeEE
Q psy8615          39 TGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY---LGQSFL  115 (128)
Q Consensus        39 ~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~---~~~~~l  115 (128)
                      .....++|||+|||++++|++|+++|++||.|.+++++.+     ++|||||+|++.+ +|.    .+++.   +.|+.|
T Consensus         7 ~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~-~A~----~~~~~~~~~~g~~v   76 (89)
T 3d2w_A            7 HHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDK-VAQ----SLCGEDLIIKGISV   76 (89)
T ss_dssp             ----CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHH-HHH----HHTTCEEEETTEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHH-HHH----HHcCCCcccCCEEE
Confidence            3455889999999999999999999999999999998864     6899999997766 766    35664   679999


Q ss_pred             EEEecccc
Q psy8615         116 KPSFNTYV  123 (128)
Q Consensus       116 ~V~~~~~~  123 (128)
                      +|.++++.
T Consensus        77 ~v~~a~~k   84 (89)
T 3d2w_A           77 HISNAEPK   84 (89)
T ss_dssp             EEEECC--
T ss_pred             EEEEcCCC
Confidence            99998764

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=4.4e-19  Score=113.81  Aligned_cols=77  Identities=16%  Similarity=0.025  Sum_probs=67.1

Q ss_pred             CCCCeEEE--cCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-C-----CC
Q psy8615          41 PEGANLFI--YHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-L-----GQ  112 (128)
Q Consensus        41 ~~~~~l~V--~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~-----~~  112 (128)
                      ....+|||  |||++++++++|+++|++||.|.++.++.      .+|||||+|.+.+ +|++|++.|||. +     ++
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~------~rgfaFV~f~~~~-~A~~Ai~~lnG~~~~~~lg~g   95 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTE-ESKRAYVTLNGKEVVDDLGQK   95 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT------TCSCEEEEESSHH-HHHHHHHHTTTCEEECTTSCE
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHH-HHHHHHHHhCCCEEccccCCC
Confidence            34678999  77999999999999999999999987653      2789999997777 999999999998 7     68


Q ss_pred             eEEEEEeccccc
Q psy8615         113 SFLKPSFNTYVL  124 (128)
Q Consensus       113 ~~l~V~~~~~~~  124 (128)
                      ++|.|.|.+.+.
T Consensus        96 ~~l~v~~a~~~p  107 (114)
T 2cq2_A           96 ITLYLNFVEKVQ  107 (114)
T ss_dssp             EECEEEEESCCC
T ss_pred             cEEEEEecccCc
Confidence            999999987653

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.76  E-value=1.2e-18  Score=116.38  Aligned_cols=78  Identities=18%  Similarity=0.285  Sum_probs=72.0

Q ss_pred             CeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEeccc
Q psy8615          44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNTY  122 (128)
Q Consensus        44 ~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~~  122 (128)
                      ++|||+|||.++++++|+++|++||.|.++++..++. |+++|||||+|.+.+ +|..|++.+||. ++|+.|+|.|.++
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~-~~~~g~afV~f~~~~-~a~~A~~~l~~~~~~g~~i~v~~~~~   78 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKN-NKNVNYAFVEYHQSH-DANIALQTLNGKQIENNIVKINWAFQ   78 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC--CCEEEEEEEESSHH-HHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCC-CCCCCEEEEEeCCHH-HHHHHHHHcCCCccCCCeeEEEEcCC
Confidence            4799999999999999999999999999999999986 889999999997777 999999999999 9999999999865


Q ss_pred             c
Q psy8615         123 V  123 (128)
Q Consensus       123 ~  123 (128)
                      .
T Consensus        79 ~   79 (166)
T 3md3_A           79 S   79 (166)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=1e-18  Score=111.74  Aligned_cols=75  Identities=13%  Similarity=0.279  Sum_probs=63.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCC---CCcceEEEEEEecCHHHHHHHHHHhcCcCCCeEEEE
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQN---NRSKCFGTIIFMRKFFILTIRFDTANDYLGQSFLKP  117 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~t---g~~~g~~fv~f~~~~~~a~~Ai~~l~g~~~~~~l~V  117 (128)
                      ...++|||+|||+++++++|+++|++||.|. +.++.++.+   |+++|||||+|++.+ +|++|++.|++ +.|+.|.+
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~-~a~~Ai~~~~~-~~G~~~~~   82 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEES-SVQALIDACLE-EDGKLYLC   82 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHH-HHHHHHHHSEE-ETTEEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHH-HHHHHHHhhhh-cCCcEEEe
Confidence            3468999999999999999999999999999 888888877   799999999997777 99999999833 44555544


Q ss_pred             E
Q psy8615         118 S  118 (128)
Q Consensus       118 ~  118 (128)
                      .
T Consensus        83 ~   83 (114)
T 2dnl_A           83 V   83 (114)
T ss_dssp             E
T ss_pred             c
Confidence            4

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

Probab=99.76  E-value=3e-18  Score=115.49  Aligned_cols=81  Identities=17%  Similarity=0.292  Sum_probs=72.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCC--CcceEEEEEEecCHHHHHHHHHHhcCc-CC---CeEE
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNN--RSKCFGTIIFMRKFFILTIRFDTANDY-LG---QSFL  115 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg--~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~---~~~l  115 (128)
                      +.++|||+|||+++++++|+++|++||.|.+++++.++.+|  +++|||||+|.+.+ +|..|++.||+. +.   ++.+
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~-~A~~A~~~l~~~~~~~~~~~~~   80 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRK-AALEAQNALHNMKVLPGMHHPI   80 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHH-HHHHHHHHHTTTCCCTTCSSCC
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHH-HHHHHHHHhcCcEEccCCccce
Confidence            46899999999999999999999999999999999999877  89999999997777 999999999997 43   5778


Q ss_pred             EEEecccc
Q psy8615         116 KPSFNTYV  123 (128)
Q Consensus       116 ~V~~~~~~  123 (128)
                      .+.+.+..
T Consensus        81 ~~~~~~~~   88 (175)
T 3nmr_A           81 QMKPADSE   88 (175)
T ss_dssp             EEEECGGG
T ss_pred             EEcccccc
Confidence            88887654

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

Probab=99.75  E-value=3.2e-18  Score=115.30  Aligned_cols=78  Identities=17%  Similarity=0.284  Sum_probs=71.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CC---CeEEE
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LG---QSFLK  116 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~---~~~l~  116 (128)
                      ...++|||+|||.++++++|+++|++||.|.++++..++. |+++|||||+|.+.+ +|.+|++.|||. +.   +++|+
T Consensus        93 ~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~-g~~~g~afV~f~~~~-~A~~A~~~l~g~~~~~g~~~~l~  170 (175)
T 3nmr_A           93 VEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPD-GLSRGCAFVTFTTRA-MAQTAIKAMHQAQTMEGCSSPMV  170 (175)
T ss_dssp             GGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSHH-HHHHHHHHHTTSCCCTTCSSCCE
T ss_pred             CCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCC-CCEEEEEEEEECCHH-HHHHHHHHhcCCcccCCCCCCeE
Confidence            3567999999999999999999999999999999999975 999999999997777 999999999997 43   49999


Q ss_pred             EEec
Q psy8615         117 PSFN  120 (128)
Q Consensus       117 V~~~  120 (128)
                      |+|+
T Consensus       171 V~~a  174 (175)
T 3nmr_A          171 VKFA  174 (175)
T ss_dssp             EEEC
T ss_pred             EEec
Confidence            9996

>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=99.75  E-value=4.7e-18  Score=118.07  Aligned_cols=78  Identities=14%  Similarity=0.084  Sum_probs=71.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCcCCCeEEEEEeccc
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDYLGQSFLKPSFNTY  122 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~~~~~~l~V~~~~~  122 (128)
                      .++|||+|||+++++++|+++|++||.|.++++..+.. |+++|||||+|++.+ +|..|++.++..++|+.|+|.|++.
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 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIE-SAKKFVETPGQKYKETDLLILFKDD  186 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTT-CCEEEEEEEEESSHH-HHHHHHHCTTCEETTEECEEEETTT
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCC-CCcccEEEEEECCHH-HHHHHHHhCCCeECCEEEEEEEhHH
Confidence            57999999999999999999999999999999999875 999999999997777 9999998776559999999999875

>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=99.75  E-value=1.9e-18  Score=115.87  Aligned_cols=79  Identities=25%  Similarity=0.370  Sum_probs=72.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      +.++|||+|||+++++++|+++|++||.|.+++++.++.+|+++|||||+|.+.+ +|..|++.  +. ++|+.|.|.+.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~-~a~~A~~~--~~~~~g~~i~v~~~   78 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPS-SVDEVVKT--QHILDGKVIDPKRA   78 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTH-HHHHHHHS--CCEETTEECCCEEC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHH-HHHHHHhc--ccccCCeEcccccc
Confidence            3679999999999999999999999999999999999999999999999998887 99999985  45 89999999887


Q ss_pred             ccc
Q psy8615         121 TYV  123 (128)
Q Consensus       121 ~~~  123 (128)
                      .+.
T Consensus        79 ~~~   81 (167)
T 2cjk_A           79 IPR   81 (167)
T ss_dssp             CCH
T ss_pred             cch
Confidence            653

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.75  E-value=7.8e-18  Score=121.95  Aligned_cols=81  Identities=14%  Similarity=0.228  Sum_probs=72.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHH----hhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCe
Q psy8615          39 TGPEGANLFIYHLPPEFSDADLA----SMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQS  113 (128)
Q Consensus        39 ~~~~~~~l~V~nLp~~~~e~~l~----~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~  113 (128)
                      +....++|||+|||+++++++|+    ++|++||.|.+|++..   +|+++|||||+|.+.+ +|.+|++.|||. +.|+
T Consensus         5 ~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~-~a~~A~~~l~g~~~~g~   80 (282)
T 3pgw_A            5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVS-SATNALRSMQGFPFYDK   80 (282)
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHH-HHHHHHHHhcCCeeCCc
Confidence            34557899999999999999976    8999999999998775   5889999999997777 999999999999 9999


Q ss_pred             EEEEEecccc
Q psy8615         114 FLKPSFNTYV  123 (128)
Q Consensus       114 ~l~V~~~~~~  123 (128)
                      .|+|.|.+..
T Consensus        81 ~l~v~~a~~~   90 (282)
T 3pgw_A           81 PMRIQYAKTD   90 (282)
T ss_pred             EEEEEEeccC
Confidence            9999998764

>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=99.75  E-value=1.5e-18  Score=111.29  Aligned_cols=73  Identities=22%  Similarity=0.246  Sum_probs=64.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeE-----E
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSF-----L  115 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~-----l  115 (128)
                      ..++|||+|||+++++++|+++|++||.|.+++++.+       |||||+|.+.+ +|+.||+.||+. ++|+.     +
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~-~a~~Ai~~l~g~~~~gr~~~~~~i   86 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKE-DMTYAVRKLDNTKFRSHEGETAYI   86 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHH-HHHHHHHHHTTCBCCCTTSCCCBC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHH-HHHHHHHHhCCCEECCcEeeeEEE
Confidence            3689999999999999999999999999999998765       89999997777 999999999999 99988     6


Q ss_pred             EEEeccc
Q psy8615         116 KPSFNTY  122 (128)
Q Consensus       116 ~V~~~~~  122 (128)
                      +|...++
T Consensus        87 ~v~~~~~   93 (115)
T 3beg_B           87 RVKVDGP   93 (115)
T ss_dssp             EEEECC-
T ss_pred             EeccCCC
Confidence            7766654

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.74  E-value=8.4e-18  Score=113.74  Aligned_cols=78  Identities=12%  Similarity=0.096  Sum_probs=70.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ....++|||+|||.++++++|+++|++||.|..+     ..+|.++|||||+|.+.+ +|.+|++.|||. ++|+.|+|+
T Consensus        96 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~-~A~~A~~~l~g~~~~g~~i~v~  169 (175)
T 1fje_B           96 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEA-DAEKNLEEKQGAEIDGRSVSLY  169 (175)
T ss_dssp             TGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECSSHH-HHHHHHHHHTEEEETTEEEEEE
T ss_pred             cccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEECCHH-HHHHHHHHhCCCEECCeEEEEE
Confidence            3456799999999999999999999999988765     556999999999997777 999999999999 999999999


Q ss_pred             ecccc
Q psy8615         119 FNTYV  123 (128)
Q Consensus       119 ~~~~~  123 (128)
                      |+++.
T Consensus       170 ~a~~k  174 (175)
T 1fje_B          170 YTGEK  174 (175)
T ss_dssp             ECSSC
T ss_pred             ecCCC
Confidence            99864

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.74  E-value=1.1e-17  Score=105.79  Aligned_cols=80  Identities=13%  Similarity=0.070  Sum_probs=69.9

Q ss_pred             CCCeEEEcCCCC-----CCCHHHHHhhhcCCCceEEEEEEecCCC-CCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeE
Q psy8615          42 EGANLFIYHLPP-----EFSDADLASMFGPFGTVLSAKVFIDKQN-NRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSF  114 (128)
Q Consensus        42 ~~~~l~V~nLp~-----~~~e~~l~~~f~~~G~i~~~~~~~~~~t-g~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~  114 (128)
                      ..+.|++.|+..     +-.+++|++.|++||.|.++.++.++.+ ++++||+||+|.+.+ +|.+|++.|||. ++||.
T Consensus         7 ~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~-~A~~Ai~~lnG~~~~Gr~   85 (105)
T 2pe8_A            7 PTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVE-SAIKAVVDLNGRYFGGRV   85 (105)
T ss_dssp             CCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHH-HHHHHHHHHTTCEETTEE
T ss_pred             CCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHH-HHHHHHHHHCCCEECCcE
Confidence            456899999952     2378999999999999999999998754 689999999997777 999999999999 99999


Q ss_pred             EEEEeccc
Q psy8615         115 LKPSFNTY  122 (128)
Q Consensus       115 l~V~~~~~  122 (128)
                      |+|.|.+.
T Consensus        86 i~v~~a~~   93 (105)
T 2pe8_A           86 VKACFYNL   93 (105)
T ss_dssp             CEEEECCH
T ss_pred             EEEEEcCH
Confidence            99999865

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.73  E-value=2.7e-17  Score=119.13  Aligned_cols=77  Identities=18%  Similarity=0.285  Sum_probs=69.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CC-CeEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LG-QSFLKP  117 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~-~~~l~V  117 (128)
                      ....++|||+|||.++++++|+++|++||.|.+++++.++     +|||||+|.+.+ +|.+|++.|||+ ++ |+.|+|
T Consensus       204 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-----~g~afV~f~~~~-~A~~A~~~l~g~~~~~g~~l~v  277 (282)
T 3pgw_A          204 NPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEV-QAGAARDALQGFKITQNNAMKI  277 (282)
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-----CcEEEEEeCCHH-HHHHHHHHcCCcEeCCCCEEEE
Confidence            3456889999999999999999999999999999998654     689999997777 999999999999 88 999999


Q ss_pred             Eeccc
Q psy8615         118 SFNTY  122 (128)
Q Consensus       118 ~~~~~  122 (128)
                      +|++.
T Consensus       278 ~~akk  282 (282)
T 3pgw_A          278 SFAKK  282 (282)
T ss_pred             EEecC
Confidence            99873

>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=99.73  E-value=1.6e-17  Score=120.41  Aligned_cols=82  Identities=20%  Similarity=0.284  Sum_probs=77.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      ..++|||+|||+++++++|+++|++||.|.+++++.++.+|.++|||||+|.+.+ +|..|++.|+|. ++|+.|+|.|.
T Consensus        94 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~-~a~~A~~~l~~~~~~g~~i~v~~a  172 (284)
T 3smz_A           94 TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKD-SAARAKSDLLGKPLGPRTLYVHWT  172 (284)
T ss_dssp             CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHH-HHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHH-HHHHHHHHhCCCEeCCcEEEEEEC
Confidence            4679999999999999999999999999999999999999999999999997777 999999999999 99999999999


Q ss_pred             cccc
Q psy8615         121 TYVL  124 (128)
Q Consensus       121 ~~~~  124 (128)
                      ++.-
T Consensus       173 ~~~~  176 (284)
T 3smz_A          173 DAGQ  176 (284)
T ss_dssp             CGGG
T ss_pred             CCCC
Confidence            8754

>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=99.73  E-value=1.8e-17  Score=120.21  Aligned_cols=82  Identities=18%  Similarity=0.202  Sum_probs=75.7

Q ss_pred             CCCCCeEEEcCCCCCC-CHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEE
Q psy8615          40 GPEGANLFIYHLPPEF-SDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKP  117 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~-~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V  117 (128)
                      ....++|||+|||+++ ++++|+++|++||.|.++++..++ +|+++|||||+|.+.+ +|.+|++.|||. ++|+.|+|
T Consensus       181 ~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~-~A~~A~~~l~g~~~~g~~l~v  258 (284)
T 3smz_A          181 LLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAE-MAEEAQQQADGLSLGGSHLRV  258 (284)
T ss_dssp             TTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECS-SCCEEEEEEEECSSHH-HHHHHHHHHTTCEETTEECEE
T ss_pred             cCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECC-CCCcccEEEEEeCCHH-HHHHHHHHhCCCccCCeEEEE
Confidence            3557899999999995 999999999999999999999987 5999999999997777 999999999999 99999999


Q ss_pred             Eecccc
Q psy8615         118 SFNTYV  123 (128)
Q Consensus       118 ~~~~~~  123 (128)
                      +|.++.
T Consensus       259 ~~a~~~  264 (284)
T 3smz_A          259 SFCAPG  264 (284)
T ss_dssp             EECCSS
T ss_pred             EEecCC
Confidence            999864

>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=99.72  E-value=8.5e-18  Score=122.30  Aligned_cols=82  Identities=20%  Similarity=0.295  Sum_probs=74.3

Q ss_pred             CCCCCeEEEcCCCCC-CCHHHHHhhhcCCCceEEEEEEecCC-CCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEE
Q psy8615          40 GPEGANLFIYHLPPE-FSDADLASMFGPFGTVLSAKVFIDKQ-NNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLK  116 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~-~~e~~l~~~f~~~G~i~~~~~~~~~~-tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~  116 (128)
                      ....++|||+|||++ +++++|+++|++||.|.+++++.++. ||.++|||||+|.+.+ +|.+|+ .|||. ++|+.|+
T Consensus       207 ~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~-~A~~A~-~l~g~~~~g~~i~  284 (292)
T 2ghp_A          207 TLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKD-SAERAL-QMNRSLLGNREIS  284 (292)
T ss_dssp             CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHH-HHHHHG-GGTTEEETTEEEE
T ss_pred             CCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHH-HHHHHH-HhcCCEECCcEEE
Confidence            445789999999999 99999999999999999999999887 6999999999997777 999999 99999 9999999


Q ss_pred             EEecccc
Q psy8615         117 PSFNTYV  123 (128)
Q Consensus       117 V~~~~~~  123 (128)
                      |+|+++.
T Consensus       285 V~~a~~k  291 (292)
T 2ghp_A          285 VSLADKK  291 (292)
T ss_dssp             EEECCCC
T ss_pred             EEEecCC
Confidence            9999864

>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=99.72  E-value=4.1e-18  Score=104.00  Aligned_cols=73  Identities=12%  Similarity=0.181  Sum_probs=62.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc---CCCeEEEE
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY---LGQSFLKP  117 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~---~~~~~l~V  117 (128)
                      ...++|||+|||+++++++|+++|++||.|.+++++.+     ++|||||+|++.+ +|++    +++.   +.++.|+|
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~-~a~~----~~~~~~~~~g~~l~v   72 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQ-IAQS----LCGEDLIIKGISVHI   72 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHH-HHHH----TTTCEEEETTEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHH-HHHH----HhcCCceeCCEEEEE
Confidence            34689999999999999999999999999999998754     6899999997766 7764    3443   68999999


Q ss_pred             Eecccc
Q psy8615         118 SFNTYV  123 (128)
Q Consensus       118 ~~~~~~  123 (128)
                      .++++.
T Consensus        73 ~~a~~~   78 (88)
T 1wf0_A           73 SNAEPK   78 (88)
T ss_dssp             ECCCCC
T ss_pred             EecCCC
Confidence            998865

>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=99.71  E-value=8.1e-18  Score=102.17  Aligned_cols=69  Identities=19%  Similarity=0.264  Sum_probs=62.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCC----C-------ceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPF----G-------TVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-  109 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~----G-------~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-  109 (128)
                      ..++|||+|||+++++++|+++|++|    |       .|.++++..+      +|||||+|.+.+ +|.+|+ .||+. 
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~-~a~~A~-~l~g~~   76 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVD-ETTQAM-AFDGII   76 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHH-HHHHHG-GGTTCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHH-HHHHHH-hcCCCE
Confidence            46799999999999999999999999    8       8999887644      789999997777 999999 99999 


Q ss_pred             CCCeEEEEE
Q psy8615         110 LGQSFLKPS  118 (128)
Q Consensus       110 ~~~~~l~V~  118 (128)
                      ++|+.|+|+
T Consensus        77 ~~g~~l~V~   85 (87)
T 2hzc_A           77 FQGQSLKIR   85 (87)
T ss_dssp             ETTEECEEE
T ss_pred             ECCeEEEEe
Confidence            999999987

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.71  E-value=1.5e-17  Score=117.71  Aligned_cols=80  Identities=19%  Similarity=0.294  Sum_probs=72.4

Q ss_pred             CCCCCCCeEEEcCCCC-CCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEE
Q psy8615          38 LTGPEGANLFIYHLPP-EFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFL  115 (128)
Q Consensus        38 ~~~~~~~~l~V~nLp~-~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l  115 (128)
                      ...+..++|||+|||+ ++++++|+++|++||.|.++++..++     +|||||+|.+.+ +|.+|++.||+. ++|+.|
T Consensus        29 ~~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~-~A~~Ai~~l~g~~~~g~~l  102 (229)
T 2adc_A           29 LAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGN-QAQLAMSHLNGHKLHGKPI  102 (229)
T ss_dssp             GGCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHH-HHHHHHHHHTTCBCSSSBC
T ss_pred             CCCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHH-HHHHHHHHhCCCeECCeEE
Confidence            3345678999999999 99999999999999999999998875     789999997777 999999999999 999999


Q ss_pred             EEEecccc
Q psy8615         116 KPSFNTYV  123 (128)
Q Consensus       116 ~V~~~~~~  123 (128)
                      +|.|.++.
T Consensus       103 ~v~~a~~~  110 (229)
T 2adc_A          103 RITLSKHQ  110 (229)
T ss_dssp             EEECCSCC
T ss_pred             EEEEecCc
Confidence            99998754

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.69  E-value=4.2e-17  Score=116.71  Aligned_cols=78  Identities=12%  Similarity=0.118  Sum_probs=68.4

Q ss_pred             CCCCCeEEEcCCCCCC---------CHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-
Q psy8615          40 GPEGANLFIYHLPPEF---------SDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-  109 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~---------~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-  109 (128)
                      ....++|||+||+.++         +|++|+.+|++||.|.+|+++.      ++|||||+|.+.+ +|+.|++.|+|. 
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~------~kG~AFV~F~~~~-~Ae~A~~am~g~~  203 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE------SKNCGFVKFKYQA-NAEFAKEAMSNQT  203 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG------GGTEEEEEESSHH-HHHHHHHHHTTCC
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC------CCCEEEEEeCCHH-HHHHHHHHhCCCE
Confidence            4457899999999998         7999999999999999999884      3889999997776 999999999999 


Q ss_pred             C------------CCeEEEEEeccccc
Q psy8615         110 L------------GQSFLKPSFNTYVL  124 (128)
Q Consensus       110 ~------------~~~~l~V~~~~~~~  124 (128)
                      +            .|+.|.|.|++...
T Consensus       204 l~~~~~~e~~~~~~gr~L~V~wA~~~p  230 (240)
T 3u1l_A          204 LLLPSDKEWDDRREGTGLLVKWANEDP  230 (240)
T ss_dssp             CCCTTSTTGGGGGGSCCCEEEECC---
T ss_pred             EeccccccccccCCCCEEEEEEccCCC
Confidence            8            89999999998654

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.68  E-value=3.6e-17  Score=112.83  Aligned_cols=76  Identities=17%  Similarity=0.259  Sum_probs=70.1

Q ss_pred             CCCeEEEcCCCC-CCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          42 EGANLFIYHLPP-EFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        42 ~~~~l~V~nLp~-~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      ..++|||+|||+ ++++++|+++|++||.|.+++++.++     +|||||+|.+.+ +|..|++.|||. ++|+.|+|.|
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~-~a~~A~~~l~~~~~~g~~l~v~~   75 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGN-QAQLAMSHLNGHKLHGKPIRITL   75 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTH-HHHHHHHHHTTCCCSSCCCEEEE
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHH-HHHHHHHHhCCCeecCeEEEEEE
Confidence            367999999999 99999999999999999999988775     789999998887 999999999999 9999999999


Q ss_pred             cccc
Q psy8615         120 NTYV  123 (128)
Q Consensus       120 ~~~~  123 (128)
                      .++.
T Consensus        76 a~~~   79 (198)
T 1qm9_A           76 SKHQ   79 (198)
T ss_dssp             CCCC
T ss_pred             ecCC
Confidence            8754

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.68  E-value=5.5e-18  Score=114.64  Aligned_cols=81  Identities=19%  Similarity=0.113  Sum_probs=70.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEE
Q psy8615          39 TGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKP  117 (128)
Q Consensus        39 ~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V  117 (128)
                      .....++|||+|||+++++++|+++|++||.+.. .++.+..+|+++|||||+|.+.+ +|.+|+ .|||. ++|+.|+|
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~-~a~~A~-~l~g~~~~g~~l~v   85 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAE-DLEKAL-ELTGLKVFGNEIKL   85 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHH-HHHHHH-HGGGEEETTEEEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHH-HHHHHH-hcCCCEeCCeEEEE
Confidence            3445789999999999999999999999998766 34555567999999999997777 999999 59999 99999999


Q ss_pred             Eeccc
Q psy8615         118 SFNTY  122 (128)
Q Consensus       118 ~~~~~  122 (128)
                      .+.++
T Consensus        86 ~~~~~   90 (175)
T 1fje_B           86 EKPKG   90 (175)
T ss_dssp             ECCCC
T ss_pred             ecCCC
Confidence            99875

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.68  E-value=9.2e-17  Score=110.77  Aligned_cols=78  Identities=24%  Similarity=0.359  Sum_probs=70.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCC-ceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CC-CeEEEE
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFG-TVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LG-QSFLKP  117 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G-~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~-~~~l~V  117 (128)
                      +..++|||+|||.++++++|+++|++|| .|.++++..+.     +|+|||+|.+.+ +|.+|++.|||. ++ |+.|+|
T Consensus       118 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~-----~g~afV~f~~~~-~A~~A~~~l~g~~~~~g~~l~v  191 (198)
T 1qm9_A          118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD-----RKMALIQMGSVE-EAVQALIDLHNHDLGENHHLRV  191 (198)
T ss_dssp             CCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTT-----SSCEEEECSSHH-HHHHHHHHHTSSCCSSCCSCCE
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCC-----CcEEEEEeCCHH-HHHHHHHHhcCCccCCCCeEEE
Confidence            4478999999999999999999999999 99999886542     789999997777 999999999999 88 999999


Q ss_pred             Eeccccc
Q psy8615         118 SFNTYVL  124 (128)
Q Consensus       118 ~~~~~~~  124 (128)
                      +|+++.+
T Consensus       192 ~~a~~~i  198 (198)
T 1qm9_A          192 SFSKSTI  198 (198)
T ss_dssp             EEECCCC
T ss_pred             EeecccC
Confidence            9999864

>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=99.67  E-value=1.3e-16  Score=112.91  Aligned_cols=78  Identities=24%  Similarity=0.359  Sum_probs=70.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCC-ceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CC-CeEEEE
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFG-TVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LG-QSFLKP  117 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G-~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~-~~~l~V  117 (128)
                      +..++|||+|||.++++++|+++|++|| .|.++++..+     .+|||||+|.+.+ +|.+|++.|||. ++ |+.|+|
T Consensus       149 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~-----~~g~afV~f~~~~-~A~~Ai~~l~g~~~~~g~~l~v  222 (229)
T 2adc_A          149 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVE-EAVQALIDLHNHDLGENHHLRV  222 (229)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS-----STTCEEEEESSHH-HHHHHHHHHTTCBSSSSCBCEE
T ss_pred             CCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC-----CCcEEEEEECCHH-HHHHHHHHHCCCccCCCCeEEE
Confidence            3468999999999999999999999999 9999988643     3789999997777 999999999999 88 999999


Q ss_pred             Eeccccc
Q psy8615         118 SFNTYVL  124 (128)
Q Consensus       118 ~~~~~~~  124 (128)
                      +|+++.+
T Consensus       223 ~~a~~~i  229 (229)
T 2adc_A          223 SFSKSTI  229 (229)
T ss_dssp             EECSSCC
T ss_pred             EEecCCC
Confidence            9999864

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.66  E-value=2.5e-16  Score=113.43  Aligned_cols=76  Identities=20%  Similarity=0.308  Sum_probs=68.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ....++|||+|||+++++++|+++|++||.|.++++..      ++|||||+|.+.+ +|..|+..+||. ++|+.|+|.
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~------~kg~afV~f~~~~-~A~~A~~~l~g~~i~g~~l~v~   91 (261)
T 3sde_A           19 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINR------DRGFGFIRLESRT-LAEIAKAELDGTILKSRPLRIR   91 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEET------TTTEEEEECSSHH-HHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCcEEEEEECCHH-HHHHHHHHcCCcEECCceeEee
Confidence            34568999999999999999999999999999998853      3789999997777 999999999999 999999999


Q ss_pred             eccc
Q psy8615         119 FNTY  122 (128)
Q Consensus       119 ~~~~  122 (128)
                      |.++
T Consensus        92 ~a~~   95 (261)
T 3sde_A           92 FATH   95 (261)
T ss_dssp             ECCC
T ss_pred             eccc
Confidence            9875

>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=7.5e-16  Score=98.08  Aligned_cols=78  Identities=12%  Similarity=0.110  Sum_probs=65.7

Q ss_pred             CCCCeEEEcCCCCCCC-----------HHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc
Q psy8615          41 PEGANLFIYHLPPEFS-----------DADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY  109 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~-----------e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~  109 (128)
                      ...+.|+|.||.....           +++|+++|++||.|.++.+ .++   .++|||||+|.+.+ +|.+|++.|||.
T Consensus        13 ~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~-~A~~Ai~~lng~   87 (112)
T 2dit_A           13 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPE-EADYCIQTLDGR   87 (112)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHH-HHHHHHHHSTTC
T ss_pred             CCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHH-HHHHHHHHcCCC
Confidence            4467899999944332           5899999999999999955 554   37999999997777 999999999999


Q ss_pred             -CCCeEEEEEecccc
Q psy8615         110 -LGQSFLKPSFNTYV  123 (128)
Q Consensus       110 -~~~~~l~V~~~~~~  123 (128)
                       ++|+.|+|.|.++.
T Consensus        88 ~~~gr~l~v~~a~~~  102 (112)
T 2dit_A           88 WFGGRQITAQAWDGT  102 (112)
T ss_dssp             EETTEECEEEECCSC
T ss_pred             EECCcEEEEEEeCCC
Confidence             99999999998764

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.65  E-value=4.5e-16  Score=112.09  Aligned_cols=79  Identities=25%  Similarity=0.252  Sum_probs=70.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcC-c-CC---CeEEE
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTAND-Y-LG---QSFLK  116 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g-~-~~---~~~l~  116 (128)
                      ..++|||+|||.++++++|+++|++||.|.+++++.|+ +|+++|||||+|.+.+ +|.+|++.||+ . +.   +++|.
T Consensus        95 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~-~A~~A~~~l~~~~~~~~~~~r~i~  172 (261)
T 3sde_A           95 HGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD-RGRATGKGFVEFAAKP-PARKALERCGDGAFLLTTTPRPVI  172 (261)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET-TSCEEEEEEEEESSHH-HHHHHHHHHHHSCEESSSSCCBCE
T ss_pred             cCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCC-CCCcCcEEEEEeCCHH-HHHHHHHHhcCCeEEecCCCceEE
Confidence            36799999999999999999999999999999999995 7999999999997777 99999999954 3 43   89999


Q ss_pred             EEeccc
Q psy8615         117 PSFNTY  122 (128)
Q Consensus       117 V~~~~~  122 (128)
                      |.+.++
T Consensus       173 v~~~~~  178 (261)
T 3sde_A          173 VEPMEQ  178 (261)
T ss_dssp             EEECCC
T ss_pred             Eeeccc
Confidence            998765

>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=99.65  E-value=1e-16  Score=112.15  Aligned_cols=70  Identities=19%  Similarity=0.263  Sum_probs=62.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCce--EEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCe
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTV--LSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQS  113 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i--~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~  113 (128)
                      ++.++|||+|||+++++++|+++|++||.|  .++++..++  |..+|||||+|++.+ +|..|+..|||+ ++|+
T Consensus       121 ~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~--~~~~g~gfV~f~~~~-~A~~Ai~~lng~~~~g~  193 (205)
T 3tyt_A          121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK--SERSSSGLLEWDSKS-DALETLGFLNHYQMKNP  193 (205)
T ss_dssp             CCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC--SSSSEEEEEECSSHH-HHHHHHHHHTTCEECCS
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC--CCCceEEEEEeCCHH-HHHHHHHHhCCCCccCC
Confidence            346789999999999999999999999999  888888775  566799999997777 999999999998 7775

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.64  E-value=2.9e-17  Score=112.87  Aligned_cols=74  Identities=16%  Similarity=0.182  Sum_probs=63.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCCC-----------ceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPFG-----------TVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-  109 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~G-----------~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-  109 (128)
                      ..++|||+|||+++++++|+++|++||           .|.++++      ++++|||||+|.+.+ +|..|+ .|||. 
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~------~~~~g~afV~F~~~~-~A~~Al-~l~g~~   74 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEFRSVD-ETTQAM-AFDGII   74 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE------ETTTTEEEEEESCSH-HHHHHG-GGTTEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe------cCCCCEEEEEeCCHH-HHHHHH-HhcCCE
Confidence            367999999999999999999999994           4555543      566899999998888 999999 89999 


Q ss_pred             CCCeEEEEEecccc
Q psy8615         110 LGQSFLKPSFNTYV  123 (128)
Q Consensus       110 ~~~~~l~V~~~~~~  123 (128)
                      ++|+.|+|.+.+..
T Consensus        75 ~~g~~i~v~~~~~~   88 (198)
T 2yh0_A           75 FQGQSLKIRRPHDY   88 (198)
T ss_dssp             ETTEEEEEECCCCC
T ss_pred             EcCceEEEeCCCCC
Confidence            99999999998653

>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=99.64  E-value=2.7e-16  Score=114.37  Aligned_cols=80  Identities=15%  Similarity=0.216  Sum_probs=68.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCCC-ceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPFG-TVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~G-~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      ..++|||+|||+++++++|+++|++|| .|.+++++.++. |.++|||||+|.+.+ +|..|++.|||. ++|+.|+|.|
T Consensus       116 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~-~~~~g~afV~f~~~~-~a~~A~~~l~g~~~~g~~l~v~~  193 (292)
T 2ghp_A          116 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF-NTSRRFAYIDVTSKE-DARYCVEKLNGLKIEGYTLVTKV  193 (292)
T ss_dssp             CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHH-HHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCC-CCcceEEEEEECCHH-HHHHHHHHhCCCEeCCcEEEEEE
Confidence            478999999999999999999999999 999999999887 889999999997777 999999999999 9999999999


Q ss_pred             cccc
Q psy8615         120 NTYV  123 (128)
Q Consensus       120 ~~~~  123 (128)
                      ..+.
T Consensus       194 a~~~  197 (292)
T 2ghp_A          194 SNPL  197 (292)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8754

>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=99.63  E-value=3.8e-17  Score=103.17  Aligned_cols=71  Identities=13%  Similarity=0.082  Sum_probs=62.0

Q ss_pred             EcCCCCCCCHHHHHhhh------------cCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeE
Q psy8615          48 IYHLPPEFSDADLASMF------------GPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSF  114 (128)
Q Consensus        48 V~nLp~~~~e~~l~~~f------------~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~  114 (128)
                      +.+||+++++++|++.|            ++||.|.++++..++. |+++|||||+|++.+ +|.+|++.|||. ++||+
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~-~~~~G~~fV~f~~~~-~A~~A~~~lng~~~~Gr~   97 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLG-DHLVGNVYVKFRREE-DAEKAVIDLNNRWFNGQP   97 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSS-SSSEEEEEEEESCHH-HHHHHHHHHTTCEETTEE
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCC-CCccEEEEEEECCHH-HHHHHHHHHCCCEECCEE
Confidence            45677777887777666            9999999999998875 899999999997777 999999999999 99999


Q ss_pred             EEEEec
Q psy8615         115 LKPSFN  120 (128)
Q Consensus       115 l~V~~~  120 (128)
                      |+|.|.
T Consensus        98 i~v~~s  103 (104)
T 1jmt_A           98 IHAELS  103 (104)
T ss_dssp             CCEEEC
T ss_pred             EEEEEc
Confidence            999985

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=99.63  E-value=8.6e-16  Score=99.05  Aligned_cols=80  Identities=13%  Similarity=0.163  Sum_probs=68.0

Q ss_pred             CCCeEEEcCC--CCCC---CHHHHHhhhcCCCceEEEEEEecCC----CCCcceEEEEEEecCHHHHHHHHHHhcCc-CC
Q psy8615          42 EGANLFIYHL--PPEF---SDADLASMFGPFGTVLSAKVFIDKQ----NNRSKCFGTIIFMRKFFILTIRFDTANDY-LG  111 (128)
Q Consensus        42 ~~~~l~V~nL--p~~~---~e~~l~~~f~~~G~i~~~~~~~~~~----tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~  111 (128)
                      ..+.|++.|+  |.++   -+++|++.|++||.|.+++++.++.    +++++||+||+|.+.+ +|.+|++.|||. ++
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e-~A~~Ai~~LnGr~f~   97 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIAS-ETHKAIQALNGRWFA   97 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHH-HHHHHHHHHTTCEET
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHH-HHHHHHHHHCCCEEC
Confidence            3567889998  3222   3689999999999999999999865    4678899999997777 999999999999 99


Q ss_pred             CeEEEEEeccc
Q psy8615         112 QSFLKPSFNTY  122 (128)
Q Consensus       112 ~~~l~V~~~~~  122 (128)
                      ||.|+|.|...
T Consensus        98 GR~i~v~~~~~  108 (118)
T 3ue2_A           98 GRKVVAEVYDQ  108 (118)
T ss_dssp             TEECEEEEECH
T ss_pred             CcEEEEEEcCh
Confidence            99999998653

>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=99.63  E-value=6.1e-16  Score=97.79  Aligned_cols=79  Identities=11%  Similarity=0.073  Sum_probs=67.2

Q ss_pred             CCeEEEcCC--CCCCC--------HHHHHhhhcCCCceEEEEEEecCCC--CCcceEEEEEEecCHHHHHHHHHHhcCc-
Q psy8615          43 GANLFIYHL--PPEFS--------DADLASMFGPFGTVLSAKVFIDKQN--NRSKCFGTIIFMRKFFILTIRFDTANDY-  109 (128)
Q Consensus        43 ~~~l~V~nL--p~~~~--------e~~l~~~f~~~G~i~~~~~~~~~~t--g~~~g~~fv~f~~~~~~a~~Ai~~l~g~-  109 (128)
                      .+.|.+.|+  |.+..        +++|++.|++||.|.+++++.++.+  ++++||+||+|++.+ +|.+|++.|||. 
T Consensus         5 s~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~-~A~~Ai~~lnG~~   83 (105)
T 3v4m_A            5 TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVF-DCQKAMQGLTGRK   83 (105)
T ss_dssp             CSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHH-HHHHHHHHHTTCE
T ss_pred             CeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHH-HHHHHHHHhCCCE
Confidence            457788887  44443        3689999999999999999988764  367999999997777 999999999999 


Q ss_pred             CCCeEEEEEeccc
Q psy8615         110 LGQSFLKPSFNTY  122 (128)
Q Consensus       110 ~~~~~l~V~~~~~  122 (128)
                      ++||+|+|+|...
T Consensus        84 f~GR~i~v~~~~~   96 (105)
T 3v4m_A           84 FANRVVVTKYCDP   96 (105)
T ss_dssp             ETTEECEEEEECH
T ss_pred             eCCCEEEEEEeCH
Confidence            9999999998754

>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=99.57  E-value=2.3e-15  Score=101.18  Aligned_cols=74  Identities=16%  Similarity=0.206  Sum_probs=64.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCC----C-------ceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPF----G-------TVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-  109 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~----G-------~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-  109 (128)
                      +.++|||+|||+++++++|+++|++|    |       .|.++++.      +++|||||+|.+.+ +|..|+ .+|+. 
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~------~~~g~afV~f~~~~-~A~~A~-~~~~~~   74 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRSVD-ETTQAM-AFDGII   74 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEE------TTTTEEEEEESSHH-HHHHHG-GGTTCE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEec------CCCCEEEEEeCCHH-HHHHHH-HhCCcE
Confidence            35799999999999999999999999    6       66666553      45899999997777 999999 89999 


Q ss_pred             CCCeEEEEEecccc
Q psy8615         110 LGQSFLKPSFNTYV  123 (128)
Q Consensus       110 ~~~~~l~V~~~~~~  123 (128)
                      ++|+.|+|.+.+..
T Consensus        75 ~~g~~i~v~~~~~~   88 (172)
T 2g4b_A           75 FQGQSLKIRRPHDY   88 (172)
T ss_dssp             ETTEECEEECCSSC
T ss_pred             ecCceeeecCCccc
Confidence            99999999997753

>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=99.54  E-value=1.1e-14  Score=108.99  Aligned_cols=77  Identities=16%  Similarity=0.036  Sum_probs=63.5

Q ss_pred             CCCCCeEEEcC--CCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-C---CCe
Q psy8615          40 GPEGANLFIYH--LPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-L---GQS  113 (128)
Q Consensus        40 ~~~~~~l~V~n--Lp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~---~~~  113 (128)
                      +....+|||+|  |+++++|++|+++|++||.|.++.+..      +||||||+|++.+ +|++|++.|||. +   .|+
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~-~A~~Ai~~lnG~~~~~~~g~   87 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTE-ESKRAYVTLNGKEVVDDLGQ   87 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHH-HHHHHHHHTTTCEEECTTSC
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHH-HHHHHHHHhCCCccccccCC
Confidence            44567999999  588999999999999999999876542      4799999997766 999999999997 3   233


Q ss_pred             --EEEEEecccc
Q psy8615         114 --FLKPSFNTYV  123 (128)
Q Consensus       114 --~l~V~~~~~~  123 (128)
                        +|.|+|...+
T Consensus        88 ~~~ly~~~~~~~   99 (345)
T 3tht_A           88 KITLYLNFVEKV   99 (345)
T ss_dssp             EEECEEEECSSE
T ss_pred             ceEEEEEEeecc
Confidence              6888887644

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.52  E-value=2.7e-14  Score=89.48  Aligned_cols=65  Identities=15%  Similarity=0.118  Sum_probs=56.4

Q ss_pred             CCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCcCCCeEEEEEeccccc
Q psy8615          53 PEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDYLGQSFLKPSFNTYVL  124 (128)
Q Consensus        53 ~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~~~~~~l~V~~~~~~~  124 (128)
                      .++++++|+++|++||.|.++.++     ++++|||||+|++.+ +|+.|++.+++ +.+++|+|.|.++..
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~-~A~~Ai~~~~~-~~g~~l~V~~a~~~~   91 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVK-AAELAVQNEVG-LVDNPLKISWLEGQP   91 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHH-HHHHHHHTCCB-CSSSBCEEECSSCCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHH-HHHHHHHhcCC-CCCCeEEEEEccCCC
Confidence            468999999999999999999987     467999999998777 99999998554 568899999988653

>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=99.43  E-value=1.4e-13  Score=88.13  Aligned_cols=75  Identities=7%  Similarity=0.032  Sum_probs=60.0

Q ss_pred             CCeEEEcCC--CCCC--------CHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CC
Q psy8615          43 GANLFIYHL--PPEF--------SDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LG  111 (128)
Q Consensus        43 ~~~l~V~nL--p~~~--------~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~  111 (128)
                      .+.|.+.|+  +.+.        -+++|++.|++||.|.++.+..+.    .+||+||+|.+.+ +|.+|++.|||. ++
T Consensus         7 s~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e-~A~~Ai~~lnG~~f~   81 (114)
T 3s6e_A            7 TQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIA-AAIAAVNALHGRWFA   81 (114)
T ss_dssp             CSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHH-HHHHHHHHHTTCEET
T ss_pred             CcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHH-HHHHHHHHhCCCEEC
Confidence            345677776  2221        134789999999999999886543    4899999997777 999999999999 99


Q ss_pred             CeEEEEEeccc
Q psy8615         112 QSFLKPSFNTY  122 (128)
Q Consensus       112 ~~~l~V~~~~~  122 (128)
                      ||.|+|.|...
T Consensus        82 GR~i~v~~~~~   92 (114)
T 3s6e_A           82 GKMITAAYVPL   92 (114)
T ss_dssp             TEECEEEEECH
T ss_pred             CEEEEEEEEcH
Confidence            99999999753

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.42  E-value=3.7e-13  Score=82.38  Aligned_cols=74  Identities=19%  Similarity=0.260  Sum_probs=61.1

Q ss_pred             CCCCCeEEEcCCC----CCCCH----HHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-C
Q psy8615          40 GPEGANLFIYHLP----PEFSD----ADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-L  110 (128)
Q Consensus        40 ~~~~~~l~V~nLp----~~~~e----~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~  110 (128)
                      +|...+|+|...+    .+..+    .+|.+.|++||.|..++++.|+        +||+|.+.+ .|.+|++ |||. +
T Consensus         4 GPpd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~-sAlaAi~-mnG~~v   73 (91)
T 2dnr_A            4 GSSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGS-SALNVLS-LNGKEL   73 (91)
T ss_dssp             CCSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHH-HHHHGGG-GTTCEE
T ss_pred             CCCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChH-HHHHHHh-cCCeEe
Confidence            4556678887665    23434    5688999999999999999874        799997766 9999998 9999 9


Q ss_pred             CCeEEEEEecccc
Q psy8615         111 GQSFLKPSFNTYV  123 (128)
Q Consensus       111 ~~~~l~V~~~~~~  123 (128)
                      +||.|+|+++++-
T Consensus        74 ~Gr~LkV~lkt~d   86 (91)
T 2dnr_A           74 LNRTITIALKSPS   86 (91)
T ss_dssp             TTEEEEEEECCCS
T ss_pred             CCeEEEEEeCCCC
Confidence            9999999999974

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.31  E-value=8.8e-12  Score=80.38  Aligned_cols=75  Identities=17%  Similarity=0.087  Sum_probs=63.8

Q ss_pred             CCCCCCeEEEcCCCCC-CCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhc--Cc-CCCeE
Q psy8615          39 TGPEGANLFIYHLPPE-FSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTAN--DY-LGQSF  114 (128)
Q Consensus        39 ~~~~~~~l~V~nLp~~-~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~--g~-~~~~~  114 (128)
                      .-+.++.|||+||+.+ +++++|+++|++||.|..|.+..+..      .|||+|.++.++|..|+..+|  +. +.+..
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 EEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNKE   87 (121)
T ss_dssp             SCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSSS
T ss_pred             cccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCcE
Confidence            3466999999999999 99999999999999999999988876      599999773338999999996  44 88877


Q ss_pred             EEEEe
Q psy8615         115 LKPSF  119 (128)
Q Consensus       115 l~V~~  119 (128)
                      +++..
T Consensus        88 ~~~ev   92 (121)
T 1owx_A           88 VTWEV   92 (121)
T ss_dssp             EEEEE
T ss_pred             EEEEE
Confidence            77654

>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=99.29  E-value=4.1e-12  Score=78.11  Aligned_cols=74  Identities=16%  Similarity=0.225  Sum_probs=62.0

Q ss_pred             CCCCCCeEEEcCCCCC-----CCH----HHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc
Q psy8615          39 TGPEGANLFIYHLPPE-----FSD----ADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY  109 (128)
Q Consensus        39 ~~~~~~~l~V~nLp~~-----~~e----~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~  109 (128)
                      .+|...+|+|..++.+     +.+    .+|.+.|++||.|..++++.|+        +||+|.+.+ +|.+||+ |||.
T Consensus        11 ~GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~-sAl~AI~-ldG~   80 (95)
T 1ufw_A           11 QGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSH-SALSVLD-VDGM   80 (95)
T ss_dssp             CCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSH-HHHHHHH-GGGS
T ss_pred             cCCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChH-HHHHHHh-cCCe
Confidence            3556778899877643     323    4588899999999999999885        999998887 9999998 9999


Q ss_pred             -CCCeEEEEEeccc
Q psy8615         110 -LGQSFLKPSFNTY  122 (128)
Q Consensus       110 -~~~~~l~V~~~~~  122 (128)
                       ++||.|+|+++++
T Consensus        81 ~v~Gr~L~V~~k~~   94 (95)
T 1ufw_A           81 KVKGRAVKISGPSS   94 (95)
T ss_dssp             EETTEEEEEECCCC
T ss_pred             eeCCeEEEEeccCC
Confidence             9999999999975

>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=99.27  E-value=1.2e-11  Score=86.84  Aligned_cols=66  Identities=11%  Similarity=0.072  Sum_probs=57.9

Q ss_pred             CCHHHHHhhhcCCCceEEEEEEecC----CCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecc
Q psy8615          55 FSDADLASMFGPFGTVLSAKVFIDK----QNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNT  121 (128)
Q Consensus        55 ~~e~~l~~~f~~~G~i~~~~~~~~~----~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~  121 (128)
                      -.+++|++.|++||.|.++.+..+.    .+|+++|++||+|.+.+ +|.+|++.|||. ++||+|.+.|..
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~-~a~~a~~~l~gr~~~gr~i~~~~~~  211 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIAS-ETHKAIQALNGRWFAGRKVVAEVYD  211 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHH-HHHHHHHHHTTCBSSSSBCEEEECC
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHH-HHHHHHHHhcCceECCeEEEEEEcC
Confidence            4567899999999999999998554    44589999999996666 999999999999 999999999864

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.38  E-value=1.4e-06  Score=54.73  Aligned_cols=70  Identities=10%  Similarity=0.058  Sum_probs=61.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCC-----CceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEE
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPF-----GTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFL  115 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~-----G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l  115 (128)
                      ..++|-+-|||+.+++..++.+.+++     |.+.++.+..|      .+-|+|+|.+.. .|.+|.-.|+|. +.|+.|
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pD------H~GAivef~d~~-~AgKasLaL~G~ef~gr~L   92 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSD------FNGAIIIFRDSK-FAAKMLMILNGSQFQGKVI   92 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETT------TTEEEEECSCHH-HHHHHHHHHSSEEETTEEE
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecC------CCceEEEEccch-hhHHHHhhcCCeeecCeEE
Confidence            36678888999999999999999999     99999887766      447999997776 999999999999 999999


Q ss_pred             EEE
Q psy8615         116 KPS  118 (128)
Q Consensus       116 ~V~  118 (128)
                      ++.
T Consensus        93 r~g   95 (117)
T 2l9w_A           93 RSG   95 (117)
T ss_dssp             EEE
T ss_pred             Eec
Confidence            875

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.88  E-value=3.9e-05  Score=47.73  Aligned_cols=74  Identities=14%  Similarity=0.075  Sum_probs=59.2

Q ss_pred             CCeEEEcCCCCCC-CH----HHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEE
Q psy8615          43 GANLFIYHLPPEF-SD----ADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLK  116 (128)
Q Consensus        43 ~~~l~V~nLp~~~-~e----~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~  116 (128)
                      +++|+|.||+.++ ..    +.++++|..|+++........-.      -.-|.|++.+ +|.+|-..|++. +.|+.|+
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSFR------Rirv~F~~~~-~A~~AR~~Lh~~~f~g~~~r   77 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFK------RVRINFSNPL-SAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTT------EEEEECSSTT-HHHHHHHTSTTSEETTEECE
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcce------EEEEEeCChH-HHHHHHHHhccceecCceeE
Confidence            6789999998764 22    46789999999888866554432      4469998888 999999999999 9999999


Q ss_pred             EEecccc
Q psy8615         117 PSFNTYV  123 (128)
Q Consensus       117 V~~~~~~  123 (128)
                      |-|+.+.
T Consensus        78 ~YFgq~~   84 (104)
T 1wey_A           78 LYFAQTL   84 (104)
T ss_dssp             EECCCCS
T ss_pred             EEecCCC
Confidence            9998743

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=97.62  E-value=0.00041  Score=42.61  Aligned_cols=55  Identities=20%  Similarity=0.340  Sum_probs=45.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhc
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTAN  107 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~  107 (128)
                      ...+++ +.|.++...||..+|++|| -..|+++.|.       -|||.|.+++ .|..|+..+.
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fg-gv~I~WidDT-------sAlvvf~~~~-~a~~al~~i~   70 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDDT-------SAFVSLSQPE-QVQIAVNTSK   70 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTC-SCCCEEEETT-------EEEEECSCHH-HHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccC-CEEEEEEcCC-------eEEEEecCHH-HHHHHHHhcc
Confidence            334556 9999999999999999999 4567788774       7999997777 8888888763

>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=97.43  E-value=0.00062  Score=41.92  Aligned_cols=53  Identities=21%  Similarity=0.358  Sum_probs=45.3

Q ss_pred             eEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhc
Q psy8615          45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTAN  107 (128)
Q Consensus        45 ~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~  107 (128)
                      .+++ +.|.++...||..+|++|| -..|+++.|.       -|||.|.+++ .|..|+..+.
T Consensus         8 V~~l-~FP~ewKt~Di~~lFs~fg-gv~I~WidDT-------sAlvvf~~~~-~a~~al~~i~   60 (101)
T 3ctr_A            8 VLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDDT-------SAFVSLSQPE-QVKIAVNTSK   60 (101)
T ss_dssp             EEEE-ECCTTCCHHHHHHHTTTSE-EEEEEEEETT-------EEEEEEEEEC-HHHHHHHHHT
T ss_pred             EEEE-eCChhhhhHHHHHHHhccC-CEEEEEEcCC-------eEEEEecCHH-HHHHHHHhcc
Confidence            3455 9999999999999999999 5668888775       7999998888 8999988774

>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=97.37  E-value=0.0021  Score=39.00  Aligned_cols=65  Identities=17%  Similarity=0.212  Sum_probs=52.7

Q ss_pred             CeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCC--cceEEEEEEecCHHHHHHHHHHhcCc
Q psy8615          44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNR--SKCFGTIIFMRKFFILTIRFDTANDY  109 (128)
Q Consensus        44 ~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~--~~g~~fv~f~~~~~~a~~Ai~~l~g~  109 (128)
                      ++|-|++||+.++|+++.+.+++...+........+.+.+  ...-|++.|.+.+ +...=.+.++|+
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e-~v~~f~~~~~g~   68 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQE-DIILFRDRFDGY   68 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSH-HHHHHHHHHTTC
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHH-HHHHHHHHhCCc
Confidence            5789999999999999999999988776666655554433  2467899997776 888899999997

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=96.56  E-value=0.0037  Score=40.81  Aligned_cols=35  Identities=11%  Similarity=-0.024  Sum_probs=28.8

Q ss_pred             EEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc
Q psy8615          72 SAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY  109 (128)
Q Consensus        72 ~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~  109 (128)
                      .++++++..  .++|||||+|.+.+ +|++|++.+++.
T Consensus         2 ~~kl~ln~~--~~~G~~fV~f~~~~-~A~~al~~~~~~   36 (158)
T 2kn4_A            2 QYKLILNGK--TLKGETTTEAVDAA-TAEKVFKQYAND   36 (158)
T ss_dssp             EEEEEEECS--SCEEEEEEECSSHH-HHHHHHHHHHHH
T ss_pred             cEEEEecCc--cccchhHHHHHHHH-hHHHHHHhhccc
Confidence            456777764  68999999997777 999999998864

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.44  E-value=0.02  Score=35.43  Aligned_cols=67  Identities=25%  Similarity=0.277  Sum_probs=48.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCC-----CceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEE
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPF-----GTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFL  115 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~-----G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l  115 (128)
                      -+.+|.|.|||.++.++.|+-+|+.-     |+|.+++..  +      +-|+|+|.+.. .+++.++. ..+ |.+.+|
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~--~------~~AvItF~d~~-va~rVL~k-~~H~L~~~~L   76 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRL--G------CGGVLTFREPA-DAERVLAQ-ADHELHGAQL   76 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEE--T------TEEEEEESSHH-HHHHHHTC-SCCBSSSSBC
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEc--C------CcEEEEEcChH-HHHHHhcC-CcceecCeEE
Confidence            36789999999999999999999862     577776543  2      46799997666 66655443 223 777777


Q ss_pred             EEE
Q psy8615         116 KPS  118 (128)
Q Consensus       116 ~V~  118 (128)
                      .|.
T Consensus        77 sV~   79 (104)
T 2dhx_A           77 SLR   79 (104)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            764

>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=96.29  E-value=0.01  Score=37.70  Aligned_cols=75  Identities=11%  Similarity=0.217  Sum_probs=53.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCC-eEEEEEe
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQ-SFLKPSF  119 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~-~~l~V~~  119 (128)
                      ..+-|.|-+.|.+.. ..+...|++||.|.+...   +   ....+-.+.|+++. +|++|+.. ||. +++ -.|-|..
T Consensus        23 ~~~wVtVFGFp~~~~-~~VL~~F~~~G~Iv~~~~---~---~~~NWihI~Y~s~~-~A~rAL~k-NG~ii~g~~mIGV~p   93 (119)
T 1wwh_A           23 DDTWVTVFGFPQASA-SYILLQFAQYGNILKHVM---S---NTGNWMHIRYQSKL-QARKALSK-DGRIFGESIMIGVKP   93 (119)
T ss_dssp             GGGEEEEECCCGGGH-HHHHHHHHTTSCEEEEEE---C---SSSSEEEEEESSHH-HHHHHHTT-TTCEETTTEECEEEE
T ss_pred             CCCEEEEECCCHHHH-HHHHHHHHhhCcEEEecc---C---CCCCeEEEEeCCHH-HHHHHHHh-CCeEecCCEEEEEEE
Confidence            356778888888864 455667999999998764   1   12458899998887 99999887 777 765 5555555


Q ss_pred             -cccccc
Q psy8615         120 -NTYVLM  125 (128)
Q Consensus       120 -~~~~~~  125 (128)
                       ..+.+|
T Consensus        94 ~~d~~vi  100 (119)
T 1wwh_A           94 CIDKNVM  100 (119)
T ss_dssp             CCCHHHH
T ss_pred             CCCHHHH
Confidence             334444

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=95.75  E-value=0.0042  Score=40.31  Aligned_cols=39  Identities=15%  Similarity=-0.117  Sum_probs=34.7

Q ss_pred             CCcceEEEEEEecCHHHHHHHHHHh-cCc-CCCeEEEEEeccc
Q psy8615          82 NRSKCFGTIIFMRKFFILTIRFDTA-NDY-LGQSFLKPSFNTY  122 (128)
Q Consensus        82 g~~~g~~fv~f~~~~~~a~~Ai~~l-~g~-~~~~~l~V~~~~~  122 (128)
                      ...+|+++++|.+.+ +|++|++.+ ||. ++| .+++.+.+.
T Consensus        10 ~~l~G~~~ve~~~~~-~A~~a~~~~~ng~~~~G-~~~~~~a~~   50 (150)
T 2i2y_A           10 KTLKGETTTEAVDAA-TAEKVFKQYANDNGVDG-EWTYDDATK   50 (150)
T ss_dssp             SSSCEEEEEECSSHH-HHTTTHHHHHHHHTCCC-EEEEETTTT
T ss_pred             ccccccceeeecCHH-HHHHHHHHHhcCCCCCC-ceecccccC
Confidence            466999999998777 999999999 999 999 999998875

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.42  E-value=0.0072  Score=46.78  Aligned_cols=51  Identities=14%  Similarity=0.278  Sum_probs=36.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHH
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILT  100 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~  100 (128)
                      .+.|||. .|...++.+|.+.|++||+|.++..-.++  |   -|+.|+|++.+ .+.
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~--g---~~~~vef~~~~-~~~  103 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF--G---LYAVVEFCQKE-SIG  103 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS--S---EEEEEECC----CCH
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC--C---eEEEEEeCCHH-HHH
Confidence            3689996 89999999999999999999998655432  3   69999997766 544

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=95.37  E-value=0.025  Score=34.55  Aligned_cols=66  Identities=17%  Similarity=0.151  Sum_probs=45.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCC--cceEEEEEEecCHHHHHHHHHHhcCc
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNR--SKCFGTIIFMRKFFILTIRFDTANDY  109 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~--~~g~~fv~f~~~~~~a~~Ai~~l~g~  109 (128)
                      .-+|-|+.||+.+||+++.+.+++.-.+........+.+-+  ...-|++.|.+.+ +...=.+..+|+
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~e-dv~~F~~~f~g~   76 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPD-DILLFRDRFDGY   76 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHH-HHHHHHHHSTTE
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHH-HHHHHHHHcCCc
Confidence            44789999999999999999888765543222222222211  1346899996665 888888899997

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=90.32  E-value=0.7  Score=36.05  Aligned_cols=55  Identities=20%  Similarity=0.347  Sum_probs=42.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhc
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTAN  107 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~  107 (128)
                      ...++++ .|..+...+|.++|+.||. .+++++.|.       .+||.|.+++ .|..+++.++
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~-v~V~widdt-------~a~V~~~~~~-~a~~~l~~~~  494 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGN-IQISWIDDT-------SAFVSLSQPE-QVQIAVNTSK  494 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCC-CEEEECSSS-------EEEEECSCHH-HHHHHHHHHT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCC-EEEEEEcCC-------eEEEEECCHH-HHHHHHHHHH
Confidence            3456665 8889999999999999994 455555442       7999997666 8988888885

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=87.47  E-value=0.46  Score=30.51  Aligned_cols=75  Identities=13%  Similarity=0.181  Sum_probs=45.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEE-EEEEe------------cCCCC-CcceEEEEEEecCHHHHHHHHHHhcC
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLS-AKVFI------------DKQNN-RSKCFGTIIFMRKFFILTIRFDTAND  108 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~-~~~~~------------~~~tg-~~~g~~fv~f~~~~~~a~~Ai~~l~g  108 (128)
                      .+.|.|-+.|.+.+...| +.|++||.|.+ .....            .+..+ ....+-.+.|+++. +|.+|+.. ||
T Consensus         7 e~~VtVFGFp~~~~~~VI-~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~-~A~rAL~~-NG   83 (132)
T 3p3d_A            7 ELAILVFGYPETMANQVI-AYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPA-SAVDALLE-NG   83 (132)
T ss_dssp             -CEEEEECCCGGGHHHHH-HHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHH-HHHHHHTT-TT
T ss_pred             ceEEEEEecCHHHHHHHH-HHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHH-HHHHHHHh-CC
Confidence            345666677777665555 56999999876 11110            00001 12457789997777 99988754 55


Q ss_pred             c-CCCeEEEEEec
Q psy8615         109 Y-LGQSFLKPSFN  120 (128)
Q Consensus       109 ~-~~~~~l~V~~~  120 (128)
                      . ++|..|-|..=
T Consensus        84 ~ii~G~mIGV~Py   96 (132)
T 3p3d_A           84 AVFNGVLLGVIPY   96 (132)
T ss_dssp             CEETTEECEEEEC
T ss_pred             eEeCcEEEEEEEC
Confidence            5 88876655443

>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=83.85  E-value=0.31  Score=29.89  Aligned_cols=20  Identities=25%  Similarity=0.341  Sum_probs=0.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHH
Q psy8615          40 GPEGANLFIYHLPPEFSDAD   59 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~   59 (128)
                      ....++|||+|||+++|++.
T Consensus        94 ~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           94 AKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             --------------------
T ss_pred             cCCCCceEeCCCCCCccccc
Confidence            34467899999999999864

---

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	128
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	5e-10
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	5e-08
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	1e-07
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	2e-07
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	3e-07
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	6e-07
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	2e-06
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	4e-06
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	5e-06
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	5e-06
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	6e-06
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	6e-06
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	7e-06
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	9e-06
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	1e-05
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	1e-05
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-05
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-05
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-05
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-05
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-05
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	2e-05
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	3e-05
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	4e-05
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-05
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	4e-05
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	6e-05
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	7e-05
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	1e-04
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	1e-04
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-04
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	2e-04
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	2e-04
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	2e-04
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	2e-04
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	3e-04
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	3e-04
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	3e-04
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	5e-04
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	5e-04
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	5e-04
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	0.001
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	0.001
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	0.003
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	0.003

>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 = 50.9 bits (121), Expect = 5e-10
 Identities = 42/65 (64%), Positives = 48/65 (73%)

Query: 31 VGSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTI 90
          +G++G Q  GPEGANLFIYHLP EF D DL  MF PFG V+SAKVFIDKQ N SKCFG +
Sbjct: 6  IGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFV 65

Query: 91 IFMRK 95
           +   
Sbjct: 66 SYDNP 70

>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 = 45.4 bits (107), Expect = 5e-08
 Identities = 12/51 (23%), Positives = 19/51 (37%)

Query: 42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          +   +F   L       DL   F   G V   ++  D+ + RSK    + F
Sbjct: 17 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEF 67

>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 = 44.2 bits (104), Expect = 1e-07
 Identities = 17/54 (31%), Positives = 27/54 (50%)

Query: 42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRK 95
          + ++L +  LP + ++ DL   F  FG VL  +V  D +   SK FG + F   
Sbjct: 7  KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEY 60

>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 = 43.8 bits (103), Expect = 2e-07
 Identities = 12/53 (22%), Positives = 28/53 (52%)

Query: 43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRK 95
            NL++ +LP   +D  L ++FG +G+++   +  DK   R +    + + ++
Sbjct: 6  DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKR 58

>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 = 43.1 bits (101), Expect = 3e-07
 Identities = 13/53 (24%), Positives = 30/53 (56%)

Query: 43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRK 95
           ANL++  LP   +  +L  +F  +G ++++++ +D+    S+  G I F ++
Sbjct: 6  DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKR 58

>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 = 42.2 bits (99), Expect = 6e-07
 Identities = 16/49 (32%), Positives = 26/49 (53%)

Query: 44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          A+L++  L P+ ++A L   F P G +LS +V  D    RS  +  + F
Sbjct: 1  ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNF 49

>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 = 40.8 bits (95), Expect = 2e-06
 Identities = 13/58 (22%), Positives = 26/58 (44%)

Query: 35 GKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          G +        L ++ L    ++ DL  +F  +G +    +  D+Q+ RS+ F  + F
Sbjct: 1  GNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF 58

>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 = 40.3 bits (94), Expect = 4e-06
 Identities = 8/56 (14%), Positives = 25/56 (44%), Gaps = 1/56 (1%)

Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFID-KQNNRSKCFGTIIFMRK 95
             + + + ++P + +  ++  +F  FG + + ++          + FG + F+ K
Sbjct: 6  QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITK 61

>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 = 39.6 bits (92), Expect = 5e-06
 Identities = 11/48 (22%), Positives = 25/48 (52%)

Query: 45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          NL + +LP + +D +L ++F   G + + ++  D +   S  +  + F
Sbjct: 4  NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDF 51

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.0 bits (93), Expect = 5e-06
 Identities = 17/57 (29%), Positives = 29/57 (50%)

Query: 33 SSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGT 89
          SSG   +      L + ++P  F D DL  MFG FG +L  ++  +++ ++   F T
Sbjct: 1  SSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVT 57

>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 = 40.0 bits (93), Expect = 6e-06
 Identities = 8/38 (21%), Positives = 18/38 (47%)

Query: 39 TGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVF 76
          + P+   ++   +    +D  +   F PFG ++  +VF
Sbjct: 14 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF 51

>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 = 39.9 bits (93), Expect = 6e-06
 Identities = 7/54 (12%), Positives = 22/54 (40%)

Query: 42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRK 95
          +   L++ +L    ++  +  +F   G +    + +DK    +  F  + +  +
Sbjct: 6  KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSR 59

>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 = 39.2 bits (91), Expect = 7e-06
 Identities = 17/50 (34%), Positives = 23/50 (46%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRK 95
          LFI  L  E +D  L S F  +GT+    V  D    RS+ FG + +   
Sbjct: 9  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATV 58

>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 = 39.2 bits (91), Expect = 9e-06
 Identities = 14/47 (29%), Positives = 25/47 (53%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          +F+  L P+  +  +   FG FG V S ++ +D + N+ + F  I F
Sbjct: 2  IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITF 48

>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 = 39.3 bits (91), Expect = 1e-05
 Identities = 14/52 (26%), Positives = 23/52 (44%)

Query: 45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKF 96
           LFI  L  E ++  L + +  +G +    V  D  + RS+ FG + F    
Sbjct: 22 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMA 73

>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 = 39.2 bits (91), Expect = 1e-05
 Identities = 10/55 (18%), Positives = 27/55 (49%)

Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRK 95
           + A +++  L  + S+  L  +F   G V++  +  D+   + + +G + F+ +
Sbjct: 7  NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSE 61

>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 = 40.4 bits (93), Expect = 1e-05
 Identities = 17/47 (36%), Positives = 23/47 (48%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          LFI  L  E +D  L S F  +GT+    V  D    RS+ FG + +
Sbjct: 9  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 55

>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 = 38.4 bits (89), Expect = 2e-05
 Identities = 15/50 (30%), Positives = 24/50 (48%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRK 95
          +FI  L  + +  DL   F  FG V+   + +D    RS+ FG ++F   
Sbjct: 2  MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKES 51

>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 = 38.7 bits (89), Expect = 2e-05
 Identities = 12/64 (18%), Positives = 19/64 (29%)

Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTII 91
          GSSG          + +  LP   S  ++   F     V +          RS     + 
Sbjct: 4  GSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQ 63

Query: 92 FMRK 95
          F  +
Sbjct: 64 FASQ 67

>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 = 38.7 bits (90), Expect = 2e-05
 Identities = 12/46 (26%), Positives = 22/46 (47%), Gaps = 1/46 (2%)

Query: 32 GSSGKQLTGPEGANLFIYHLPPE-FSDADLASMFGPFGTVLSAKVF 76
          GSSGK       + +FI +L       +D+ ++F  +G ++   V 
Sbjct: 4  GSSGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH 49

>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 = 38.1 bits (88), Expect = 2e-05
 Identities = 12/47 (25%), Positives = 23/47 (48%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          L++  L  E  D  L + F PFG +   ++ +D +  + + F  + F
Sbjct: 8  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 54

>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 = 37.7 bits (87), Expect = 2e-05
 Identities = 17/50 (34%), Positives = 23/50 (46%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRK 95
          +FI  L  + +   L   FG FG V    V  D    RS+ FG + FM +
Sbjct: 3  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 52

>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 = 38.1 bits (88), Expect = 3e-05
 Identities = 12/53 (22%), Positives = 21/53 (39%), Gaps = 3/53 (5%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDK---QNNRSKCFGTIIFMRK 95
          LFI +L    ++  L  +F   G + S  +   K       S  FG + + + 
Sbjct: 1  LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 53

>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 = 37.4 bits (86), Expect = 4e-05
 Identities = 10/52 (19%), Positives = 25/52 (48%)

Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
           EG  LF+  +  E  + ++   F  +G + +  + +D++   SK +  + +
Sbjct: 5  VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEY 56

>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 = 37.3 bits (86), Expect = 4e-05
 Identities = 11/50 (22%), Positives = 20/50 (40%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRK 95
          LFI  LP   +D  +  +   FG + +  +  D     SK +    ++  
Sbjct: 4  LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDI 53

>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 = 37.3 bits (86), Expect = 4e-05
 Identities = 14/46 (30%), Positives = 21/46 (45%)

Query: 44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGT 89
           N+FI +L     +  L   F  FG +LS KV  D+  ++   F  
Sbjct: 9  GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVH 54

>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 = 37.5 bits (86), Expect = 6e-05
 Identities = 12/63 (19%), Positives = 24/63 (38%), Gaps = 8/63 (12%)

Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKV--------FIDKQNNRSKCFGTIIF 92
           + + +++  L    +  DLA  F   G V   K         ++DK+  + K   T+ +
Sbjct: 6  SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSY 65

Query: 93 MRK 95
             
Sbjct: 66 EDP 68

>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 = 37.0 bits (85), Expect = 7e-05
 Identities = 18/64 (28%), Positives = 26/64 (40%), Gaps = 4/64 (6%)

Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTII 91
          GSSG          LF+ +L    S+ DL  +F  +G +      ID    + K F  + 
Sbjct: 1  GSSG----SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVT 56

Query: 92 FMRK 95
          FM  
Sbjct: 57 FMFP 60

>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 = 36.7 bits (84), Expect = 1e-04
 Identities = 13/55 (23%), Positives = 22/55 (40%)

Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRK 95
           EG  +FI +L  +  +  L  +   FG +   +V +      SK      FM +
Sbjct: 6  TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQ 60

>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 = 36.2 bits (83), Expect = 1e-04
 Identities = 15/63 (23%), Positives = 27/63 (42%), Gaps = 6/63 (9%)

Query: 33 SSGKQLTGPEGAN---LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGT 89
          S G  + GP G N   +++ +LPP+    D+  +F  +G +   +    K       F  
Sbjct: 1  SGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAI---RDIDLKNRRGGPPFAF 57

Query: 90 IIF 92
          + F
Sbjct: 58 VEF 60

>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 = 36.3 bits (83), Expect = 1e-04
 Identities = 7/48 (14%), Positives = 17/48 (35%), Gaps = 5/48 (10%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKV-----FIDKQNNRSKCFG 88
          L++ ++P   ++  +   F     +           +  Q N+ K F 
Sbjct: 4  LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFA 51

>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 = 35.8 bits (82), Expect = 2e-04
 Identities = 9/63 (14%), Positives = 21/63 (33%), Gaps = 4/63 (6%)

Query: 33 SSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          SSGK    P    + + ++P   S  ++   F  +  +  +      +         + F
Sbjct: 3  SSGK----PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAF 58

Query: 93 MRK 95
            +
Sbjct: 59 ESR 61

>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 = 35.8 bits (82), Expect = 2e-04
 Identities = 9/44 (20%), Positives = 20/44 (45%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGT 89
          L++ +L  + ++  +  +F   G   S K+  +  +N   CF  
Sbjct: 11 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVE 54

>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 = 35.5 bits (81), Expect = 2e-04
 Identities = 14/49 (28%), Positives = 26/49 (53%)

Query: 45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFM 93
          NL + +LP   +  +  S+FG  G + S K+  DK   +S  +G + ++
Sbjct: 4  NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYI 52

>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 = 35.9 bits (82), Expect = 2e-04
 Identities = 14/64 (21%), Positives = 21/64 (32%)

Query: 32 GSSGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTII 91
          GSSG +L        F+ +LP + ++  +   F                  R K FG   
Sbjct: 4  GSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAE 63

Query: 92 FMRK 95
          F   
Sbjct: 64 FEDL 67

>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 = 35.8 bits (82), Expect = 3e-04
 Identities = 9/57 (15%), Positives = 23/57 (40%), Gaps = 5/57 (8%)

Query: 41 PEGAN--LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRK 95
          P   N  L+I +LP + +  ++  +FG +G +             ++    +++   
Sbjct: 3  PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDI 56

>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 = 35.2 bits (80), Expect = 3e-04
 Identities = 9/50 (18%), Positives = 20/50 (40%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRK 95
          L++ + PP ++  ++  +      V  +      + N S+ F  I    K
Sbjct: 4  LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSK 53

>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 = 35.4 bits (81), Expect = 3e-04
 Identities = 15/52 (28%), Positives = 26/52 (50%)

Query: 41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
           + A + + +L  +  + DL  +F PFG++    +  DK   +SK F  I F
Sbjct: 6  DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISF 57

>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 = 34.7 bits (79), Expect = 5e-04
 Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 1/48 (2%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTV-LSAKVFIDKQNNRSKCFGTIIF 92
          +FI +L PE  +  L   F  FG +  + K+  D     SK +  I F
Sbjct: 1  IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINF 48

>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 = 34.3 bits (78), Expect = 5e-04
 Identities = 7/47 (14%), Positives = 21/47 (44%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIF 92
          +F+  +  +  +  L   F  +G +   ++  D+ + + + F  + F
Sbjct: 5  IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 51

>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 = 34.8 bits (79), Expect = 5e-04
 Identities = 13/56 (23%), Positives = 21/56 (37%)

Query: 40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRK 95
          G     L++ +L P  ++ DL S+F  F       +       R +    I F  K
Sbjct: 15 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNK 70

>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 = 33.9 bits (77), Expect = 0.001
 Identities = 5/52 (9%), Positives = 15/52 (28%), Gaps = 2/52 (3%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQN--NRSKCFGTIIFMRK 95
          LFI  +P      ++          +   +         +++ F  + +   
Sbjct: 4  LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESH 55

>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 = 33.2 bits (75), Expect = 0.001
 Identities = 15/50 (30%), Positives = 23/50 (46%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRK 95
          +F+  L    +  D+   F  FG V  A +  DK  NR + FG + F  +
Sbjct: 2  IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESE 51

>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 = 32.5 bits (73), Expect = 0.003
 Identities = 7/52 (13%), Positives = 17/52 (32%), Gaps = 3/52 (5%)

Query: 45 NLFIYHLPPEFSDADLASMF---GPFGTVLSAKVFIDKQNNRSKCFGTIIFM 93
           +F+  L    +D ++       G FG +    +        S+      ++
Sbjct: 10 LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYV 61

>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 = 32.2 bits (73), Expect = 0.003
 Identities = 13/42 (30%), Positives = 19/42 (45%)

Query: 46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCF 87
          L + +L    SDAD+  +F  FGT+  A V  D+        
Sbjct: 3  LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTA 44

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	128
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.93
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.93
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.93
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.93
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.93
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.93
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.92
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.92
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.92
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.92
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.92
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.91
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.91
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.91
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.91
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.9
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.9
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.9
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.9
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.9
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.9
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.9
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.9
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.9
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.9
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.89
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.89
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.89
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.89
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.88
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.88
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.88
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.88
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.88
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.88
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.87
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.87
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.87
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.87
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.87
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.86
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.86
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.86
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.86
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.86
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.86
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.86
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.85
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.85
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.85
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.85
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.85
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.85
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.85
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.84
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.84
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.84
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.83
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.83
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.82
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.82
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.82
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.82
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.82
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.82
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.81
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.81
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.81
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.8
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.8
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.79
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.79
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.79
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.79
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.79
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.79
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.76
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.74
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.74
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.72
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	99.7
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.67
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.66
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.61
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.5
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.48
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.47
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.69
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.41
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	96.49
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	95.09

>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=99.93  E-value=3.5e-26  Score=142.94  Aligned_cols=89  Identities=51%  Similarity=0.826  Sum_probs=81.5

Q ss_pred             CCCCCCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCC
Q psy8615          34 SGKQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQ  112 (128)
Q Consensus        34 ~~~~~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~  112 (128)
                      .+.+.+.+++++|||+|||+++++++|+++|++||.+.+++++.++.+|.++|||||+|.+.+ +|..|++.|||+ ++|
T Consensus         9 ~~~~~~~p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~-~A~~Ai~~lng~~~~g   87 (102)
T d2cpza1           9 AGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPV-SAQAAIQSMNGFQIGM   87 (102)
T ss_dssp             BSCCCCCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHH-HHHHHHHHHTTCEETT
T ss_pred             CCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHH-HHHHHHHHhCCCEECC
Confidence            344455667889999999999999999999999999999999999999999999999997777 999999999999 999


Q ss_pred             eEEEEEecccc
Q psy8615         113 SFLKPSFNTYV  123 (128)
Q Consensus       113 ~~l~V~~~~~~  123 (128)
                      +.|+|+|+++.
T Consensus        88 ~~i~V~~a~~k   98 (102)
T d2cpza1          88 KRLKVQLKRSK   98 (102)
T ss_dssp             EECEEECCCCS
T ss_pred             EEEEEEEeCCC
Confidence            99999998764

>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=99.93  E-value=2.5e-26  Score=138.14  Aligned_cols=79  Identities=19%  Similarity=0.319  Sum_probs=75.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecc
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNT  121 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~  121 (128)
                      .++|||+|||.++++++|+++|++||.|.+++++.++.+|+++|||||+|.+.+ +|++|++.|||. ++|+.|+|+|++
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~-~A~~ai~~lng~~~~g~~l~v~~a~   80 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEM-DSQRAIKVLNGITVRNKRLKVSYAR   80 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHH-HHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHH-HHHHHHHHhCCCEECCEEEEEEEcC
Confidence            578999999999999999999999999999999999999999999999998777 999999999999 999999999998


Q ss_pred             c
Q psy8615         122 Y  122 (128)
Q Consensus       122 ~  122 (128)
                      |
T Consensus        81 p   81 (82)
T d1b7fa1          81 P   81 (82)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.93  E-value=1.2e-25  Score=137.53  Aligned_cols=83  Identities=20%  Similarity=0.332  Sum_probs=78.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ..+.++|||+|||.++++++|+++|++||.|.+++++.|+.+|.++|||||+|.+.+ +|.+|++.|||+ ++|+.|+|+
T Consensus         5 ~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~-~A~~Ai~~l~g~~~~g~~i~v~   83 (90)
T d2cq0a1           5 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRE-DAARAIAGVSGFGYDHLILNVE   83 (90)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHH-HHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHH-HHHHHHHHhCCCEECCEEEEEE
Confidence            345678999999999999999999999999999999999999999999999997777 999999999999 999999999


Q ss_pred             ecccc
Q psy8615         119 FNTYV  123 (128)
Q Consensus       119 ~~~~~  123 (128)
                      |++|.
T Consensus        84 ~akp~   88 (90)
T d2cq0a1          84 WAKPS   88 (90)
T ss_dssp             ESSCC
T ss_pred             eeeCC
Confidence            99975

>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=99.93  E-value=1.3e-25  Score=134.97  Aligned_cols=80  Identities=24%  Similarity=0.370  Sum_probs=76.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecc
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNT  121 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~  121 (128)
                      .++|||+|||.+++|++|+++|++||.|.+++++.|+.+|+++|||||+|.+.+ +|+.|++.|||. ++|+.|+|+|++
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~-~a~~a~~~l~g~~~~g~~l~v~~Ak   80 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPK-DAEKAINTLNGLRLQTKTIKVSYAR   80 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHH-HHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHH-HHHHHHHHhCCCEECCEEEEEEEee
Confidence            468999999999999999999999999999999999999999999999997777 999999999999 999999999999


Q ss_pred             cc
Q psy8615         122 YV  123 (128)
Q Consensus       122 ~~  123 (128)
                      |+
T Consensus        81 Ps   82 (82)
T d1fxla1          81 PS   82 (82)
T ss_dssp             CC
T ss_pred             Cc
Confidence            74

>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=99.93  E-value=1.1e-25  Score=137.10  Aligned_cols=82  Identities=13%  Similarity=0.205  Sum_probs=76.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      +.++++|||+|||.++++++|+++|++||.|.+++++.|+.||+++|||||+|.+.+ +|++|++.|||. ++|+.|+|+
T Consensus         4 s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~-~A~~A~~~lng~~l~g~~l~V~   82 (88)
T d1rk8a_           4 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHK-QALAAKEALNGAEIMGQTIQVD   82 (88)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHH-HHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHH-HHHHHHHHcCCCEECCEEEEEE
Confidence            445889999999999999999999999999999999999999999999999997777 999999999999 999999999


Q ss_pred             eccc
Q psy8615         119 FNTY  122 (128)
Q Consensus       119 ~~~~  122 (128)
                      |+++
T Consensus        83 ~a~~   86 (88)
T d1rk8a_          83 WCFV   86 (88)
T ss_dssp             ESEE
T ss_pred             EecC
Confidence            9875

>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=99.93  E-value=1e-25  Score=138.68  Aligned_cols=87  Identities=14%  Similarity=0.138  Sum_probs=80.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEE
Q psy8615          39 TGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKP  117 (128)
Q Consensus        39 ~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V  117 (128)
                      +....++|||+|||.++++++|+++|++||.|.+++++.|+.||.++|||||+|.+.+ +|+.|++.|||+ ++|+.|+|
T Consensus         5 ~~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~-~A~~Ai~~l~g~~~~g~~l~V   83 (93)
T d1x5ua1           5 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEE-DADYAIKIMDMIKLYGKPIRV   83 (93)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHH-HHHHHHHHSSSCBCSSCBCEE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHH-HHHHHHHHcCCCEECCEEEEE
Confidence            3445689999999999999999999999999999999999999999999999997776 999999999999 99999999


Q ss_pred             Eeccccccc
Q psy8615         118 SFNTYVLMN  126 (128)
Q Consensus       118 ~~~~~~~~~  126 (128)
                      +|+++.--|
T Consensus        84 ~~A~~~~~n   92 (93)
T d1x5ua1          84 NKASAHNKN   92 (93)
T ss_dssp             EETTTTSCC
T ss_pred             EEcCCCCCC
Confidence            999876544

>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=99.92  E-value=1.1e-25  Score=136.40  Aligned_cols=83  Identities=19%  Similarity=0.229  Sum_probs=78.6

Q ss_pred             CeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEeccc
Q psy8615          44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNTY  122 (128)
Q Consensus        44 ~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~~  122 (128)
                      .+|||+|||++++|++|+++|++||+|.++++++|+.||+++|||||+|.+.+ +|..|++.||++ ++|++|+|.|+++
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~-~A~~a~~~l~~~~l~g~~l~V~~A~~   80 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDIN-VTDQAIAGLNGMQLGDKKLLVQRASV   80 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSH-HHHHHHHTSSSCCCSSSCCEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHH-HHHHHHHHhCCCEECCEEEEEEECCC
Confidence            47999999999999999999999999999999999999999999999998888 999999999999 9999999999998


Q ss_pred             ccccc
Q psy8615         123 VLMNV  127 (128)
Q Consensus       123 ~~~~~  127 (128)
                      ..-|+
T Consensus        81 ~~~~a   85 (85)
T d2u2fa_          81 GAKNA   85 (85)
T ss_dssp             CCCCC
T ss_pred             CCCCc
Confidence            76653

>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=99.92  E-value=2e-25  Score=133.71  Aligned_cols=77  Identities=23%  Similarity=0.298  Sum_probs=73.8

Q ss_pred             eEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEeccc
Q psy8615          45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNTY  122 (128)
Q Consensus        45 ~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~~  122 (128)
                      +|||+|||++++|++|+++|++||+|.+++++.|+.||+++|||||+|.+.+ +|..|++.|||. ++|++|+|+|++.
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 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPA-DAERALDTMNFDVIKGKPVRIMWSQR   79 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHH-HHHHHHTTSTTCEETTEECEEEECCC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHH-HHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            6999999999999999999999999999999999999999999999997777 999999999999 9999999999863

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

Probab=99.92  E-value=7.7e-25  Score=143.52  Aligned_cols=81  Identities=19%  Similarity=0.326  Sum_probs=76.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      ...++|||+|||+++++++|+++|++||.|.+++++.|+.||+++|||||+|.+.+ +|.+|++.|||+ ++|+.|+|.|
T Consensus        40 ~~~~~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          40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGS-SAQQAIAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHH-HHHHHHHHTTTEECSSCEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHH-HHHHHHHHhCCCEECCEEEEEEE
Confidence            33568999999999999999999999999999999999999999999999997777 999999999999 9999999999


Q ss_pred             ccc
Q psy8615         120 NTY  122 (128)
Q Consensus       120 ~~~  122 (128)
                      +++
T Consensus       119 a~~  121 (139)
T d1u6fa1         119 AAS  121 (139)
T ss_dssp             SSC
T ss_pred             cCC
Confidence            864

>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=99.92  E-value=2.3e-25  Score=135.97  Aligned_cols=81  Identities=19%  Similarity=0.258  Sum_probs=76.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      ..++|||+|||+++++++|+++|++||+|.+++++.|+.+|+++|||||+|.+.+ +|+.|++.+|+. ++|+.|+|.|+
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~-~A~~ai~~l~~~~i~g~~l~v~~a   82 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE-DAAAAIDNMNESELFGRTIRVNLA   82 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHH-HHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHH-HHHHHHHHcCCCEECCEEEEEEEe
Confidence            3568999999999999999999999999999999999999999999999998777 999999999999 99999999999


Q ss_pred             ccc
Q psy8615         121 TYV  123 (128)
Q Consensus       121 ~~~  123 (128)
                      ++.
T Consensus        83 ~p~   85 (89)
T d2cqba1          83 KPM   85 (89)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            864

>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=99.92  E-value=1.2e-24  Score=131.64  Aligned_cols=80  Identities=18%  Similarity=0.363  Sum_probs=73.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCC--eEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQ--SFLK  116 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~--~~l~  116 (128)
                      +.+.++|||+|||++++|++|+++|++||.|.++++++|+.+|+++|||||+|.+.+ +|..|++.|||. +.|  ++|+
T Consensus         3 ~~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~-~A~~Ai~~l~g~~~~g~~~~l~   81 (85)
T d1b7fa2           3 SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKRE-EAQEAISALNNVIPEGGSQPLS   81 (85)
T ss_dssp             TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHH-HHHHHHHHHTTCCCTTCSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHH-HHHHHHHHHCCCEeCCCCeEEE
Confidence            345788999999999999999999999999999999999999999999999998777 999999999998 644  8999


Q ss_pred             EEec
Q psy8615         117 PSFN  120 (128)
Q Consensus       117 V~~~  120 (128)
                      |+|+
T Consensus        82 V~~A   85 (85)
T d1b7fa2          82 VRLA   85 (85)
T ss_dssp             EEEC
T ss_pred             EEEC
Confidence            9985

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.91  E-value=1.2e-24  Score=133.71  Aligned_cols=81  Identities=11%  Similarity=0.179  Sum_probs=76.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      ...++|||+|||+++++++|+++|++||+|.+++++.++.+|.++|||||+|.+.+ +|..|++.|||. ++|++|+|.|
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~-~A~~Ai~~l~g~~~~gr~i~V~~   83 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRA-DAENAMRYINGTRLDDRIIRTDW   83 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHH-HHHHHHHHTTTSEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHH-HHHHHHHHhCCCEECCEEEEEEE
Confidence            45789999999999999999999999999999999999999999999999997777 999999999999 9999999999


Q ss_pred             ccc
Q psy8615         120 NTY  122 (128)
Q Consensus       120 ~~~  122 (128)
                      +..
T Consensus        84 a~~   86 (93)
T d1h2vz_          84 DAG   86 (93)
T ss_dssp             ESC
T ss_pred             cCC
Confidence            864

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.91  E-value=1e-24  Score=132.03  Aligned_cols=78  Identities=19%  Similarity=0.413  Sum_probs=72.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCC--eEEEEE
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQ--SFLKPS  118 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~--~~l~V~  118 (128)
                      ++++|||+|||+++++++|+++|++||+|.+++++.|+.+|+++|||||+|.+.+ +|..|++.|||. ++|  ++|+|+
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~-~a~~Ai~~lng~~~~G~~~~i~V~   83 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRI-EAEEAIKGLNGQKPSGATEPITVK   83 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHH-HHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHH-HHHHHHHHhCCCEeCCCCEEEEEE
Confidence            4689999999999999999999999999999999999999999999999997777 999999999999 776  669999


Q ss_pred             ec
Q psy8615         119 FN  120 (128)
Q Consensus       119 ~~  120 (128)
                      |+
T Consensus        84 ~A   85 (85)
T d1fxla2          84 FA   85 (85)
T ss_dssp             EC
T ss_pred             eC
Confidence            85

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.91  E-value=1.5e-24  Score=134.61  Aligned_cols=81  Identities=20%  Similarity=0.271  Sum_probs=76.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      ..++|||+|||+++++++|+++|++||.|.+++++.|+.||+++|||||+|.+.+ +|..|++.||+. ++|+.|+|.++
T Consensus         7 ~~~~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_           7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPE-HAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHH-HHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHH-HHHHHHHHcCCCEECCEEEEEEEC
Confidence            3668999999999999999999999999999999999999999999999997777 999999999999 99999999998


Q ss_pred             ccc
Q psy8615         121 TYV  123 (128)
Q Consensus       121 ~~~  123 (128)
                      ++.
T Consensus        86 ~~~   88 (99)
T d1whwa_          86 TIK   88 (99)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            864

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.91  E-value=2.6e-24  Score=129.58  Aligned_cols=75  Identities=20%  Similarity=0.284  Sum_probs=71.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEE
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKP  117 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V  117 (128)
                      +.++|||+|||+++++++|+++|++||.|.+++++.++.+|+++|||||+|.+.+ +|..|++.||+. ++|+.|+|
T Consensus         8 ~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           8 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD-DAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHH-HHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHH-HHHHHHHHcCCCEECCEEeEC
Confidence            3578999999999999999999999999999999999999999999999997777 999999999999 99999987

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.90  E-value=1.3e-24  Score=130.32  Aligned_cols=79  Identities=14%  Similarity=0.193  Sum_probs=68.4

Q ss_pred             CeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEeccc
Q psy8615          44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNTY  122 (128)
Q Consensus        44 ~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~~  122 (128)
                      |+|||+|||+++++++|+++|++||.|..+.++.+..+|+++|||||+|.+.+ +|.+|++.|||. ++|+.|+|+|++|
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e-~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKE-DARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHH-HHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHH-HHHHHHHHhCCCEECCEEEEEEEccC
Confidence            68999999999999999999999999999988888888999999999997777 999999999999 9999999999987


Q ss_pred             c
Q psy8615         123 V  123 (128)
Q Consensus       123 ~  123 (128)
                      .
T Consensus        81 ~   81 (81)
T d2ghpa1          81 L   81 (81)
T ss_dssp             C
T ss_pred             c
Confidence            3

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.90  E-value=3.7e-24  Score=133.84  Aligned_cols=82  Identities=20%  Similarity=0.286  Sum_probs=75.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCcCCCeEEEEEe
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDYLGQSFLKPSF  119 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~~~~~~l~V~~  119 (128)
                      +...++|||+|||++++|++|+++|++||.|.+++++.|+.||+++|||||+|.+.+ +|.+|++.+|+.++|+.|+|.|
T Consensus         7 d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~-~A~~Ai~~~~~~l~Gr~l~V~~   85 (103)
T d2cqda1           7 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRA-AAERACKDPNPIIDGRKANVNL   85 (103)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHH-HHHHHHTCSSCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHH-HHHHHHHHCCCcCCCEEEEEEE
Confidence            444678999999999999999999999999999999999999999999999997777 9999999998779999999999


Q ss_pred             ccc
Q psy8615         120 NTY  122 (128)
Q Consensus       120 ~~~  122 (128)
                      +..
T Consensus        86 a~~   88 (103)
T d2cqda1          86 AYL   88 (103)
T ss_dssp             STT
T ss_pred             cCC
Confidence            764

>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=99.90  E-value=1.8e-24  Score=128.68  Aligned_cols=75  Identities=25%  Similarity=0.381  Sum_probs=70.6

Q ss_pred             CeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        44 ~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      |+|||+|||+++++++|+++|++||.|.+++++.|+.||+++|||||+|.+.+ +|.+|++ +|+. ++|+.|+|..+
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 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQA-GVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTT-HHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHH-HHHHHHH-cCCCEECCeEEEEEEC
Confidence            68999999999999999999999999999999999999999999999998777 9999997 6888 99999998764

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.90  E-value=1.7e-23  Score=128.54  Aligned_cols=85  Identities=22%  Similarity=0.353  Sum_probs=76.8

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEE
Q psy8615          38 LTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLK  116 (128)
Q Consensus        38 ~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~  116 (128)
                      ......++|||+|||+++++++|+++|++||+|.+++++.++.  .++|||||+|.+.+ +|.+|++.||+. ++|+.|+
T Consensus         6 ~~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~--~~kg~afV~f~~~~-~a~~Ai~~l~~~~~~g~~l~   82 (93)
T d2cq3a1           6 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSA-DADRAREKLHGTVVEGRKIE   82 (93)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHH-HHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeecccccccc--CCcceeEEEECCHH-HHHHHHHHcCCCEECCEEEE
Confidence            3445577899999999999999999999999999999998874  47999999998777 999999999999 9999999


Q ss_pred             EEecccccc
Q psy8615         117 PSFNTYVLM  125 (128)
Q Consensus       117 V~~~~~~~~  125 (128)
                      |.|+++..+
T Consensus        83 V~~A~~r~~   91 (93)
T d2cq3a1          83 VNNATARVM   91 (93)
T ss_dssp             EEECCSSCC
T ss_pred             EEecCcCCC
Confidence            999998765

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.90  E-value=6.5e-24  Score=130.70  Aligned_cols=82  Identities=13%  Similarity=0.243  Sum_probs=74.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecC-CCCCcceEEEEEEecCHHHHHHHHHHh-cCc-CCCeEEEE
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDK-QNNRSKCFGTIIFMRKFFILTIRFDTA-NDY-LGQSFLKP  117 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~-~tg~~~g~~fv~f~~~~~~a~~Ai~~l-~g~-~~~~~l~V  117 (128)
                      ...++|||+|||+++++++|+++|++||.|.+++++.++ .+|+++|||||+|.+.+ +|..|++.| |+. ++|+.|+|
T Consensus         6 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~-~A~~Ai~~l~~~~~~~Gr~l~V   84 (94)
T d2cpha1           6 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQ-DAKKAFNALCHSTHLYGRRLVL   84 (94)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHH-HHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHH-HHHHHHHHccCCcEECCEEEEE
Confidence            346789999999999999999999999999999998875 47999999999997777 999999998 888 99999999


Q ss_pred             Eecccc
Q psy8615         118 SFNTYV  123 (128)
Q Consensus       118 ~~~~~~  123 (128)
                      .|++..
T Consensus        85 ~~A~~~   90 (94)
T d2cpha1          85 EWADSE   90 (94)
T ss_dssp             EECCCC
T ss_pred             EEcCCC
Confidence            999864

>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=99.90  E-value=6.7e-24  Score=128.21  Aligned_cols=80  Identities=16%  Similarity=0.184  Sum_probs=72.9

Q ss_pred             EEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCC---CcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecc
Q psy8615          46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNN---RSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNT  121 (128)
Q Consensus        46 l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg---~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~  121 (128)
                      |||+|||+++++++|+++|++||.|.+++++.++.++   .++|||||+|.+.+ +|.+|++.|||. ++|+.|+|.|++
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~-~A~~A~~~~~~~~~~g~~i~V~~a~   79 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPE-QAQKALKQLQGHTVDGHKLEVRISE   79 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHH-HHHHHHHHSTTCEETTEECEEECSS
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHH-HHHHHHHHhCCCEECCEEEEEEECC
Confidence            7999999999999999999999999999999988765   46899999998777 999999999999 999999999987


Q ss_pred             ccccc
Q psy8615         122 YVLMN  126 (128)
Q Consensus       122 ~~~~~  126 (128)
                      +..-+
T Consensus        80 ~~~kp   84 (85)
T d2cpfa1          80 RATKP   84 (85)
T ss_dssp             CSSCC
T ss_pred             CCCCC
Confidence            65433

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.90  E-value=1.8e-23  Score=127.84  Aligned_cols=81  Identities=21%  Similarity=0.297  Sum_probs=73.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCcCCCeEEEEEec
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDYLGQSFLKPSFN  120 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~~~~~~l~V~~~  120 (128)
                      ...++|||+|||+++++++|+++|++||.|.+++++.|+.||+++|||||+|.+.+ +|.+|++..+ .++|+.|.|.++
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~-~a~~al~~~~-~l~Gr~i~v~~a   83 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYE-TQVKVMSQRH-MIDGRWCDCKLP   83 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHH-HHHHHHHSCE-EETTEEEEEECC
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHH-HHHHHHhcCC-ccCCEEeEEEeC
Confidence            34679999999999999999999999999999999999999999999999997776 9999998433 389999999998


Q ss_pred             ccc
Q psy8615         121 TYV  123 (128)
Q Consensus       121 ~~~  123 (128)
                      ++.
T Consensus        84 ~~k   86 (90)
T d2cqga1          84 NSK   86 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            763

>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=99.90  E-value=4.5e-24  Score=133.09  Aligned_cols=78  Identities=17%  Similarity=0.238  Sum_probs=73.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecc
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNT  121 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~  121 (128)
                      .++|||+|||+++++++|+++|++||.|.+++++.|+.||+++|||||+|.+.+ +|..|++ |||. ++|+.|+|.+++
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e-~a~~A~~-l~g~~~~G~~l~V~~a~   95 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQ-SVPLAIG-LTGQRLLGVPIIVQASQ   95 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGG-GHHHHHH-HTTEEETTEEEEEEEHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHH-HHHHHHH-HCCCEECCEEEEEEECC
Confidence            468999999999999999999999999999999999999999999999998877 9999995 9999 999999999976


Q ss_pred             c
Q psy8615         122 Y  122 (128)
Q Consensus       122 ~  122 (128)
                      +
T Consensus        96 ~   96 (101)
T d2cq4a1          96 A   96 (101)
T ss_dssp             H
T ss_pred             C
Confidence            4

>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=99.90  E-value=1.6e-23  Score=130.47  Aligned_cols=85  Identities=20%  Similarity=0.277  Sum_probs=77.0

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEE
Q psy8615          38 LTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLK  116 (128)
Q Consensus        38 ~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~  116 (128)
                      ..+.+.++|||+|||.++++++|+++|++||.|..+.+..+. +++++|||||+|.+.+ +|.+|++.|||. +.|+++.
T Consensus        13 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~-~A~~Ai~~lng~~i~gr~~~   90 (101)
T d1x5oa1          13 QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTE-KCEAVIGHFNGKFIKTPPGV   90 (101)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHH-HHHHHHHHHBTCCCCCCTTS
T ss_pred             cccCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHH-HHHHHHHHhCCCEECCcCCc
Confidence            344557899999999999999999999999999999988885 6999999999997777 999999999999 9999999


Q ss_pred             EEeccccc
Q psy8615         117 PSFNTYVL  124 (128)
Q Consensus       117 V~~~~~~~  124 (128)
                      |.+++|..
T Consensus        91 v~~~~Pl~   98 (101)
T d1x5oa1          91 SAPTEPLL   98 (101)
T ss_dssp             CCCSSCBE
T ss_pred             cCCCCCcc
Confidence            99888754

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.90  E-value=5.3e-24  Score=126.88  Aligned_cols=75  Identities=28%  Similarity=0.325  Sum_probs=71.1

Q ss_pred             eEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecc
Q psy8615          45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNT  121 (128)
Q Consensus        45 ~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~  121 (128)
                      +|||+|||+++++++|+++|++||+|.++++..++ +|+++|||||+|.+.+ +|..|++.|||. ++|++|+|+|.+
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-SGRSLGTADVHFERKA-DALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHH-HHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHH-HHHHHHHHhCCCEECCEEEEEEEee
Confidence            69999999999999999999999999999999987 5999999999997777 999999999999 999999999976

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.89  E-value=4.3e-24  Score=130.34  Aligned_cols=81  Identities=17%  Similarity=0.244  Sum_probs=76.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      +..+|||+|||+++++++|+++|++||.|.++.++.++.+|.++|||||+|.+.+ +|+.|++.|||+ ++|+.|+|.|+
T Consensus         4 ~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~-~a~~Ai~~l~~~~~~g~~l~V~~a   82 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENID-DAKDAMMAMNGKSVDGRQIRVDQA   82 (90)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHH-HHHHHHHHHTTCCTTSCCCEEEEE
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHH-HHHHHHHHcCCCEECCEEEEEEEc
Confidence            4678999999999999999999999999999999999999999999999997777 999999999999 99999999998


Q ss_pred             ccc
Q psy8615         121 TYV  123 (128)
Q Consensus       121 ~~~  123 (128)
                      ++.
T Consensus        83 ~~~   85 (90)
T d1x5sa1          83 GKS   85 (90)
T ss_dssp             ECC
T ss_pred             CCC
Confidence            764

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.89  E-value=1.7e-23  Score=127.81  Aligned_cols=82  Identities=13%  Similarity=0.192  Sum_probs=74.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      +.+.++|||+|||.++++++|+++|++||+|.+++++.|+.++  +|||||+|.+.+ +|..|++.+||. ++|+.|+|.
T Consensus         5 ~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~-~A~~A~~~l~~~~~~g~~i~v~   81 (90)
T d2cqia1           5 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHR-DAAAALAAMNGRKILGKEVKVN   81 (90)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHH-HHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHH-HHHHHHHHcCCCEECCEEEEEE
Confidence            4457799999999999999999999999999999999987644  899999997777 999999999999 999999999


Q ss_pred             eccccc
Q psy8615         119 FNTYVL  124 (128)
Q Consensus       119 ~~~~~~  124 (128)
                      |+++..
T Consensus        82 ~a~~~~   87 (90)
T d2cqia1          82 WATTPS   87 (90)
T ss_dssp             ECCCTT
T ss_pred             EcCCCC
Confidence            998753

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.89  E-value=7.7e-24  Score=132.45  Aligned_cols=79  Identities=16%  Similarity=0.281  Sum_probs=74.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecc
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNT  121 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~  121 (128)
                      .++|||+|||+++++++|+++|++||.|.+++++.++.||+++|||||+|.+.+ +|..|++.||+. ++|+.|+|.|++
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~-~a~~ai~~l~~~~~~g~~i~V~~a~   86 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE-TALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHH-HHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHH-HHHHHHHHcCCCEECCEEEEEEECC
Confidence            457999999999999999999999999999999999999999999999997777 999999999999 999999999976


Q ss_pred             c
Q psy8615         122 Y  122 (128)
Q Consensus       122 ~  122 (128)
                      +
T Consensus        87 ~   87 (104)
T d1p1ta_          87 S   87 (104)
T ss_dssp             C
T ss_pred             C
Confidence            5

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.89  E-value=6.8e-24  Score=127.64  Aligned_cols=77  Identities=25%  Similarity=0.333  Sum_probs=71.9

Q ss_pred             EEEcCCCCCCCHHHHHhhhcCCCceEEE-EEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecccc
Q psy8615          46 LFIYHLPPEFSDADLASMFGPFGTVLSA-KVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNTYV  123 (128)
Q Consensus        46 l~V~nLp~~~~e~~l~~~f~~~G~i~~~-~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~~~  123 (128)
                      |||+|||+++++++|+++|++||.|.++ +++.++.||+++|||||+|.+.+ +|..|++.|||. ++|++|+|+|+++.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~-~a~~Ai~~~~g~~~~gr~l~v~~a~~k   79 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFD-ASDAAIEAMNGQYLCNRPITVSYAFKK   79 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHH-HHHHHHHTTTTCEETTEECEEEESCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHH-HHHHHHHhCCCcEECCEEEEEEEecCC
Confidence            7999999999999999999999999764 78999999999999999998777 999999999999 99999999998763

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.88  E-value=7.8e-23  Score=126.25  Aligned_cols=83  Identities=20%  Similarity=0.255  Sum_probs=75.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhc------Cc-CCC
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTAN------DY-LGQ  112 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~------g~-~~~  112 (128)
                      ..++++|||+|||+++++++|+++|++||.+.++.++.++.+++++|||||+|.+.+ +|.+|++.+|      |. +.|
T Consensus         5 ~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~-~a~~ai~~l~~~~~~~g~~~~g   83 (98)
T d1x4ha1           5 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQE-AAQKCLAAASLEAEGGGLKLDG   83 (98)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHH-HHHHHHHHHCTTTTTCCEESSS
T ss_pred             CCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHH-HHHHHHHHcccccccCCcEECC
Confidence            345789999999999999999999999999999999999999999999999997777 9999999987      56 889


Q ss_pred             eEEEEEecccc
Q psy8615         113 SFLKPSFNTYV  123 (128)
Q Consensus       113 ~~l~V~~~~~~  123 (128)
                      +.|+|+|+++.
T Consensus        84 r~l~v~~a~~k   94 (98)
T d1x4ha1          84 RQLKVDLAVTR   94 (98)
T ss_dssp             CEEEEECCCCC
T ss_pred             EEEEEEECCCC
Confidence            99999998763

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=2.2e-23  Score=130.34  Aligned_cols=78  Identities=21%  Similarity=0.286  Sum_probs=72.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecc
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNT  121 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~  121 (128)
                      .++|||+|||+++++++|+++|++||.|.++.++.|+.+++++|||||+|.+.+ +|..|++ +++. ++|+.|+|.+++
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~-~a~~al~-~~~~~l~G~~i~V~~a~   97 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMA-EVDAAMA-ARPHSIDGRVVEPKRAV   97 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHH-HHHHHHT-SCSEEETTEEEEEECCS
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHH-HHHHHHH-hCCCeECCEEEEEEECc
Confidence            479999999999999999999999999999999999999999999999997777 9998885 7888 999999999987


Q ss_pred             c
Q psy8615         122 Y  122 (128)
Q Consensus       122 ~  122 (128)
                      +
T Consensus        98 ~   98 (103)
T d1x4ba1          98 A   98 (103)
T ss_dssp             S
T ss_pred             c
Confidence            6

>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=99.88  E-value=7.1e-23  Score=123.55  Aligned_cols=76  Identities=25%  Similarity=0.330  Sum_probs=70.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      .++|||+|||+++++++|+++|++||.|.+++++.|+.||+++|||||+|.+.+ +|.+|++ +++. +.|+.|+|..+
T Consensus         6 ~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~-~a~~ai~-~~~~~i~Gr~i~V~~A   82 (84)
T d1l3ka1           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE-EVDAAMN-ARPHKVDGRVVEPKRA   82 (84)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHH-HHHHHHH-TCSCEETTEECEEEEC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHH-HHHHHHH-hCCCEECCEEEEEEee
Confidence            468999999999999999999999999999999999999999999999997766 9999997 4777 99999999765

>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=99.88  E-value=2.3e-23  Score=126.24  Aligned_cols=80  Identities=21%  Similarity=0.321  Sum_probs=68.8

Q ss_pred             CCCeEEEcCCCCCCC-HHHHHhhhcCCCceEEEEEEe-cCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          42 EGANLFIYHLPPEFS-DADLASMFGPFGTVLSAKVFI-DKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~-e~~l~~~f~~~G~i~~~~~~~-~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ++++|||+|||++++ |++|+++|++||.|.++++.. ++.+|+++|||||+|.+.+ +|..|++ ||+. ++|+.|+|+
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~-~a~~Al~-~n~~~~~gr~l~V~   80 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKD-SAERALQ-MNRSLLGNREISVS   80 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHH-HHHHHGG-GTTEEETTEEEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHH-HHHHHHh-cCCCEECCEEEEEE
Confidence            478999999999976 566999999999999999876 4578999999999997766 9999995 9999 999999999


Q ss_pred             ecccc
Q psy8615         119 FNTYV  123 (128)
Q Consensus       119 ~~~~~  123 (128)
                      |+++.
T Consensus        81 ~a~~k   85 (86)
T d2ghpa3          81 LADKK   85 (86)
T ss_dssp             ECCCC
T ss_pred             EcCCC
Confidence            99874

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=4.2e-23  Score=122.06  Aligned_cols=72  Identities=25%  Similarity=0.442  Sum_probs=67.6

Q ss_pred             eEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        45 ~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      +|||+|||++++|++|+++|++||+|.+++++.|+.||+++|||||+|.+.+ +|++|++ +++. ++|+.|+|.
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~-~a~~Al~-~~~~~l~Gr~i~V~   73 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESE-SVDKVMD-QKEHKLNGKVIDPK   73 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHH-HHHHHHH-TCCCCBTTBCCEEC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHH-HHHHHHh-cCCCEECCCEEEee
Confidence            5899999999999999999999999999999999999999999999997777 9999997 6877 999999885

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=8.1e-23  Score=126.89  Aligned_cols=84  Identities=18%  Similarity=0.235  Sum_probs=75.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceE--------EEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-
Q psy8615          39 TGPEGANLFIYHLPPEFSDADLASMFGPFGTVL--------SAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-  109 (128)
Q Consensus        39 ~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~--------~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-  109 (128)
                      ++.+.++|||+|||+++++++|+++|++||.|.        .+.+..++.+|+++|||||+|.+.+ +|..|++.|||+ 
T Consensus         4 ~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~-~a~~Ai~~l~g~~   82 (101)
T d2cpea1           4 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPP-TAKAAVEWFDGKD   82 (101)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHH-HHHHHHHHHTTCE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHH-HHHHHHHHhCCCE
Confidence            345678999999999999999999999999874        5677888899999999999997777 999999999999 


Q ss_pred             CCCeEEEEEecccc
Q psy8615         110 LGQSFLKPSFNTYV  123 (128)
Q Consensus       110 ~~~~~l~V~~~~~~  123 (128)
                      ++|+.|+|+|+++.
T Consensus        83 ~~gr~i~V~~a~~~   96 (101)
T d2cpea1          83 FQGSKLKVSLARKK   96 (101)
T ss_dssp             ETTEECEEECSSCC
T ss_pred             ECCEEEEEEEcCCC
Confidence            99999999999764

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=3e-22  Score=119.22  Aligned_cols=76  Identities=9%  Similarity=0.160  Sum_probs=69.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      .++|||+|||+++++++|+++|++||.+..+++..++.+++++|||||+|.+.+ ++.+|+ .+|+. ++|+.|+|..+
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 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD-SVDKIV-IQKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHH-HHHHHH-HCSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHH-HHHHHH-HhCCCEECCEEEEEEEC
Confidence            368999999999999999999999999999999999999999999999997765 777777 58999 99999999753

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=7.4e-23  Score=124.64  Aligned_cols=78  Identities=24%  Similarity=0.305  Sum_probs=71.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecc
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNT  121 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~  121 (128)
                      ..+|||+|||+++++++|+++|++||.|.+++++.++.  .++|||||+|++.+ +|..|++.|||. ++|+.|+|+|++
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~--~~kg~afV~f~~~~-~A~~Ai~~l~g~~~~g~~i~V~~a~   84 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN--GSKGYGFVHFETQE-AAERAIEKMNGMLLNDRKVFVGRFK   84 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTT--BCCSCEEEEESCHH-HHHHHTTSSSEEEETTEEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecC--CCcceeEEEECCHH-HHHHHHHHcCCCEECCEEEEEEECC
Confidence            45799999999999999999999999999999998874  47899999997777 999999999999 999999999988


Q ss_pred             cc
Q psy8615         122 YV  123 (128)
Q Consensus       122 ~~  123 (128)
                      +.
T Consensus        85 ~~   86 (89)
T d1cvja2          85 SR   86 (89)
T ss_dssp             CT
T ss_pred             CC
Confidence            63

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=2.9e-23  Score=122.87  Aligned_cols=74  Identities=22%  Similarity=0.350  Sum_probs=68.0

Q ss_pred             eEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        45 ~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      +|||+|||+++++++|+++|++||.|.+++++.|+.||+++|||||+|++.+ +|.+|++. ++. ++|+.++|..+
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 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEE-PVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSH-HHHHHTTC-SSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHH-HHHHHHhh-CCCEECCEEeEEEEC
Confidence            6999999999999999999999999999999999999999999999998887 99999976 555 99999988753

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=4e-22  Score=126.31  Aligned_cols=77  Identities=14%  Similarity=0.291  Sum_probs=70.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      ..++|||+|||.++++++|+++|++||.|.+|++..+   +.++|||||+|.+.+ +|..|++.|||+ ++|+.|+|.|.
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~-~A~~Ai~~l~g~~~~gr~l~V~~a   81 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIF-DAKNACDHLSGFNVCNRYLVVLYY   81 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHH-HHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHH-HHHHHHHHhCCCEECCEEEEEEEc
Confidence            3678999999999999999999999999999988754   677999999997777 999999999999 99999999997


Q ss_pred             cc
Q psy8615         121 TY  122 (128)
Q Consensus       121 ~~  122 (128)
                      +.
T Consensus        82 ~~   83 (114)
T d2f9da1          82 NA   83 (114)
T ss_dssp             CH
T ss_pred             CC
Confidence            64

>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=99.87  E-value=3.2e-22  Score=121.86  Aligned_cols=76  Identities=17%  Similarity=0.274  Sum_probs=68.9

Q ss_pred             CCCeEEEcCCCCCCCHHHH---HhhhcCCCceEEEEEEecCCCCCcc---eEEEEEEecCHHHHHHHHHHhcCc-CCCeE
Q psy8615          42 EGANLFIYHLPPEFSDADL---ASMFGPFGTVLSAKVFIDKQNNRSK---CFGTIIFMRKFFILTIRFDTANDY-LGQSF  114 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l---~~~f~~~G~i~~~~~~~~~~tg~~~---g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~  114 (128)
                      ....|||+|||+++++++|   +++|++||+|.++.++.++.++.++   |||||+|++.+ +|..|++.|||. ++|++
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~-~A~~Ai~~lng~~~~gr~   85 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSE-DALRAIQCVNNVVVDGRT   85 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHH-HHHHHHHHHTTEEETTEE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccch-hHHHHHHHhCCCEECCEE
Confidence            3567999999999999999   7789999999999999998776654   89999997777 999999999999 99999


Q ss_pred             EEEE
Q psy8615         115 LKPS  118 (128)
Q Consensus       115 l~V~  118 (128)
                      |+|+
T Consensus        86 lkvS   89 (89)
T d2cpia1          86 LKAS   89 (89)
T ss_dssp             EEEE
T ss_pred             EEEC
Confidence            9986

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=2.3e-22  Score=124.16  Aligned_cols=76  Identities=16%  Similarity=0.314  Sum_probs=70.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      +..++|||+|||.++++++|+++|++||.|.+++++.+      +|||||+|++.+ +|..|++.|||. ++|+.|+|+|
T Consensus        16 ~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~-~A~~Ai~~l~~~~i~g~~l~v~~   88 (96)
T d1x4ga1          16 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHE-SAAHAIVSVNGTTIEGHVVKCYW   88 (96)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHH-HHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHH-HHHHHHHHhCCCEECCEEEEEEE
Confidence            44678999999999999999999999999999999865      689999997777 999999999999 9999999999


Q ss_pred             cccc
Q psy8615         120 NTYV  123 (128)
Q Consensus       120 ~~~~  123 (128)
                      +++.
T Consensus        89 ak~~   92 (96)
T d1x4ga1          89 GKES   92 (96)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9874

>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=99.86  E-value=6.7e-22  Score=121.68  Aligned_cols=79  Identities=15%  Similarity=0.258  Sum_probs=70.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ....++|||+|||+++++++|+++|++||.|..+++..+   +.++|||||+|++.+ +|..|++.||++ ++|+.|+|+
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e-~a~~Ai~~l~g~~~~g~~l~V~   86 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPR-DAEDAVYGRDGYDYDGYRLRVE   86 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHH-HHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHH-HHHHHHHHhCCCEECCEEEEEE
Confidence            345679999999999999999999999999999886544   567899999997777 999999999999 999999999


Q ss_pred             eccc
Q psy8615         119 FNTY  122 (128)
Q Consensus       119 ~~~~  122 (128)
                      |++.
T Consensus        87 ~a~~   90 (95)
T d1x4aa1          87 FPRS   90 (95)
T ss_dssp             CCCC
T ss_pred             eccC
Confidence            9875

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.86  E-value=1.5e-22  Score=119.26  Aligned_cols=74  Identities=22%  Similarity=0.321  Sum_probs=69.4

Q ss_pred             eEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        45 ~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      +|||+|||++++|++|+++|++||.+..+.++.++.+|.++|||||+|.+.+ +|..|++ +|+. ++|+.|+|+++
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~-~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESED-IVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHH-HHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHH-HHHHHHh-cCCCEECCeEEEEEEC
Confidence            5899999999999999999999999999999999999999999999997766 9999986 9999 99999999874

>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=99.86  E-value=5.4e-23  Score=127.98  Aligned_cols=81  Identities=22%  Similarity=0.282  Sum_probs=76.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      +.++|||+|||.++++++|+++|++||.|..+.+..+..+|+++|||||+|.+.+ +|..|++.|||. ++|++|+|+|+
T Consensus        17 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          17 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKE-IAWQALHLVNGYKLYGKILVIEFG   95 (102)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHH-HHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHH-HHHHHHHHhCCCEECCEEEEEEeC
Confidence            4678999999999999999999999999999999998888999999999997777 999999999999 99999999999


Q ss_pred             ccc
Q psy8615         121 TYV  123 (128)
Q Consensus       121 ~~~  123 (128)
                      ++.
T Consensus        96 k~k   98 (102)
T d2cpxa1          96 KNK   98 (102)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            863

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.86  E-value=7e-22  Score=118.80  Aligned_cols=78  Identities=15%  Similarity=0.290  Sum_probs=69.4

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-C-CCeEE
Q psy8615          38 LTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-L-GQSFL  115 (128)
Q Consensus        38 ~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~-~~~~l  115 (128)
                      .+.++.++|||+|||.++++++|+++|++||.|.+++++.++     +|||||+|.+.+ +|..|++.|||+ + +|++|
T Consensus         3 ~~~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~-~A~~A~~~l~g~~~~~~~~i   76 (83)
T d2b0ga1           3 TEQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFTTEL-QSNAAKEALQGFKITPTHAM   76 (83)
T ss_dssp             CCCSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT-----CSCEEEEESSHH-HHHHHHHHHTTCBSSTTCBC
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc-----ceeEEEecCCHH-HHHHHHHHhCCcEeCCCcEE
Confidence            345567899999999999999999999999999999987543     689999998777 999999999998 6 57999


Q ss_pred             EEEecc
Q psy8615         116 KPSFNT  121 (128)
Q Consensus       116 ~V~~~~  121 (128)
                      +|+|+|
T Consensus        77 ~v~~ak   82 (83)
T d2b0ga1          77 KITFAK   82 (83)
T ss_dssp             EEEECC
T ss_pred             EEEEec
Confidence            999987

>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=99.86  E-value=3e-22  Score=117.31  Aligned_cols=70  Identities=26%  Similarity=0.437  Sum_probs=66.6

Q ss_pred             EEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEE
Q psy8615          46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLK  116 (128)
Q Consensus        46 l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~  116 (128)
                      |||+|||+++++++|+++|++||.|.++++..++.++.++|||||+|.+.+ +|.+|++.|||. +.|+.||
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~-~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPS-AAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHH-HHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHH-HHHHHHHHhCCCEECCEECc
Confidence            799999999999999999999999999999999999999999999997777 999999999999 9998764

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.86  E-value=1.4e-21  Score=118.28  Aligned_cols=75  Identities=21%  Similarity=0.389  Sum_probs=69.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      ..++|||+|||.++++++|+++|++||.|.++++..+      +|||||+|++.+ +|..|++.|||. ++|+.|+|+|+
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~-~A~~A~~~l~g~~i~g~~l~V~~A   79 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRT-LAEIAKVELDNMPLRGKQLRVRFA   79 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSH-HHHHHHHHHTTCCBTTBCCEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHH-HHHHHHHHhCCCEECCEEEEEEEC
Confidence            3578999999999999999999999999999998755      679999998888 999999999999 99999999999


Q ss_pred             ccc
Q psy8615         121 TYV  123 (128)
Q Consensus       121 ~~~  123 (128)
                      ++.
T Consensus        80 ~~~   82 (86)
T d2cpja1          80 CHS   82 (86)
T ss_dssp             SCC
T ss_pred             CCc
Confidence            875

>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=99.85  E-value=2.5e-22  Score=123.81  Aligned_cols=80  Identities=11%  Similarity=0.122  Sum_probs=71.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCc-eEEEEEEecC-CCCCcceEEEEEEecCHHHHHHHHHHhcC--c-CCCeEEEE
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGT-VLSAKVFIDK-QNNRSKCFGTIIFMRKFFILTIRFDTAND--Y-LGQSFLKP  117 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~-i~~~~~~~~~-~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g--~-~~~~~l~V  117 (128)
                      .|+|||+|||.++++++|+++|++||+ |.+++++.|+ .+|+++|||||+|.+.+ +|..|++.|++  + ++|++|+|
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~-~A~~Ai~~l~~~~~~~~g~~i~V   79 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHR-AAAMARRKLMPGRIQLWGHQIAV   79 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHH-HHHHHHTTTTTCCSCBTTBCCEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHH-HHHHHHHHHcCCCeEECCEEEEE
Confidence            478999999999999999999999996 8999988875 46899999999998877 99999999975  3 78999999


Q ss_pred             Eecccc
Q psy8615         118 SFNTYV  123 (128)
Q Consensus       118 ~~~~~~  123 (128)
                      +|+++.
T Consensus        80 ~~A~p~   85 (96)
T d2disa1          80 DWAEPE   85 (96)
T ss_dssp             EESCSS
T ss_pred             EEcCCC
Confidence            999863

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.85  E-value=6.9e-22  Score=119.44  Aligned_cols=79  Identities=13%  Similarity=0.130  Sum_probs=69.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      +..+.|||+|||+++++++|+++|+.||.+.....+.+..+|+++|+|||+|.+.+ +|.+|++.||+. ++|++|+|++
T Consensus         7 p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e-~a~~Ai~~l~~~~l~gr~i~v~l   85 (86)
T d2cqpa1           7 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRD-EATAAVIDLNDRPIGSRKVKLVL   85 (86)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHH-HHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcH-HHHHHHHHcCCCEECCEEEEEEE
Confidence            44678999999999999999999999999877544455567999999999997777 999999999999 9999999987


Q ss_pred             c
Q psy8615         120 N  120 (128)
Q Consensus       120 ~  120 (128)
                      +
T Consensus        86 ~   86 (86)
T d2cqpa1          86 G   86 (86)
T ss_dssp             S
T ss_pred             C
Confidence            4

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=1.3e-21  Score=118.70  Aligned_cols=79  Identities=22%  Similarity=0.336  Sum_probs=69.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-C-CCeEEEEE
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-L-GQSFLKPS  118 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~-~~~~l~V~  118 (128)
                      ++.++|||+|||.++++++|+++|++||.|.++....+    +.+|||||+|++.+ +|.+|+..|||+ + .|+.|+|+
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~----~~~~~afV~f~~~~-~A~~A~~~l~~~~i~~g~~l~v~   82 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVE-EAVQALIDLHNHDLGENHHLRVS   82 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS----SSTTCEEEEESSHH-HHHHHHHHHTTCBSSSSCBCEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee----cccceeEEEECCHH-HHHHHHHhccCCEecCCCEEEEE
Confidence            34678999999999999999999999999988876544    45889999997777 999999999998 7 47999999


Q ss_pred             eccccc
Q psy8615         119 FNTYVL  124 (128)
Q Consensus       119 ~~~~~~  124 (128)
                      |+|..+
T Consensus        83 ~sk~~i   88 (88)
T d2adca2          83 FSKSTI   88 (88)
T ss_dssp             ECSSCC
T ss_pred             eCCCCC
Confidence            999764

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.85  E-value=7.1e-23  Score=125.29  Aligned_cols=80  Identities=19%  Similarity=0.089  Sum_probs=71.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ....++|||+|||+++++++|+++|++||.|.+++++.+ .+|+++|||||+|.+.+ +|.+|++ ||+. ++|+.|+|.
T Consensus        10 ~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e-~a~~Al~-~~g~~~~g~~i~V~   86 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAE-DLEKALE-LTGLKVFGNEIKLE   86 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHH-HHHHHHH-GGGEEETTEEEEEE
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHH-HHHHHHh-cCCcEECCEEEEEE
Confidence            344678999999999999999999999999999888655 56999999999997777 9999996 9999 999999999


Q ss_pred             eccc
Q psy8615         119 FNTY  122 (128)
Q Consensus       119 ~~~~  122 (128)
                      +++.
T Consensus        87 ~ak~   90 (91)
T d1fjeb1          87 KPKG   90 (91)
T ss_dssp             CCCC
T ss_pred             ecCC
Confidence            9874

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=3.1e-21  Score=116.50  Aligned_cols=77  Identities=13%  Similarity=0.068  Sum_probs=70.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecc
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNT  121 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~  121 (128)
                      .++|||+|||.++++++|+++|+.||+|.++++..++ +|+++|||||+|.+.+ +|.+|++ +++. ++|+.|+|.|++
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e-~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIE-SAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHH-HHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHH-HHHHHHH-HCCCEECCEEEEEEEcC
Confidence            5689999999999999999999999999999998876 6999999999997776 9999985 6888 999999999986


Q ss_pred             c
Q psy8615         122 Y  122 (128)
Q Consensus       122 ~  122 (128)
                      .
T Consensus        83 d   83 (85)
T d1zh5a2          83 D   83 (85)
T ss_dssp             G
T ss_pred             C
Confidence            4

>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=99.85  E-value=2.8e-21  Score=120.56  Aligned_cols=79  Identities=16%  Similarity=0.245  Sum_probs=68.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecC-CCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDK-QNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~-~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      +.++|||+|||+++++++|+++|++|| +.+++++.++ .+|+++|||||+|.+.+ +|++|+ .+|+. ++|+.|+|.|
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e-~a~~~~-~~~~~~~~gr~l~V~~   90 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLD-SLLSAL-SLNEESLGNKRIRVDV   90 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHH-HHHHHH-GGGTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHH-HHHHHH-HcCCCEECCEEEEEEE
Confidence            368999999999999999999999999 7778777665 46889999999997776 887555 69999 9999999999


Q ss_pred             cccc
Q psy8615         120 NTYV  123 (128)
Q Consensus       120 ~~~~  123 (128)
                      +++.
T Consensus        91 a~~~   94 (104)
T d1wi8a_          91 ADQA   94 (104)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8753

>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=99.85  E-value=3.2e-21  Score=119.35  Aligned_cols=74  Identities=14%  Similarity=0.264  Sum_probs=66.6

Q ss_pred             CCCCeEEEcCCC-CCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          41 PEGANLFIYHLP-PEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        41 ~~~~~l~V~nLp-~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ...++|||+||| ..+++++|+++|++||.|.++++        ++|||||+|++.+ +|.+|++.|||. +.|+.|+|.
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~-~A~~Ai~~lng~~~~g~~l~V~   83 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNER-NARAAVAGEDGRMIAGQVLDIN   83 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHH-HHHHHHHTTTTCEETTEECEEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHH-HHHHHHHHcCCCEECCEEEEEE
Confidence            446789999996 57889999999999999999987        3789999998777 999999999999 999999999


Q ss_pred             ecccc
Q psy8615         119 FNTYV  123 (128)
Q Consensus       119 ~~~~~  123 (128)
                      |+++.
T Consensus        84 ~a~~~   88 (98)
T d1wf2a_          84 LAAEP   88 (98)
T ss_dssp             ETTSC
T ss_pred             ECCCC
Confidence            99764

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=1.7e-21  Score=116.12  Aligned_cols=75  Identities=16%  Similarity=0.236  Sum_probs=67.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      .+++|||+|++  +++++|+++|++||.|.++++..+      +|||||+|++.+ +|..|++.|||. ++|+.|+|+|+
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~-~A~~Ai~~lng~~~~g~~l~V~~a   74 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKME-SADQAVAELNGTQVESVQLKVNIA   74 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHH-HHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccH-HHHHHHHHhCCCEECCEEEEEEEe
Confidence            46799999986  899999999999999999988643      679999997776 999999999999 99999999999


Q ss_pred             ccccc
Q psy8615         121 TYVLM  125 (128)
Q Consensus       121 ~~~~~  125 (128)
                      ++.+|
T Consensus        75 ~~~P~   79 (79)
T d2bz2a1          75 RKQPM   79 (79)
T ss_dssp             CSSCC
T ss_pred             cCCCC
Confidence            98876

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=7.5e-21  Score=118.36  Aligned_cols=85  Identities=12%  Similarity=0.207  Sum_probs=73.9

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeE
Q psy8615          36 KQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSF  114 (128)
Q Consensus        36 ~~~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~  114 (128)
                      .......+.+|||+|||++++|++|+++|+.|| +.++.++.+.. |+.+|||||+|.+.+ +|++|++ +|+. ++||.
T Consensus         8 ~~~~~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~~-g~~~G~afVeF~~~~-~a~~Al~-~~~~~i~gR~   83 (102)
T d1weza_           8 SSFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPD-GRVTGEADVEFATHE-DAVAAMA-KDKANMQHRY   83 (102)
T ss_dssp             SSCCCSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESSS-SCEEEEEEEECSSSH-HHHHHHT-TSSCCSSSSC
T ss_pred             CCCcCCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEecC-CcceEEEEEEECCHH-HHHHHHH-cCCCEECCEE
Confidence            334556678999999999999999999999998 45788888865 899999999998888 9999986 8999 99999


Q ss_pred             EEEEeccccc
Q psy8615         115 LKPSFNTYVL  124 (128)
Q Consensus       115 l~V~~~~~~~  124 (128)
                      |+|.|++..-
T Consensus        84 I~V~~s~~~~   93 (102)
T d1weza_          84 VELFLNSTAG   93 (102)
T ss_dssp             CEEEEECCCC
T ss_pred             EEEEEcCCCC
Confidence            9999988754

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.84  E-value=4.8e-21  Score=118.00  Aligned_cols=78  Identities=12%  Similarity=0.096  Sum_probs=69.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ..+.++|||+|||+++++++|+++|++||.|..++     .+|+++|||||+|.+.+ +|..|++.||+. ++|+.|+|.
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~-----~~~~~~~~afV~f~~~~-~A~~A~~~l~~~~~~gr~i~V~   86 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEA-DAEKNLEEKQGAEIDGRSVSLY   86 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEE-----ETTEEEEEEEEEESSHH-HHHHHHHHTTEEEETTEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeee-----ecCccccEEEEEeCCHH-HHHHHHHHcCCCEECCEEEEEE
Confidence            34467999999999999999999999999887653     35889999999997776 999999999999 999999999


Q ss_pred             ecccc
Q psy8615         119 FNTYV  123 (128)
Q Consensus       119 ~~~~~  123 (128)
                      |.++.
T Consensus        87 ~a~~k   91 (96)
T d1fjca_          87 YTGEK   91 (96)
T ss_dssp             ECSSS
T ss_pred             EeCCC
Confidence            99874

>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=99.83  E-value=2.2e-20  Score=116.57  Aligned_cols=83  Identities=12%  Similarity=0.119  Sum_probs=73.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ..+...|||+|||++++|++|+++|..+|.+....++.+..+++++|||||+|.+.+ +|.+|++ +|+. ++||.|+|.
T Consensus        12 ~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e-~a~~a~~-~~~~~i~gR~i~V~   89 (104)
T d1wg5a_          12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQE-IAEKALK-KHKERIGHRYIEIF   89 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHH-HHHHHHT-TTTCCSSSSCCEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHH-HHHHHHh-hCCCEEcceEEEEE
Confidence            344567999999999999999999999999988777777778999999999997777 9998885 8888 999999999


Q ss_pred             eccccc
Q psy8615         119 FNTYVL  124 (128)
Q Consensus       119 ~~~~~~  124 (128)
                      +.++.-
T Consensus        90 ~~~~~~   95 (104)
T d1wg5a_          90 KSSRAE   95 (104)
T ss_dssp             EECTTT
T ss_pred             ECCHHH
Confidence            988753

>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=99.83  E-value=9e-21  Score=114.48  Aligned_cols=74  Identities=14%  Similarity=0.095  Sum_probs=66.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecc
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNT  121 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~  121 (128)
                      .++|||+|||+++++++|+++|++||.+..+++.      +++|||||+|.+.+ +|..|++.|||. ++|+.|+|+|++
T Consensus         8 ~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~------~~rg~afV~f~~~~-~A~~Ai~~l~~~~i~g~~i~V~~ak   80 (86)
T d2cpda1           8 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNRE-DAVEAMKALNGKVLDGSPIEVTLAK   80 (86)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEE------ECSSEEEEEESSHH-HHHHHHHHHSSEEETTEEEEEECCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEc------cccEEEEEEeCCHH-HHHHHHHHcCCCEECCEEEEEEecc
Confidence            3589999999999999999999999998877653      45789999997777 999999999999 999999999998


Q ss_pred             cc
Q psy8615         122 YV  123 (128)
Q Consensus       122 ~~  123 (128)
                      |.
T Consensus        81 P~   82 (86)
T d2cpda1          81 PV   82 (86)
T ss_dssp             CC
T ss_pred             CC
Confidence            75

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=1.5e-20  Score=118.05  Aligned_cols=80  Identities=16%  Similarity=0.181  Sum_probs=71.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-C--CCeEEEEEe
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-L--GQSFLKPSF  119 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~--~~~~l~V~~  119 (128)
                      ..+|||+|||+++++++|+++|++||.|.++.+..++    .+|||||+|++.+ +|+.|++.|||. +  +++.|+|.|
T Consensus         7 ~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e-~A~~Ai~~ln~~~l~~~~~~l~v~~   81 (108)
T d2adba1           7 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPV-SAQHAKLSLDGQNIYNACCTLRIDF   81 (108)
T ss_dssp             EEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHH-HHHHHHHHHHSCCSSTTCCCCEEEE
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHH-HHHHHHHHHCCCEeccCCcEEEEEe
Confidence            4579999999999999999999999999999998775    3899999998777 999999999998 5  578999999


Q ss_pred             cccccccc
Q psy8615         120 NTYVLMNV  127 (128)
Q Consensus       120 ~~~~~~~~  127 (128)
                      +++.-+|+
T Consensus        82 s~~~~~~~   89 (108)
T d2adba1          82 SKLTSLNV   89 (108)
T ss_dssp             CSSCSCCC
T ss_pred             cCCccccc
Confidence            98865543

>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=99.82  E-value=9.2e-21  Score=119.23  Aligned_cols=74  Identities=12%  Similarity=0.123  Sum_probs=67.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecc
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNT  121 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~  121 (128)
                      .++|||+|||+++++++|+++|++||.|.+|.+.      .++|||||+|.+.+ +|.+|++.|||. +.|++|+|.|+.
T Consensus        10 ~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~------~~kg~afV~f~~~~-~A~~A~~~lng~~~~gr~l~v~~a~   82 (111)
T d1whxa_          10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP------EGGITAIVEFLEPL-EARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC------SSSSCEEEEESCHH-HHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCEEEEECCCCCCCHHHHHhhhhccCCccEEEee------ccCceEEEEEcCHH-HHHHHHHHHcCCccCCCeEEEEECC
Confidence            5789999999999999999999999999998763      34789999997777 999999999999 999999999986


Q ss_pred             cc
Q psy8615         122 YV  123 (128)
Q Consensus       122 ~~  123 (128)
                      ..
T Consensus        83 ~~   84 (111)
T d1whxa_          83 IG   84 (111)
T ss_dssp             TT
T ss_pred             CC
Confidence            54

>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=99.82  E-value=1.8e-20  Score=110.62  Aligned_cols=74  Identities=19%  Similarity=0.237  Sum_probs=65.9

Q ss_pred             CeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecc
Q psy8615          44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNT  121 (128)
Q Consensus        44 ~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~  121 (128)
                      ++|||+|||+++++++|+++|++||.|.++++..++.  ..+|||||+|++.+ +|.+|+ .+|+. ++|++|.|...|
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~--~~~~~afV~F~~~~-~a~~Al-~~~~~~i~g~~i~V~~~T   75 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFARYD-GALAAI-TKTHKVVGQNEIIVSHLT   75 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT--SSSEEEEEEESSHH-HHHHHH-TTTTCEETTEECEEEECC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecc--ccceEEEEEEcchH-HhHHHH-HhcCcEECCEEEEEEECC
Confidence            5899999999999999999999999999999999875  34679999997766 999998 48998 999999998643

>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=99.82  E-value=7.2e-21  Score=119.44  Aligned_cols=75  Identities=17%  Similarity=0.266  Sum_probs=68.2

Q ss_pred             CCeEEEcCCCC-CCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          43 GANLFIYHLPP-EFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        43 ~~~l~V~nLp~-~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      .++|||+|||+ .+++++|+++|++||.|.+++++.++     +|||||+|++.+ +|.+|++.|||. +.|+.|+|.|+
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~~~-~A~~ai~~lng~~l~g~~l~v~~s   75 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGN-QAQLAMSHLNGHKLHGKPIRITLS   75 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHH-HHHHHHHHHTTCBCSSSBCEEECC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHH-HHHHHHHHhCCCEECCEEEEEEEC
Confidence            46899999965 59999999999999999999998774     789999998777 999999999999 99999999998


Q ss_pred             ccc
Q psy8615         121 TYV  123 (128)
Q Consensus       121 ~~~  123 (128)
                      +..
T Consensus        76 ~~~   78 (109)
T d2adca1          76 KHQ   78 (109)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            754

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.82  E-value=1.7e-20  Score=110.64  Aligned_cols=73  Identities=11%  Similarity=0.161  Sum_probs=64.3

Q ss_pred             EEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEeccccc
Q psy8615          46 LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNTYVL  124 (128)
Q Consensus        46 l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~~~~  124 (128)
                      |||+|||.++++++|+++|++|| +..+++      ++++|||||+|.+.+ +|++|++.|||+ +.|++|+|+|++...
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~-~A~~Ai~~ln~~~~~g~~l~V~~a~~d~   72 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGE-QAEAAINTFHQSRLRERELSVQLQPTDA   72 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHH-HHHHHHHHHTTEESSSCEEEEEECCSTT
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHH-HHHHHHHHhCCccCCCCEEEEEEeCCCC
Confidence            79999999999999999999999 444432      466899999997777 999999999999 999999999998776


Q ss_pred             cc
Q psy8615         125 MN  126 (128)
Q Consensus       125 ~~  126 (128)
                      |.
T Consensus        73 ~l   74 (75)
T d1wi6a1          73 LL   74 (75)
T ss_dssp             CC
T ss_pred             cc
Confidence            53

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=4.6e-21  Score=114.46  Aligned_cols=73  Identities=16%  Similarity=0.291  Sum_probs=65.0

Q ss_pred             CeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcC-c-CCCeEEEEEecc
Q psy8615          44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTAND-Y-LGQSFLKPSFNT  121 (128)
Q Consensus        44 ~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g-~-~~~~~l~V~~~~  121 (128)
                      .+|||+|||.++++++|+++|++||.+.++++..      .+|||||+|.+.+ +|.+|++.||| . ++|++|+|+|++
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~------~rg~aFV~f~~~~-~A~~Ai~~lng~~~~~G~~i~V~~a~   74 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQN-WAIRAIETLSGKVELHGKIMEVDYSV   74 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHH-HHHHHHHHHTTTCEETTEECEEEECC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec------ccceEEEEECCHH-HHHHHHHHhCCCeEECCEEEEEEEcC
Confidence            4799999999999999999999999987766654      4789999997777 99999999998 5 999999999988


Q ss_pred             cc
Q psy8615         122 YV  123 (128)
Q Consensus       122 ~~  123 (128)
                      +.
T Consensus        75 ~k   76 (80)
T d2cqha1          75 SK   76 (80)
T ss_dssp             CC
T ss_pred             Cc
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=99.81  E-value=6.7e-20  Score=111.07  Aligned_cols=79  Identities=15%  Similarity=0.150  Sum_probs=69.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhc--Cc-CCCeEE
Q psy8615          39 TGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTAN--DY-LGQSFL  115 (128)
Q Consensus        39 ~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~--g~-~~~~~l  115 (128)
                      ++++.++|||+|||.++++++|+++|++||.|.++++..+      +|||||+|++.+ +|.+|++.++  +. ++|++|
T Consensus         4 ~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e-~A~~a~~~~~~~~~~~~g~~l   76 (88)
T d2cq1a1           4 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEE-AAITMVNYYSAVTPHLRNQPI   76 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHH-HHHHHHHHHHHSCCEETTEEC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHH-HHHHHHHHHccCCCccCCCEE
Confidence            4556789999999999999999999999999999988754      579999997777 9999999765  55 999999


Q ss_pred             EEEeccccc
Q psy8615         116 KPSFNTYVL  124 (128)
Q Consensus       116 ~V~~~~~~~  124 (128)
                      +|+|+++.-
T Consensus        77 ~v~~sk~~~   85 (88)
T d2cq1a1          77 YIQYSNHKE   85 (88)
T ss_dssp             EEEECSCSS
T ss_pred             EEEECCCCC
Confidence            999998753

>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=99.81  E-value=1.7e-20  Score=113.89  Aligned_cols=74  Identities=9%  Similarity=0.147  Sum_probs=64.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecc
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNT  121 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~  121 (128)
                      .++|||+|||+++++++|+++|++|| +..+.+      ++++|||||+|.+.+ +|+.|++.||++ ++|+.|+|+|++
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~------~~~kg~afV~f~~~~-~A~~Ai~~ln~~~~~G~~l~V~~a~   76 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV------DRNKRTAFVTLLNGE-QAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE------EGGGTEEEECCSCHH-HHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcC-ceeeee------eccCCceEEEECCHH-HHHHHHHHhCCCEECCEEEEEEEcC
Confidence            56899999999999999999999999 333322      456899999997777 999999999999 999999999987


Q ss_pred             ccc
Q psy8615         122 YVL  124 (128)
Q Consensus       122 ~~~  124 (128)
                      ...
T Consensus        77 ~~~   79 (88)
T d1wg1a_          77 TDA   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            643

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=1.4e-20  Score=114.81  Aligned_cols=77  Identities=14%  Similarity=0.244  Sum_probs=68.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHh----hhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEE
Q psy8615          43 GANLFIYHLPPEFSDADLAS----MFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKP  117 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~----~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V  117 (128)
                      .++|||+|||+++++++|++    +|++||+|.++++..   +++++|||||+|.+.+ +|..|++.+||. ++|+.|+|
T Consensus         3 ~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~-~A~~A~~~~~~~~~~g~~l~v   78 (91)
T d1nu4a_           3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVS-SATNALRSMQGFPFYDKPMRI   78 (91)
T ss_dssp             CSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHH-HHHHHHHHHTTCEETTEECEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHH-HHHHHHHHhCCCEECCEEEEE
Confidence            57899999999999998864    589999999987643   4788999999997777 999999999999 99999999


Q ss_pred             Eecccc
Q psy8615         118 SFNTYV  123 (128)
Q Consensus       118 ~~~~~~  123 (128)
                      .|++..
T Consensus        79 ~~ak~~   84 (91)
T d1nu4a_          79 QYAKTD   84 (91)
T ss_dssp             EECSSC
T ss_pred             EEeCCC
Confidence            999863

>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=99.80  E-value=3.1e-19  Score=111.29  Aligned_cols=81  Identities=14%  Similarity=0.017  Sum_probs=69.5

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhc--Cc-CCC
Q psy8615          36 KQLTGPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTAN--DY-LGQ  112 (128)
Q Consensus        36 ~~~~~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~--g~-~~~  112 (128)
                      .+...++...|||+|||.+++|++|+.+|++||.|.++.+..+      +|+|||+|++.+ +|+.|++.++  +. ++|
T Consensus         8 ~~~~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e-~A~~ai~~~~~~~~~~~g   80 (104)
T d1wexa_           8 SHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENID-SAKECVTFAADVPVYIAG   80 (104)
T ss_dssp             SCCCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHH-HHHHHHHHHHHSCCBSSS
T ss_pred             CCCcCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHH-HHHHHHHHHcCCCcEEee
Confidence            3344556779999999999999999999999999999987643      679999997777 9999999884  45 899


Q ss_pred             eEEEEEecccc
Q psy8615         113 SFLKPSFNTYV  123 (128)
Q Consensus       113 ~~l~V~~~~~~  123 (128)
                      ++|+|+|++..
T Consensus        81 ~~l~v~~s~~~   91 (104)
T d1wexa_          81 QQAFFNYSTSK   91 (104)
T ss_dssp             SBCEEEECSSS
T ss_pred             EEEEEEEcCCC
Confidence            99999999764

>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=99.80  E-value=4e-20  Score=115.07  Aligned_cols=79  Identities=10%  Similarity=-0.043  Sum_probs=69.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecc
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNT  121 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~  121 (128)
                      .++|||+|||+++++++|+++|+.||.+..+..+.+..+|+++|||||+|.+.+ +|++|++ +|+. ++|+.|.|.+.+
T Consensus         8 ~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~-~a~~Al~-~n~~~i~gr~i~V~~~~   85 (103)
T d2cpya1           8 KVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNED-DARKSER-LHRKKLNGREAFVHVVT   85 (103)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHH-HHHHHGG-GCSEEETTEEEEEEEEC
T ss_pred             ceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHH-HHHHHHh-cCCCeECCcEEEEEECC
Confidence            467999999999999999999999999887555666667999999999997777 9999996 8999 999999999876


Q ss_pred             cc
Q psy8615         122 YV  123 (128)
Q Consensus       122 ~~  123 (128)
                      ..
T Consensus        86 ~~   87 (103)
T d2cpya1          86 LE   87 (103)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=1.1e-19  Score=114.82  Aligned_cols=81  Identities=15%  Similarity=0.169  Sum_probs=71.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEe
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSF  119 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~  119 (128)
                      ..+++|||+|||+++++++|+++|+.||.+..+.++.+..+|.++|||||+|.+.+ +|.+|++ +|+. ++|+.|+|..
T Consensus        16 ~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e-~a~~al~-~~~~~i~gR~i~V~~   93 (112)
T d1wela1          16 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEA-DYKAALC-RHKQYMGNRFIQVHP   93 (112)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSH-HHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHH-HHHHHHH-cCCCcCCCEEEEEEE
Confidence            34678999999999999999999999999987666777778999999999998887 9998885 8999 9999999987


Q ss_pred             cccc
Q psy8615         120 NTYV  123 (128)
Q Consensus       120 ~~~~  123 (128)
                      .+..
T Consensus        94 ~~~~   97 (112)
T d1wela1          94 ITKK   97 (112)
T ss_dssp             ECHH
T ss_pred             cChH
Confidence            6543

>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=99.79  E-value=1.5e-19  Score=111.68  Aligned_cols=73  Identities=21%  Similarity=0.208  Sum_probs=66.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      ..++|||+|||+++++++|+++|++||.|.++++..       +|||||+|.+.+ +|++|++.|||. +.|+.|+|.|.
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~-~a~~Ai~~lng~~~~g~~i~v~~~   85 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKE-DMEYALRKLDDTKFRSHEGETSYI   85 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHH-HHHHHHHHHSSEEEECTTSCEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHH-HHHHHHHHhCCCEeCCeEEEEEEE
Confidence            356899999999999999999999999999998752       579999997777 999999999999 99999999997


Q ss_pred             cc
Q psy8615         121 TY  122 (128)
Q Consensus       121 ~~  122 (128)
                      +.
T Consensus        86 ~~   87 (98)
T d1wg4a_          86 RV   87 (98)
T ss_dssp             EE
T ss_pred             ec
Confidence            64

>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=4.4e-19  Score=109.24  Aligned_cols=76  Identities=21%  Similarity=0.241  Sum_probs=67.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCC--eEEEE
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQ--SFLKP  117 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~--~~l~V  117 (128)
                      ++.++|||+|||+++++++|+++|++||.|..+++..+      ++||||+|.+.+ +|+.|++.||+. ++|  +.|+|
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~-~A~~A~~~l~~~~i~g~~~~l~v   87 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLD-AAQAACAKMRGFPLGGPDRRLRV   87 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHH-HHHHHHHHHTTCBCSSSSCBCEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHH-HHHHHHHHhCCCEeCCCceEEEE
Confidence            34679999999999999999999999999999987644      679999997777 999999999999 765  68999


Q ss_pred             Eecccc
Q psy8615         118 SFNTYV  123 (128)
Q Consensus       118 ~~~~~~  123 (128)
                      +|+++.
T Consensus        88 ~~ak~~   93 (97)
T d1whya_          88 DFAKSG   93 (97)
T ss_dssp             EECCCC
T ss_pred             EeCCCC
Confidence            999864

>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=1.8e-20  Score=113.50  Aligned_cols=70  Identities=23%  Similarity=0.247  Sum_probs=63.7

Q ss_pred             eEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEeccc
Q psy8615          45 NLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNTY  122 (128)
Q Consensus        45 ~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~~  122 (128)
                      +|||+|||+++++++|+++|++||.|.++++..|       |||||+|.+.+ +|+.|++.|||. +.|+.|+|.|.++
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~-~a~~Ai~~l~g~~~~g~~i~v~~~~~   72 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKE-DMTYAVRKLDNTKFRSHEGETAYIRV   72 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHH-HHHHHHHHHTTCBCCCTTSCCCBCEE
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHH-HHHHHHHHhCCCEECCcEeEEeEEec
Confidence            6999999999999999999999999999987543       79999997777 999999999999 9999999888654

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=4.5e-20  Score=111.90  Aligned_cols=74  Identities=14%  Similarity=0.227  Sum_probs=64.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          42 EGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        42 ~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      ..++|||+|||++++|++|+++|++||.|.++++.     ..++|||||+|.+.+ +|+.|+.  +++ ++|+.|+|.|+
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~-----~~~~gfafV~f~~~~-~a~~a~~--~~~~i~g~~l~v~~a   75 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP-----KPFRAFAFVTFADDQ-IAQSLCG--EDLIIKGISVHISNA   75 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECC-----SSCCSCCEEECSCHH-HHHHTTT--CEEEETTEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEe-----eccCceEEEEECCHH-HHHHHHh--CCCEECCEEeEEEeC
Confidence            36799999999999999999999999999998754     456899999997776 9999985  777 99999999998


Q ss_pred             ccc
Q psy8615         121 TYV  123 (128)
Q Consensus       121 ~~~  123 (128)
                      ++.
T Consensus        76 ~~k   78 (88)
T d1wf0a_          76 EPK   78 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            764

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.79  E-value=3.2e-19  Score=110.36  Aligned_cols=76  Identities=14%  Similarity=0.180  Sum_probs=66.3

Q ss_pred             CCCCCeEEEcCCCCC-CCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHH--HhcCc-CCCeEE
Q psy8615          40 GPEGANLFIYHLPPE-FSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFD--TANDY-LGQSFL  115 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~-~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~--~l~g~-~~~~~l  115 (128)
                      ...+++|||+|||.+ +++++|+++|++||.|.++++..+      +|+|||+|.+.+ +|..|++  .+++. ++|+.|
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~-~A~~Ai~~~~~~~~~~~gr~l   87 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETRE-DAMAMVDHCLKKALWFQGRCV   87 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHH-HHHHHHHHHHHSCCCSSSSCC
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchH-HHHHHHHHHhcCCceECCEEE
Confidence            345779999999985 899999999999999999998754      679999997777 9999998  46777 999999


Q ss_pred             EEEeccc
Q psy8615         116 KPSFNTY  122 (128)
Q Consensus       116 ~V~~~~~  122 (128)
                      +|+|++.
T Consensus        88 ~V~~s~~   94 (99)
T d1x4fa1          88 KVDLSEK   94 (99)
T ss_dssp             EEEEECS
T ss_pred             EEEEcCC
Confidence            9999864

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=2.8e-18  Score=115.76  Aligned_cols=81  Identities=9%  Similarity=0.108  Sum_probs=73.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEE
Q psy8615          40 GPEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPS  118 (128)
Q Consensus        40 ~~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~  118 (128)
                      ....++|||+|||+.+++++|+++|+.||.|..+.++.|+.+|+++|||||+|.+.+ +|.+|++ +++. ++|+.|+|.
T Consensus        94 ~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e-~A~~Al~-~~~~~~~G~~i~V~  171 (183)
T d1u1qa_          94 HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD-SVDKIVI-QKYHTVNGHNCEVR  171 (183)
T ss_dssp             TCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHH-HHHHHHT-SSCEEETTEEEEEE
T ss_pred             ccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHH-HHHHHHH-hCCCeECCEEEEEE
Confidence            344679999999999999999999999999999999999999999999999997776 9999997 6777 999999999


Q ss_pred             eccc
Q psy8615         119 FNTY  122 (128)
Q Consensus       119 ~~~~  122 (128)
                      ++.+
T Consensus       172 ~A~~  175 (183)
T d1u1qa_         172 KALS  175 (183)
T ss_dssp             ECCC
T ss_pred             ecCC
Confidence            9754

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.74  E-value=8.4e-19  Score=109.39  Aligned_cols=78  Identities=14%  Similarity=0.061  Sum_probs=67.3

Q ss_pred             CCCCeEEEcCCCCCC-CH----HHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeE
Q psy8615          41 PEGANLFIYHLPPEF-SD----ADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSF  114 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~-~e----~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~  114 (128)
                      ...++|||+||+.++ ++    ++|+++|++||.|.++++..      ++|||||+|++.+ +|.+|++.|||+ ++|+.
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k------~~~~afV~f~~~~-~A~~Ai~~lng~~~~g~~   75 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK------SFKRVRINFSNPL-SAADARLRLHKTEFLGKE   75 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET------TTTEEEEECSSTT-HHHHHHHTSTTSEETTEE
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec------CCCEEEEEECCHH-HHHHHHHHhcccccCCCE
Confidence            346789999999875 33    56999999999999998873      4779999998888 999999999999 99999


Q ss_pred             EEEEecccccc
Q psy8615         115 LKPSFNTYVLM  125 (128)
Q Consensus       115 l~V~~~~~~~~  125 (128)
                      |+|.|+++...
T Consensus        76 l~v~~a~~~~~   86 (104)
T d1weya_          76 MKLYFAQTLHI   86 (104)
T ss_dssp             CEEECCCCSSC
T ss_pred             eEEeecccCCC
Confidence            99999987643

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.74  E-value=4.2e-18  Score=103.34  Aligned_cols=75  Identities=9%  Similarity=-0.003  Sum_probs=65.4

Q ss_pred             CCCCeEEEcCCCCC-CCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHh--cCc-CCCeEEE
Q psy8615          41 PEGANLFIYHLPPE-FSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTA--NDY-LGQSFLK  116 (128)
Q Consensus        41 ~~~~~l~V~nLp~~-~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l--~g~-~~~~~l~  116 (128)
                      .....|||+|||.. +++++|.++|++||.|.++.+..+      +++|||+|++.+ +|..|++.+  ++. ++|++|+
T Consensus         6 ~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~------k~~afV~f~~~~-~A~~A~~~l~~~~~~~~gr~l~   78 (89)
T d1x4da1           6 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTE-DAQAAVDYYTTTPALVFGKPVR   78 (89)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHH-HHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc------ceEEEEEEcchh-hHHHHHHHHhhCCCccCCceEE
Confidence            34668999999986 789999999999999999998755      459999997777 999999976  566 9999999


Q ss_pred             EEeccc
Q psy8615         117 PSFNTY  122 (128)
Q Consensus       117 V~~~~~  122 (128)
                      |+|++.
T Consensus        79 V~~s~~   84 (89)
T d1x4da1          79 VHLSQK   84 (89)
T ss_dssp             EEEECC
T ss_pred             EEECCC
Confidence            999874

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=2.8e-20  Score=113.14  Aligned_cols=77  Identities=14%  Similarity=0.106  Sum_probs=66.3

Q ss_pred             CeEEEcCCCCCCCHHHHHhhhcCCCceEEEEE-----EecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEE
Q psy8615          44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKV-----FIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKP  117 (128)
Q Consensus        44 ~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~-----~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V  117 (128)
                      ++|||+|||.+++|++|+++|++||.+.++.+     ..+..+++++|||||+|.+.+ +|+.|++ |||+ +.|+.|+|
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e-~a~~a~~-l~g~~~~Gr~l~V   79 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD-ETTQAMA-FDGIIFQGQSLKI   79 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCT-TTTTGGG-GSSCCSSSSCCCC
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHH-HHHHHHh-hCCcEECCEEEEE
Confidence            58999999999999999999999998766543     456677899999999998877 8999985 9999 99999999


Q ss_pred             Eeccc
Q psy8615         118 SFNTY  122 (128)
Q Consensus       118 ~~~~~  122 (128)
                      +..+.
T Consensus        80 ~r~k~   84 (90)
T d1u2fa_          80 RRPHD   84 (90)
T ss_dssp             BCTTC
T ss_pred             CCCCC
Confidence            76543

>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=99.70  E-value=2.4e-19  Score=111.93  Aligned_cols=75  Identities=12%  Similarity=0.053  Sum_probs=69.1

Q ss_pred             CeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEec
Q psy8615          44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFN  120 (128)
Q Consensus        44 ~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~  120 (128)
                      +.++|.+++.+++|++|+++|++||+|.++++..+ .+|+++|||||+|++.+ +|.+|++.|||+ ++||+|+|+|.
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-LGDHLVGNVYVKFRREE-DAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCS-SSSSSEEEEEEEESCHH-HHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecC-CCCCEeeEEEEEEechh-HHHHHHHHHCCCEECCEEEEEEEC
Confidence            46888999999999999999999999999998766 46999999999997777 999999999999 99999999985

>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=99.67  E-value=7.4e-17  Score=101.72  Aligned_cols=75  Identities=19%  Similarity=0.108  Sum_probs=61.8

Q ss_pred             CCCCCCe-EEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEE
Q psy8615          39 TGPEGAN-LFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLK  116 (128)
Q Consensus        39 ~~~~~~~-l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~  116 (128)
                      +.+.|+. +||||||+++|+++|+++|++||+|.+|+++.+      +|||||.|.++.++|..|+..+|+. +.++.+.
T Consensus         6 ~~~~g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~   79 (113)
T d1owxa_           6 EEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKE   79 (113)
T ss_dssp             SCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSS
T ss_pred             CCCCCCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceE
Confidence            4455675 499999999999999999999999999998744      7899999987644889999999997 6555544


Q ss_pred             EEe
Q psy8615         117 PSF  119 (128)
Q Consensus       117 V~~  119 (128)
                      |.|
T Consensus        80 v~~   82 (113)
T d1owxa_          80 VTW   82 (113)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            444

>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=99.66  E-value=1.7e-16  Score=106.76  Aligned_cols=78  Identities=23%  Similarity=0.312  Sum_probs=69.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCcCCCeEEEEEecc
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDYLGQSFLKPSFNT  121 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~~~~~~l~V~~~~  121 (128)
                      .++|||+|||+++++++|+++|++||.|.+++++.++.+|.++|||||+|.+.+ +|..|+..+++.++++.+.+....
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~-~a~~a~~~~~~~~~~~~~~~~~~~   83 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE-EVDAAMNARPHKVDGRVVEPKRAV   83 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHH-HHHHHHHTCSCEETTEECEEEECC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHH-HHHHHHHhcCCcccccchhhhhhh
Confidence            368999999999999999999999999999999999999999999999997777 999999887777777777766543

>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=99.61  E-value=2.5e-16  Score=97.44  Aligned_cols=61  Identities=15%  Similarity=0.047  Sum_probs=53.5

Q ss_pred             CCCeEEEc--CCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc
Q psy8615          42 EGANLFIY--HLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY  109 (128)
Q Consensus        42 ~~~~l~V~--nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~  109 (128)
                      +..++||+  |||.++++++|+++|++||.|.++++..+      +|||||+|.+.+ +|..|++.|||+
T Consensus        17 pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e-~A~~A~~~lng~   79 (101)
T d2cq2a1          17 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTE-ESKRAYVTLNGK   79 (101)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHH-HHHHHHHHTTTC
T ss_pred             CCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHH-HHHHHHHHhCCC
Confidence            34578885  59999999999999999999999887644      579999997777 999999999998

>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=99.50  E-value=1.2e-14  Score=86.42  Aligned_cols=69  Identities=13%  Similarity=0.216  Sum_probs=57.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeE-EEEEec
Q psy8615          43 GANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSF-LKPSFN  120 (128)
Q Consensus        43 ~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~-l~V~~~  120 (128)
                      .+.|+|+++|++.+++.|+ .|++||+|.++++.      +.+||+||+|++.+ +|++|++ +||. ++|+. +.|.-.
T Consensus         4 ~~wV~V~G~p~~~~~~il~-~F~~~G~I~~~~~~------~~~~~~fV~f~~~~-~A~~Al~-~nG~~~~g~~~vgV~~~   74 (81)
T d1wwha1           4 DTWVTVFGFPQASASYILL-QFAQYGNILKHVMS------NTGNWMHIRYQSKL-QARKALS-KDGRIFGESIMIGVKPC   74 (81)
T ss_dssp             GGEEEEECCCGGGHHHHHH-HHHTTSCEEEEEEC------SSSSEEEEEESSHH-HHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             ccEEEEECCChHHHHHHHH-HHHhhhhhheEEec------CCCCEEEEEEcccH-HHHHHHh-cCCCeECCcEEEEEEeC
Confidence            4679999999999977665 69999999998753      44789999997777 9999995 9999 99875 456544

>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=99.48  E-value=3.7e-14  Score=87.13  Aligned_cols=75  Identities=15%  Similarity=0.173  Sum_probs=62.6

Q ss_pred             CCeEEEcCC--CCCCC---------HHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-C
Q psy8615          43 GANLFIYHL--PPEFS---------DADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-L  110 (128)
Q Consensus        43 ~~~l~V~nL--p~~~~---------e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~  110 (128)
                      ...|+|.|+  |.+..         +++|++.|++||.|..+++..+    ..+||+||+|++.+ +|.+|++.|||. +
T Consensus         8 ~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e-~A~~A~~~lng~~~   82 (99)
T d2dita1           8 ERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPE-EADYCIQTLDGRWF   82 (99)
T ss_dssp             CCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHH-HHHHHHHHSTTCEE
T ss_pred             ccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHH-HHHHHHHHhCCcEE
Confidence            568999998  54422         3678999999999999987654    45799999997776 999999999999 9


Q ss_pred             CCeEEEEEeccc
Q psy8615         111 GQSFLKPSFNTY  122 (128)
Q Consensus       111 ~~~~l~V~~~~~  122 (128)
                      +|++|+|.|...
T Consensus        83 ~gr~i~v~~~~g   94 (99)
T d2dita1          83 GGRQITAQAWDG   94 (99)
T ss_dssp             TTEECEEEECCS
T ss_pred             CCEEEEEEEeCC
Confidence            999999998643

>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=99.47  E-value=2.9e-14  Score=88.37  Aligned_cols=80  Identities=11%  Similarity=0.070  Sum_probs=65.6

Q ss_pred             CCCeEEEcCC--CCCCC--------HHHHHhhhcCCCceEEEEEEecCCCC--CcceEEEEEEecCHHHHHHHHHHhcCc
Q psy8615          42 EGANLFIYHL--PPEFS--------DADLASMFGPFGTVLSAKVFIDKQNN--RSKCFGTIIFMRKFFILTIRFDTANDY  109 (128)
Q Consensus        42 ~~~~l~V~nL--p~~~~--------e~~l~~~f~~~G~i~~~~~~~~~~tg--~~~g~~fv~f~~~~~~a~~Ai~~l~g~  109 (128)
                      +...|.+.|+  |.++.        .++|++.|++||.|.++.+.+++.+.  ...|++||+|.+.+ +|.+|++.|||.
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e-~A~~A~~~l~Gr   81 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVF-DCQKAMQGLTGR   81 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHH-HHHHHHHHHSSC
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHH-HHHHHHHHHCCC
Confidence            3557888998  55443        24689999999999999998876543  34689999997777 999999999999


Q ss_pred             -CCCeEEEEEeccc
Q psy8615         110 -LGQSFLKPSFNTY  122 (128)
Q Consensus       110 -~~~~~l~V~~~~~  122 (128)
                       ++||.|+|.|-..
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             9999999999653

>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=97.69  E-value=4.5e-05  Score=42.60  Aligned_cols=60  Identities=15%  Similarity=0.110  Sum_probs=47.6

Q ss_pred             HHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEecc
Q psy8615          58 ADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNT  121 (128)
Q Consensus        58 ~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~  121 (128)
                      +.|...|.+++.|.++.+....+ |.  -.|-|...+.. +|..|+..|+.+ +|+|.|.|+|.+
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~d-g~--~~A~V~v~~~q-~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHTD-YQ--LKAVVQMENLQ-DAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCCS-TT--CCEEEEESSHH-HHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHhheeEEEEEEEeccC-Cc--EEEEEEcCCHH-HHHHHHHHHHHHhcCCeEEEEEEec
Confidence            34567788999999988765533 33  35667775666 999999999999 999999999986

>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=97.41  E-value=0.00083  Score=39.31  Aligned_cols=65  Identities=17%  Similarity=0.222  Sum_probs=54.1

Q ss_pred             CeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCc--ceEEEEEEecCHHHHHHHHHHhcCc
Q psy8615          44 ANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRS--KCFGTIIFMRKFFILTIRFDTANDY  109 (128)
Q Consensus        44 ~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~--~g~~fv~f~~~~~~a~~Ai~~l~g~  109 (128)
                      |+|-|+.||+..+|+++.+.+++.|.+........+.+-+.  ..-|++.|.+.+ +...-.+..+|+
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~-~v~~F~~~f~g~   68 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQE-DIILFRDRFDGY   68 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSH-HHHHHHHHHTTC
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHH-HHHHHHHHcCCc
Confidence            68999999999999999999999998887777666555443  357899997777 888888999997

>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=96.49  E-value=0.0023  Score=37.25  Aligned_cols=54  Identities=13%  Similarity=0.120  Sum_probs=43.2

Q ss_pred             HHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhcCc-CCCeEEEEEeccc
Q psy8615          59 DLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTANDY-LGQSFLKPSFNTY  122 (128)
Q Consensus        59 ~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~g~-~~~~~l~V~~~~~  122 (128)
                      +|.+.|+.||+|.-+|++.|        --.|+|.+.. .|..| -.++|. +.|+.|+|+...+
T Consensus        40 ~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~-SAL~a-l~l~g~~v~G~~l~It~~~~   94 (95)
T d1ufwa_          40 ELMQTLGSYGTIVLVRINQG--------QMLVTFADSH-SALSV-LDVDGMKVKGRAVKISGPSS   94 (95)
T ss_dssp             HHHHHHHHHSCCSEEEEETT--------EEEEECSCSH-HHHHH-HHGGGSEETTEEEEEECCCC
T ss_pred             HHHHHHhhCCeEEEEEEeCC--------eEEEEECCcH-HHHHH-hccCCeEEcceEEEEecCCC
Confidence            56777889999999998866        4589997777 77755 457777 9999999987654

>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=95.09  E-value=0.087  Score=30.74  Aligned_cols=58  Identities=19%  Similarity=0.359  Sum_probs=42.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHhhhcCCCceEEEEEEecCCCCCcceEEEEEEecCHHHHHHHHHHhc
Q psy8615          41 PEGANLFIYHLPPEFSDADLASMFGPFGTVLSAKVFIDKQNNRSKCFGTIIFMRKFFILTIRFDTAN  107 (128)
Q Consensus        41 ~~~~~l~V~nLp~~~~e~~l~~~f~~~G~i~~~~~~~~~~tg~~~g~~fv~f~~~~~~a~~Ai~~l~  107 (128)
                      +....+|.-..|..+...+|.++|++||.|. +..+.|.       -|||...+.+ ++..++..++
T Consensus        13 p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIddT-------Sa~V~L~~~e-~~~~v~~~~~   70 (100)
T d1whva_          13 PKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDDT-------SAFVSLSQPE-QVQIAVNTSK   70 (100)
T ss_dssp             CCCCSEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEETT-------EEEEECSCHH-HHHHHHHHHH
T ss_pred             CCcceeEEEeCCcccchhHHHHHhcCCCceE-EEEecCc-------eEEEEecCHH-HHHHHHHHhc
Confidence            3345688879999999999999999999764 3444443       6899985554 7776665544