Citrus Sinensis ID: 045516

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------670-----
Protein Sequence
VDAAPVVATPTKSAKKGGKREAEDAIEKLVSAKKQKGNDGVAQAVKKAKVEAKTQKKNKNDETSSSSSEEDSSDSEEEQKVKAVVTNKGGKAAKPPVKESSSEEEDSSSDEEPPKKQPVAAKNGAVAATAKKSKPDSSSSDSSDDDSDEDEVPTSIKKLPVAAAKNGPSAPQKKKDDSSDSSDEESDESSDEDDKSTKAIPQPKKLPASTAKKGTVAATKKSTGSSDDDSSSSEDSSESEEDNGAPAKVTSEAKKLPAVKNVPAPAAKKKTESSDSSDEESEDSSDEDEEPTHVTKATPVKKLSAVVTKNKVESSSSSDESESEEEKPPAKMDVDSSSEEESSDEEPQKKKDVKPNTKALKKESSSDEEDSDDEDEGEEEEASKTPKKNVTDVKMVDAESGKKAAQTPFTPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDEAKQRGDFGSGGGRSGGRGGRSGGRDFGRSGGRDGGRFGGRGRGGRDGGRGGRGRGRGTPNRPSLAAAGTGKKTTFGDD
Secondary Structure (PSIPRED)
cccccccccccccccccccccHHHHHHHHHHHHHccccccccHHHHHHHHHHHHccccccccccccccccccccHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHcccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccHHccccccccccccccccHHHHHHHcccccccccccccccccccccccccccccccccccEEEEccccccccHHHHHHHHHHcccEEEEEEEEccccccccEEEEEEccHHHHHHHHHHcccEEccEEEEEcccccccccccccccccccccccccccccccEEEEccccccccHHHHHHHHHHHHcccccEEEEEEcccccccccccEEEEEEccHHHHHHHHHHcccEEccEEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccEEcccccccccccHHHHHHHHHHHHHHHHHHHccccHHHHHHHEEEEEEEEEcccccccccccccccccccHcHcccccccccccccccccccccccccccccccccccccccHHHHccHHHHHHccccccccccccccccccccccccccccccccHcccccccccccccccccccccccccccccccccHHcccccccccccHcccccccccccccccccccccccHHcccccccccccHHccHHHccccccccccccHcccccccccHHccccccccccccccHHHHcccccccHHHccccccccccccccHHHccccccccHHHHccccccccccccccHHHccccccccccccccccccccccccccccHHHHHHHHHHccccEcccccccccccccccccccccccEEEEccccccccHHHHHHHHHHcccEEEEEEEEccccccccEEEEEEccHHHHHHHHHHccccccccEEEEEEcccccHccHHHcccHHHHccccccccccEEEEEEcccccccHHHHHHHHHHHHHHcccEEEEEEEEcccccccccEEEEEcccHHHHHHHHHHcccEEcccEEEEEEcccHHHHcHHccccHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
vdaapvvatptksakkggkREAEDAIEKLVSAKKQKGNDGVAQAVKKAKVEAKTqkknkndetssssseedssdseeEQKVKAVVTnkggkaakppvkessseeedsssdeeppkkqpvaaknGAVAatakkskpdssssdssdddsdedevptsiKKLPvaaakngpsapqkkkddssdssdeesdessdeddkstkaipqpkklpastakkgtvaatkkstgssdddssssedsseseedngapakvtseakklpavknvpapaakkktessdssdeesedssdedeepthvtkatpvkkLSAVVTKNkvesssssdeseseeekppakmdvdssseeessdeepqkkkdvkpntkalkkesssdeedsddedegeeeeasktpkknvtdvkmvdaesgkkaaqtpftpqsggsktlfvgnlpfsveqADVQNFFSEVAEVVDVRlssdadgrfkgyghvefasVEDAHKAIELNGQMLGNRAIRLDFArergaytpysggnesnsfqkggrgqaAHTIFIkgfdssvgeDQVRASLEEhfgscgeitrisvpkdydtgsvkgiayldftdadsFNKALEmsgteiggySLVVDeakqrgdfgsgggrsggrggrsggrdfgrsggrdggrfggrgrggrdggrggrgrgrgtpnrpslaaagtgkkttfgdd
Flexible Loop (DISEMBL)
vdaapvvatptksakkggkreaEDAIEKLvsakkqkgndgvAQAVKKAKveaktqkknkndetssssseedssdseeeQKVKAvvtnkggkaakppvkessseeedsssdeeppkkqpvaakngavaatakkskpdssssdssdddsdedeVPTSIKklpvaaakngpsapqkkkddssdssdeesdessdeddkstkaipqpkklpastakkgtvaatkkstgssdddssssedsseseedngapakvtseakklpavknvpapaakkktessdssdeesedssdedeepthvtkatpvkklsavvtknkvesssssdeseseeekppakmdvdssseeessdeepqkkkdvkpntkalkkesssdeedsddedegeeeeasktpkknvtdvKMVDAEsgkkaaqtpftpqsggSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARERGAYTpysggnesnsfqKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHfgscgeitrisvpkdydtGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDEAKQRgdfgsgggrsggrggrsggrdfgrsggrdggrfggrgrggrdggrggrgrgrgtpnrpslaaagtgkkttfgdd
Low Complexity Region (SEG)
VDAAPVVATPTKSAKKGGKREAEDAIEKLVSAKKQKGNDGvaqavkkakveaktqkknkndetssssseedssdseeeQKVKAVVTNKGGKAAKPPVKessseeedsssdeePPKKQPVaakngavaatakkSKPdssssdssdddsdedeVPTSIKKLPVAAAKNGPSAPQkkkddssdssdeesdessdeddksTKAIPQPKKLPastakkgtvaatkkstgssdddssssedsseseedNGAPAKVTSEakklpavknvpapaakkkTessdssdeesedssdedeePTHVTKATPVKKLSAVVTKNKVesssssdeseseeeKPPAKMDVdssseeessdeePQKKKDVKPNTKALKKesssdeedsddedegeeeeasKTPKKNVTDVKMVDAESGKKAAQTPFTPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDEAKQrgdfgsgggrsggrggrsggrdfgrsggrdggrfggrgrggrdggrggrgrgrgTPNRPSLAAAGTGKKTTFGDD
Disordered region (IsUnstruct)
*********************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARERGAYT******************AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVV********************************************************************************
Disordered Region (DISOPRED)
****P*****************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRL********************************IFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLV*********************************************************************************
Disordered Region (DISEMBL)
***********************DAIEKLVSA*************************************************KAVVT*******************************************************************TSIKKLPVA**************************************PQPKK*******************************************VTSEAKKLPAVKNV**********************************ATPVKKLSAV********************************************************************************KKNVTDVKMVDAESGKKAAQTPFTPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARERGAYTPYSGGNES*********QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDEAKQRGDFGS*************GRDFGRSGGRDGGRFGGRG*************************************
Disordered Region (DISPRO)
****PVVATP*************DAIEKLVSAKKQKGNDGVAQAVKKAKVEAKTQKKN***************************************************************************************************************************************************************************************************************************************EP**************************************************************************************************************************GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARE*********************GQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDEAKQRGDFGSGGGRSGGRGGRSGGRDFGRSGGRDGGRFGGRGRGGRDGGRGGRGRGRGTP*******************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
VDAAPVVATPTKSAKKGGKREAEDAIEKLVSAKKQKGNDGVxxxxxxxxxxxxxxxxxxxxxTSSSSSEEDSSDSEEEQKVKAVVTNKGGKAAKPPVKESSSEEEDSSSDEEPPKKQPVAAKNGAVAATAKKSKPDSSSSDSSDDDSDEDEVPTSIKKLPVAAAKNGPSAPQKKKDDSSDSSDEESDESSDEDDKSTKAIPQPKKLPASTAKKGTVAATKKSTGSSDDDSSSSEDSSESEEDNGAPAKVTSEAKKLPAVKNVPAPAAKKKTESSDSSDEESEDSSDEDEEPTHVTKATPVKKLSAVVTKNKVESSSSSDESESEEEKPPAKMDVDSSSEEESSDEEPQKKKDVKPNTKALKKESSSDEEDSDDEDEGEEEEASKTPKKNVTDVKMVDAESGKKAAQTPFTPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDEAKQRGDFGSGGGRSGGRGGRSGGRDFGRSGGRDGGRFGGRGRGGRDGGRGGRGRGRGTPNRPSLAAAGTGKKTTFGDD
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	675	2.2.26 [Sep-21-2011]
Q7XTT4	707	Nucleolin 2 OS=Oryza sati	yes	no	0.343	0.328	0.554	3e-71
Q1PEP5	636	Nucleolin 2 OS=Arabidopsi	yes	no	0.411	0.437	0.481	4e-67
Q6Z1C0	572	Nucleolin 1 OS=Oryza sati	no	no	0.284	0.335	0.576	3e-61
Q9FVQ1	557	Nucleolin 1 OS=Arabidopsi	no	no	0.308	0.373	0.544	5e-60
Q86U06	439	Probable RNA-binding prot	yes	no	0.277	0.425	0.303	5e-15
Q5RC80	524	RNA-binding protein 39 OS	no	no	0.274	0.353	0.294	1e-13
Q8VH51	530	RNA-binding protein 39 OS	yes	no	0.274	0.349	0.294	2e-13
Q14498	530	RNA-binding protein 39 OS	no	no	0.274	0.349	0.294	2e-13
P09405	707	Nucleolin OS=Mus musculus	no	no	0.297	0.284	0.3	3e-12
P49314	292	31 kDa ribonucleoprotein,	N/A	no	0.259	0.599	0.300	6e-12

>sp|Q7XTT4|NUCL2_ORYSJ Nucleolin 2 OS=Oryza sativa subsp. japonica GN=Os04g0620700 PE=2 SV=2

 Score =  270 bits (689), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 137/247 (55%), Positives = 174/247 (70%), Gaps = 15/247 (6%)

Query: 383 SKTPKKNVTDVKMVDAESGKKAAQT-PFTP-----QSGGSKTLFVGNLPFSVEQADVQNF 436
           +KTP+K  T V +   +S  K  Q  P TP     Q+ GSKTLFVGNLP++VEQ  V+ F
Sbjct: 409 AKTPQKKETAVSVGSNKSATKPGQEEPKTPASNQNQATGSKTLFVGNLPYNVEQEQVKQF 468

Query: 437 FSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARERGA 496
           F E  EVVD+R S+  DG F+G+GHVEFA+ E A KA+EL G  L  R +RLD ARERGA
Sbjct: 469 FQEAGEVVDIRFSTFEDGNFRGFGHVEFATAEAAKKALELAGHDLMGRPVRLDLARERGA 528

Query: 497 YTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPK 556
           YTP SG + S SF+K  +  + +TIFIKGFD+S+   Q+R SLEEHFGSCGEITR+S+PK
Sbjct: 529 YTPGSGRDNS-SFKKPAQS-SGNTIFIKGFDTSLDIHQIRNSLEEHFGSCGEITRVSIPK 586

Query: 557 DYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDEAKQRGDFGSGGGRSGGRGG 616
           DY+TG+ KG+AY+DF D  S +KA E++G+++GGYSL VDEA+ R D       +   GG
Sbjct: 587 DYETGASKGMAYMDFADNGSLSKAYELNGSDLGGYSLYVDEARPRPD-------NNREGG 639

Query: 617 RSGGRDF 623
            SGGRDF
Sbjct: 640 FSGGRDF 646

Involved in pre-rRNA processing and ribosome assembly.
Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q1PEP5|NUCL2_ARATH Nucleolin 2 OS=Arabidopsis thaliana GN=NUCL2 PE=2 SV=1

 Score =  256 bits (654), Expect = 4e-67,   Method: Compositional matrix adjust.
 Identities = 144/299 (48%), Positives = 193/299 (64%), Gaps = 21/299 (7%)

Query: 385 TPKKNVTDVKMVDAE--SGKKAAQTPFTPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAE 442
           TPKK  +DV+MVDAE  S  K  +TP     GGSKTLF GNL + + ++D++NFF E  E
Sbjct: 350 TPKKKDSDVEMVDAEQKSNAKQPKTPTNQTQGGSKTLFAGNLSYQIARSDIENFFKEAGE 409

Query: 443 VVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARERGAYTPYSG 502
           VVDVRLSS  DG FKGYGH+EFAS E+A KA+E+NG++L  R +RLD A ERG  TP + 
Sbjct: 410 VVDVRLSSFDDGSFKGYGHIEFASPEEAQKALEMNGKLLLGRDVRLDLANERG--TPRN- 466

Query: 503 GNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGS 562
              SN  +K G G  + TI+++GF SS+GED+++  L  HF  CGE+TR+ VP D +TG+
Sbjct: 467 ---SNPGRK-GEGSQSRTIYVRGFSSSLGEDEIKKELRSHFSKCGEVTRVHVPTDRETGA 522

Query: 563 VKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDEAKQR-GDFGSGGGRSGGRGGRSGGR 621
            +G AY+D T    F++AL++SG+EIGG ++ V+E++ R  D G    R+  RG    GR
Sbjct: 523 SRGFAYIDLTSG--FDEALQLSGSEIGGGNIHVEESRPRDSDEGRSSNRAPARGA-PRGR 579

Query: 622 DFGRSGGRDGGRFGGRGRGGRDGGRGG-RG----RGRGTPNRPSLAAAGTGKKTTFGDD 675
              R+    GGRF  R   GR   RG  RG    RGRG P++PS+  +  G KT F D+
Sbjct: 580 HSDRAP--RGGRFSDRAPRGRHSDRGAPRGRFSTRGRG-PSKPSVMESSKGTKTVFNDE 635

Involved in pre-rRNA processing and ribosome assembly.

Arabidopsis thaliana (taxid: 3702)

>sp|Q6Z1C0|NUCL1_ORYSJ Nucleolin 1 OS=Oryza sativa subsp. japonica GN=Os08g0192900 PE=2 SV=1

 Score =  236 bits (603), Expect = 3e-61,   Method: Compositional matrix adjust.
 Identities = 113/196 (57%), Positives = 149/196 (76%), Gaps = 4/196 (2%)

Query: 406 QTPFTPQSGG--SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVE 463
           +TP + QS G  S TLF+GNL F++ Q  V+ FF EV EV+ VRL++  DG  +G+GHV+
Sbjct: 298 KTPASNQSQGTESATLFMGNLSFNLNQDQVKEFFQEVGEVISVRLATHEDGSSRGFGHVQ 357

Query: 464 FASVEDAHKAIELNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFI 523
           FAS E+A KA+EL+G  L  R +RLD A ERGAYTP+S  N++ SFQK  RG ++ +IF+
Sbjct: 358 FASSEEAKKALELHGCDLDGRPVRLDLAHERGAYTPHSR-NDTGSFQKQNRG-SSQSIFV 415

Query: 524 KGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEM 583
           KGFDSS+ E ++R SLE HF  CGEITR+SVP D +TG+ KGIAY+DF D  SF+KALE+
Sbjct: 416 KGFDSSLEESKIRESLEGHFADCGEITRVSVPMDRETGASKGIAYIDFKDQASFSKALEL 475

Query: 584 SGTEIGGYSLVVDEAK 599
           SG+++GGY+L VDEAK
Sbjct: 476 SGSDLGGYNLYVDEAK 491

Involved in pre-rRNA processing and ribosome assembly.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9FVQ1|NUCL1_ARATH Nucleolin 1 OS=Arabidopsis thaliana GN=NUCL1 PE=1 SV=1

 Score =  233 bits (593), Expect = 5e-60,   Method: Compositional matrix adjust.
 Identities = 122/224 (54%), Positives = 160/224 (71%), Gaps = 16/224 (7%)

Query: 385 TPKKNVTDVKMVDAE-SGKKAAQTPFTPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEV 443
           TPKK  +DV+MVDAE S  K  +TP TP +GGSKTLF  NL F++E+ADV+NFF E  EV
Sbjct: 264 TPKKKSSDVEMVDAEKSSAKQPKTPSTPAAGGSKTLFAANLSFNIERADVENFFKEAGEV 323

Query: 444 VDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARERG------A 496
           VDVR S++  DG F+G+GHVEFAS E+A KA+E +G+ L  R IRLD A+ERG      A
Sbjct: 324 VDVRFSTNRDDGSFRGFGHVEFASSEEAQKALEFHGRPLLGREIRLDIAQERGERGERPA 383

Query: 497 YTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPK 556
           +TP SG     +F+ GG G     IF+KGFD+S+ ED ++ +L EHF SCGEI  +SVP 
Sbjct: 384 FTPQSG-----NFRSGGDGGDEKKIFVKGFDASLSEDDIKNTLREHFSSCGEIKNVSVPI 438

Query: 557 DYDTGSVKGIAYLDFTDADSFNKALEMSGTEI-GGYSLVVDEAK 599
           D DTG+ KGIAYL+F++     KALE++G+++ GG+ LVVDE +
Sbjct: 439 DRDTGNSKGIAYLEFSEGK--EKALELNGSDMGGGFYLVVDEPR 480

Involved in pre-rRNA processing and ribosome assembly. Is associated with intranucleolar chromatin and pre-ribosomal particles and plays a role in controlling activation and repression of a specific subset of rRNA genes located in distinctive nucleolar organizer regions. Binds specifically rDNA chromatin and may be required to maintain rDNA chromatin structure, but is probably not required for the overall histone methylation status of 45S rRNA genes.

Arabidopsis thaliana (taxid: 3702)

>sp|Q86U06|RBM23_HUMAN Probable RNA-binding protein 23 OS=Homo sapiens GN=RBM23 PE=1 SV=1

 Score = 83.6 bits (205), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 61/201 (30%), Positives = 100/201 (49%), Gaps = 14/201 (6%)

Query: 409 FTPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRF-KGYGHVEFASV 467
            +P+   ++T+F   L   +   D+++FFS V +V DVR+ SD + R  KG  +VEF  +
Sbjct: 158 LSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEI 217

Query: 468 EDAHKAIELNGQ-MLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGF 526
           +    AI L GQ +LG   I      E+           +N+ QKG  G     +++   
Sbjct: 218 QSVPLAIGLTGQRLLGVPIIVQASQAEKNRLAAM-----ANNLQKGNGGPM--RLYVGSL 270

Query: 527 DSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSG 585
             ++ ED +R   E      G+I  I + KD DTG  KG  ++ F+D++   +ALE ++G
Sbjct: 271 HFNITEDMLRGIFEPF----GKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNG 326

Query: 586 TEIGGYSLVVDEAKQRGDFGS 606
            E+ G  + V    +R D G+
Sbjct: 327 FELAGRPMRVGHVTERLDGGT 347

Probable RNA-binding protein. May be involved in pre-mRNA splicing process.

Homo sapiens (taxid: 9606)

>sp|Q5RC80|RBM39_PONAB RNA-binding protein 39 OS=Pongo abelii GN=RBM39 PE=2 SV=1

 Score = 79.0 bits (193), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 58/197 (29%), Positives = 92/197 (46%), Gaps = 12/197 (6%)

Query: 409 FTPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRF-KGYGHVEFASV 467
            TP+   ++T+F   L   +   D++ FFS V +V DVR+ SD + R  KG  +VEF  V
Sbjct: 145 LTPEERDARTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDV 204

Query: 468 EDAHKAIELNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFD 527
                AI L GQ    R + +    +            +N+ QKG  G     +++    
Sbjct: 205 SSVPLAIGLTGQ----RVLGVPIIVQASQAEKNRAAAMANNLQKGSAGPM--RLYVGSLH 258

Query: 528 SSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGT 586
            ++ ED +R   E      G I  I +  D +TG  KG  ++ F+D++   KALE ++G 
Sbjct: 259 FNITEDMLRGIFEPF----GRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGF 314

Query: 587 EIGGYSLVVDEAKQRGD 603
           E+ G  + V    +R D
Sbjct: 315 ELAGRPMKVGHVTERTD 331

Transcriptional coactivator for steroid nuclear receptors ESR1/ER-alpha and ESR2/ER-beta, and JUN/AP-1 (By similarity). May be involved in pre-mRNA splicing process.

Pongo abelii (taxid: 9601)

>sp|Q8VH51|RBM39_MOUSE RNA-binding protein 39 OS=Mus musculus GN=Rbm39 PE=1 SV=2

 Score = 78.6 bits (192), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 58/197 (29%), Positives = 92/197 (46%), Gaps = 12/197 (6%)

Query: 409 FTPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRF-KGYGHVEFASV 467
            TP+   ++T+F   L   +   D++ FFS V +V DVR+ SD + R  KG  +VEF  V
Sbjct: 145 LTPEERDARTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDV 204

Query: 468 EDAHKAIELNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFD 527
                AI L GQ    R + +    +            +N+ QKG  G     +++    
Sbjct: 205 SSVPLAIGLTGQ----RVLGVPIIVQASQAEKNRAAAMANNLQKGSAGPM--RLYVGSLH 258

Query: 528 SSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGT 586
            ++ ED +R   E      G I  I +  D +TG  KG  ++ F+D++   KALE ++G 
Sbjct: 259 FNITEDMLRGIFEPF----GRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGF 314

Query: 587 EIGGYSLVVDEAKQRGD 603
           E+ G  + V    +R D
Sbjct: 315 ELAGRPMKVGHVTERTD 331

Transcriptional coactivator for steroid nuclear receptors ESR1/ER-alpha and ESR2/ER-beta, and JUN/AP-1. May be involved in pre-mRNA splicing process.

Mus musculus (taxid: 10090)

>sp|Q14498|RBM39_HUMAN RNA-binding protein 39 OS=Homo sapiens GN=RBM39 PE=1 SV=2

 Score = 78.2 bits (191), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 58/197 (29%), Positives = 92/197 (46%), Gaps = 12/197 (6%)

Query: 409 FTPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRF-KGYGHVEFASV 467
            TP+   ++T+F   L   +   D++ FFS V +V DVR+ SD + R  KG  +VEF  V
Sbjct: 145 LTPEERDARTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDV 204

Query: 468 EDAHKAIELNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFD 527
                AI L GQ    R + +    +            +N+ QKG  G     +++    
Sbjct: 205 SSVPLAIGLTGQ----RVLGVPIIVQASQAEKNRAAAMANNLQKGSAGPM--RLYVGSLH 258

Query: 528 SSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGT 586
            ++ ED +R   E      G I  I +  D +TG  KG  ++ F+D++   KALE ++G 
Sbjct: 259 FNITEDMLRGIFEPF----GRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGF 314

Query: 587 EIGGYSLVVDEAKQRGD 603
           E+ G  + V    +R D
Sbjct: 315 ELAGRPMKVGHVTERTD 331

Transcriptional coactivator for steroid nuclear receptors ESR1/ER-alpha and ESR2/ER-beta, and JUN/AP-1 (By similarity). May be involved in pre-mRNA splicing process.

Homo sapiens (taxid: 9606)

>sp|P09405|NUCL_MOUSE Nucleolin OS=Mus musculus GN=Ncl PE=1 SV=2

 Score = 74.3 bits (181), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 72/240 (30%), Positives = 118/240 (49%), Gaps = 39/240 (16%)

Query: 370 DSDDEDEGEEEEASKTPKKNVTDVKMVDAESGKKAAQTPFT-PQSGGSKTLFVGNLPFSV 428
           ++D E   EE++ ++   ++V+       E G++  +T  T   SG SKTL + NL +S 
Sbjct: 441 EADAEKNLEEKQGAEIDGRSVSL--YYTGEKGQRQERTGKTSTWSGESKTLVLSNLSYSA 498

Query: 429 EQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQM-LGNRAIR 487
            +  ++  F    +   +++  +  G+ KGY  +EFAS EDA +A+    +M +  R IR
Sbjct: 499 TKETLEEVFE---KATFIKVPQNPHGKPKGYAFIEFASFEDAKEALNSCNKMEIEGRTIR 555

Query: 488 LDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHF-GSC 546
           L+                SNS     R Q + T+F+KG    + ED    +L+E F GS 
Sbjct: 556 LEL-------------QGSNS-----RSQPSKTLFVKG----LSEDTTEETLKESFEGSV 593

Query: 547 GEITRISVPKDYDTGSVKGIAYLDFT---DADSFNKALEMSGTEIGGYSLVVDEAKQRGD 603
               R  +  D +TGS KG  ++DF    DA +  +A+E    EI G  + +D AK +G+
Sbjct: 594 ----RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAME--DGEIDGNKVTLDWAKPKGE 647

Nucleolin is the major nucleolar protein of growing eukaryotic cells. It is found associated with intranucleolar chromatin and pre-ribosomal particles. It induces chromatin decondensation by binding to histone H1. It is thought to play a role in pre-rRNA transcription and ribosome assembly. May play a role in the process of transcriptional elongation. Binds RNA oligonucleotides with 5'-UUAGGG-3' repeats more tightly than the telomeric single-stranded DNA 5'-TTAGGG-3' repeats.

Mus musculus (taxid: 10090)

>sp|P49314|ROC2_NICPL 31 kDa ribonucleoprotein, chloroplastic OS=Nicotiana plumbaginifolia PE=2 SV=1

 Score = 73.2 bits (178), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 62/206 (30%), Positives = 104/206 (50%), Gaps = 31/206 (15%)

Query: 419 LFVGNLPFSVEQADVQNFF-----SEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKA 473
           LFVGNLPFSV+ A +   F      E+ EV+  +LS    GR +G+G V  ++ E+   A
Sbjct: 90  LFVGNLPFSVDSAALAGLFERAGNVEIVEVIYDKLS----GRSRGFGFVTMSTKEEVEAA 145

Query: 474 -IELNGQMLGNRAIRLD------------FARERGAYTPYSGGNESNSFQKGGRG----Q 516
             + NG  +  RAIR++            F   RG  + Y GG + NS   G RG     
Sbjct: 146 EQQFNGYEIDGRAIRVNAGPAPAKRENSSFGGGRGGNSSYGGGRDGNSSFGGARGGRSVD 205

Query: 517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADS 576
           +++ +++   + S G D +  +L+E F   G +    V  D D+G  +G  ++ ++ A  
Sbjct: 206 SSNRVYVG--NLSWGVDDL--ALKELFSEQGNVVDAKVVYDRDSGRSRGFGFVTYSSAKE 261

Query: 577 FNKALE-MSGTEIGGYSLVVDEAKQR 601
            N A++ ++G ++ G S+ V  A++R
Sbjct: 262 VNDAIDSLNGIDLDGRSIRVSAAEER 287

Nicotiana plumbaginifolia (taxid: 4092)

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	675
359472731	664	PREDICTED: uncharacterized protein LOC10	0.810	0.823	0.480	1e-101
297737935	691	unnamed protein product [Vitis vinifera]	0.32	0.312	0.691	4e-86
940288	611	protein localized in the nucleoli of pea	0.423	0.468	0.583	9e-80
356538573	748	PREDICTED: uncharacterized protein LOC10	0.388	0.350	0.580	4e-78
356544468	744	PREDICTED: uncharacterized protein LOC10	0.385	0.349	0.594	5e-76
357473911	623	RNA-binding protein [Medicago truncatula	0.32	0.346	0.608	3e-74
357473909	635	RNA-binding protein [Medicago truncatula	0.32	0.340	0.608	3e-74
118486193	590	unknown [Populus trichocarpa]	0.322	0.369	0.592	1e-73
1279563	635	nuM1 [Medicago sativa]	0.318	0.338	0.606	2e-73
224096554	548	predicted protein [Populus trichocarpa]	0.322	0.397	0.592	3e-73

>gi|359472731|ref|XP_002277195.2| PREDICTED: uncharacterized protein LOC100262769 [Vitis vinifera]

 Score =  375 bits (962), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 299/622 (48%), Positives = 380/622 (61%), Gaps = 75/622 (12%)

Query: 1   VDAAPVVATPTKSAKKGGKREAEDAIEKLVSAKKQKGNDGVAQAVKKAKVEAKTQKKNKN 60
           VDA PVV  P+K  KKG KR+AED++EK+VSAKKQK ++GV Q V+K KVE K Q+K + 
Sbjct: 12  VDATPVVTPPSKPTKKG-KRQAEDSVEKVVSAKKQKKDNGVEQVVQKQKVEVKKQQKVET 70

Query: 61  DETSSSSSEED----SSDSEEEQKVKAVVTNKGGKAAKPPVKESSSEEEDSSSDEEPPKK 116
            +     +       SSDS+EE K     + KG   AKPP K +  E             
Sbjct: 71  KKKKKEETSSSEDLTSSDSDEEPKA-TTASKKGAIPAKPPAKATVEES------------ 117

Query: 117 QPVAAKNGAVAATAKKSKPDSSSSDSSDDDSDEDEVPTSIKKLPVAAAKNG----PSAPQ 172
                               SS  +SS D+  + +V    KK P++A+KNG    P A  
Sbjct: 118 --------------------SSDEESSSDEEPDSKVAVPSKKKPISASKNGTAAGPVAAA 157

Query: 173 KKKDDSSDSSDEESDESSDEDDKSTKAIPQPKKLPAST--AKKGTVAATKKSTGSSDDDS 230
           KK  DSS S   +  +S +E  ++ K   QPKKLPA+   AK G+V A KK   SSD   
Sbjct: 158 KKVSDSSSSDSSDDSDSDEEIKEANKVSSQPKKLPATAKAAKNGSVVAPKKKEESSDSSD 217

Query: 231 SSSEDSSESEEDNGAPAKVTSEAKKLP--AVKNVPAPAAKKKTESSDSSDEESEDSSDED 288
           S S    E E+     +KV S+AKKLP  + KNVP  A KK   S  S + +S++     
Sbjct: 218 SDSSSDEEDEKA----SKVASQAKKLPPSSQKNVPVAAPKKAESSDSSDESDSDEEEPAA 273

Query: 289 EEPTHVTKATPVKKLSAVVTKNKVESSSSSDESESEEEKPPAKMDVDSSSEEESSDEEPQ 348
            +     K          V  +   S +SS+E E  ++KP  K D       + SDEEPQ
Sbjct: 274 AKNVAAAKNVIAAAPKKKVQSSDSSSETSSEEEEEPQKKPAPKEDSSEDDSSDESDEEPQ 333

Query: 349 KKKDVKPNTKALKKESSSDEEDSDDEDEGEEEEASKTPKKNVTDVKMVDAE--------- 399
           KKK        LK++SS ++   ++    +EEE SKTPKKN TDV+MVDAE         
Sbjct: 334 KKK--------LKEDSSEEDSSEEES---DEEEPSKTPKKNGTDVEMVDAETPAKQTDSK 382

Query: 400 SGKKAAQTPFTPQ--SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFK 457
           SGKKA +TP TPQ  S GSKTLFVGNL FSV++ DV++FF +  EVVDVR SSDADGRFK
Sbjct: 383 SGKKAPKTPATPQVESTGSKTLFVGNLSFSVQKEDVEHFFKDAGEVVDVRFSSDADGRFK 442

Query: 458 GYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQA 517
           G+GHVEFA+ E A KA+++NG+ L  RA+RLD ARERGAYTPYSG  ESNSFQKGG    
Sbjct: 443 GFGHVEFATPEAAQKALKMNGKDLLGRAVRLDLARERGAYTPYSG-KESNSFQKGG--SQ 499

Query: 518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSF 577
           A TIF++GFD S  EDQVR++LEE+FGSCG+I+RIS+PKDY++GSVKGIAY+DFTD DSF
Sbjct: 500 AQTIFVRGFDKSGDEDQVRSTLEEYFGSCGDISRISIPKDYESGSVKGIAYMDFTDGDSF 559

Query: 578 NKALEMSGTEIGGYSLVVDEAK 599
           NKALE++GTE+GGY+L V+EAK
Sbjct: 560 NKALELNGTELGGYTLNVEEAK 581

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297737935|emb|CBI27136.3| unnamed protein product [Vitis vinifera]

 Score =  325 bits (834), Expect = 4e-86,   Method: Compositional matrix adjust.
 Identities = 159/230 (69%), Positives = 189/230 (82%), Gaps = 14/230 (6%)

Query: 383 SKTPKKNVTDVKMVDAE---------SGKKAAQTPFTPQ--SGGSKTLFVGNLPFSVEQA 431
           SKTPKKN TDV+MVDAE         SGKKA +TP TPQ  S GSKTLFVGNL FSV++ 
Sbjct: 403 SKTPKKNGTDVEMVDAETPAKQTDSKSGKKAPKTPATPQVESTGSKTLFVGNLSFSVQKE 462

Query: 432 DVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFA 491
           DV++FF +  EVVDVR SSDADGRFKG+GHVEFA+ E A KA+++NG+ L  RA+RLD A
Sbjct: 463 DVEHFFKDAGEVVDVRFSSDADGRFKGFGHVEFATPEAAQKALKMNGKDLLGRAVRLDLA 522

Query: 492 RERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITR 551
           RERGAYTPYSG  ESNSFQKGG    A TIF++GFD S  EDQVR++LEE+FGSCG+I+R
Sbjct: 523 RERGAYTPYSG-KESNSFQKGG--SQAQTIFVRGFDKSGDEDQVRSTLEEYFGSCGDISR 579

Query: 552 ISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDEAKQR 601
           IS+PKDY++GSVKGIAY+DFTD DSFNKALE++GTE+GGY+L V+EAK R
Sbjct: 580 ISIPKDYESGSVKGIAYMDFTDGDSFNKALELNGTELGGYTLNVEEAKPR 629

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|940288|gb|AAA74208.1| protein localized in the nucleoli of pea nuclei; ORF; putative [Pisum sativum]

 Score =  304 bits (779), Expect = 9e-80,   Method: Compositional matrix adjust.
 Identities = 175/300 (58%), Positives = 214/300 (71%), Gaps = 14/300 (4%)

Query: 383 SKTPKKNVTDVKMVDAE-SGKKAAQTPFTP-QSGGSKTLFVGNLPFSVEQADVQNFFSEV 440
           SKTP+K   DV+M+DA+ S KKA  TP TP ++GGSKTLFVGNL FSV+++D+++FF E 
Sbjct: 319 SKTPQKKTKDVEMIDADKSSKKAPATPATPSENGGSKTLFVGNLSFSVQRSDIESFFQEC 378

Query: 441 AEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARERGAYTPY 500
            EVVDVRL+SD DGRFKG+GHVEFA+ E A  A+ELNGQ L  R +RLD ARERGA+TP 
Sbjct: 379 GEVVDVRLASDEDGRFKGFGHVEFATAEAAQSALELNGQELLQRGVRLDLARERGAFTPN 438

Query: 501 SGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDT 560
           S GN     Q  GRGQ + T+F++GFD S+GED++RA LE+HF SCG+ +R+S+PKDYDT
Sbjct: 439 STGN-----QNSGRGQ-SQTVFVRGFDKSLGEDEIRAKLEQHFASCGQASRVSIPKDYDT 492

Query: 561 GSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDEAKQRGDFGSGGGRSGGRGGRSGG 620
           G  KG AY+DF D+DSFNKA+E+ G+E+ GY L +DEAK R +    GGR   RGG S G
Sbjct: 493 GYSKGFAYMDFKDSDSFNKAIELHGSELDGYPLSIDEAKPR-ESTGFGGRGTPRGGGSRG 551

Query: 621 RDFGRSGGRDGGRF-----GGRGRGGRDGGRGGRGRGRGTPNRPSLAAAGTGKKTTFGDD 675
           R         GGRF     GGR  G   G  G RG GR   N+PSLA  GTGKKTTF DD
Sbjct: 552 RGGRFGDRNSGGRFGDRSGGGRSGGRDGGRGGRRGGGRFGFNKPSLAPEGTGKKTTFADD 611

Source: Pisum sativum

Species: Pisum sativum

Genus: Pisum

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356538573|ref|XP_003537777.1| PREDICTED: uncharacterized protein LOC100786132 [Glycine max]

 Score =  299 bits (765), Expect = 4e-78,   Method: Compositional matrix adjust.
 Identities = 159/274 (58%), Positives = 201/274 (73%), Gaps = 12/274 (4%)

Query: 331 KMDVDSSSEEESSDEEPQKKKDVKPNTKALKKESSSDEEDSDDEDEGEEEEASKTPKKNV 390
           KMD+D   +     EEPQKKK       A+K    S +   +D ++  EE+ SKTP+K  
Sbjct: 397 KMDIDDDDDSSDESEEPQKKK-------AVKNSKESSDSSEEDSEDESEEKPSKTPQKRG 449

Query: 391 TDVKMVDAE-SGKKAAQTPFTPQ--SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVR 447
            DV+MVDA  S KKA +TP TP+  SG SKTLFVGNLPFSVE+ADV+ FF +  EVVDVR
Sbjct: 450 RDVEMVDAALSEKKAPKTPVTPREESGTSKTLFVGNLPFSVERADVEGFFKDAGEVVDVR 509

Query: 448 LSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARERGAYTPYSGGNESN 507
            ++D  G+FKG+GHVEFA+ E A  A+ LNGQ L NR +RLD ARERGAYTP S    ++
Sbjct: 510 FATDDTGKFKGFGHVEFATAEAAQNALGLNGQQLFNRELRLDLARERGAYTPNSSNWNNS 569

Query: 508 SFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIA 567
           S QK  RGQ+  TIF++GFD+S+GED++R SL+EHFGSCG+ITR+S+PKDY++G+VKG A
Sbjct: 570 S-QKSERGQS-QTIFVRGFDTSLGEDEIRGSLQEHFGSCGDITRVSIPKDYESGAVKGFA 627

Query: 568 YLDFTDADSFNKALEMSGTEIGGYSLVVDEAKQR 601
           Y+DF DADS  KALE+  TE+GGY+L VDEAK R
Sbjct: 628 YVDFGDADSMGKALELHETELGGYTLTVDEAKPR 661

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356544468|ref|XP_003540672.1| PREDICTED: uncharacterized protein LOC100779929 [Glycine max]

 Score =  292 bits (747), Expect = 5e-76,   Method: Compositional matrix adjust.
 Identities = 163/274 (59%), Positives = 207/274 (75%), Gaps = 14/274 (5%)

Query: 331 KMDVDSSSEEESSDEEPQKKKDVKPNTKALKKESSSDEEDSDDEDEGEEEEASKTPKKNV 390
           KMD+D  S +ES   EPQKKK VK N K       S +   +D ++  EEE SKTP+K  
Sbjct: 394 KMDIDDDSSDESE--EPQKKKTVK-NPK------ESSDSSEEDSEDESEEEPSKTPQKRD 444

Query: 391 TDVKMVDA-ESGKKAAQTPFTP--QSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVR 447
            DV+MVDA  SGKKA +TP TP  ++G SKTLFVGNLPFSVE+ADV++FF +  EVVDVR
Sbjct: 445 RDVEMVDAASSGKKAPKTPVTPKEETGASKTLFVGNLPFSVERADVEDFFKDAGEVVDVR 504

Query: 448 LSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARERGAYTPYSGGNESN 507
            ++D  G+FKG+GHVEFA+   A KA+ LNGQ L NR +RLD ARERGAYTP S    ++
Sbjct: 505 FATDDTGKFKGFGHVEFATAAAAQKALGLNGQQLFNRELRLDLARERGAYTPNSSNWNNS 564

Query: 508 SFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIA 567
           S QK GRGQ + T+F++GFD+S+GED++R SL+EHFGSCG+ITR+S+PKDY++G+VKG A
Sbjct: 565 S-QKSGRGQ-SQTVFVRGFDTSLGEDEIRGSLQEHFGSCGDITRVSIPKDYESGAVKGFA 622

Query: 568 YLDFTDADSFNKALEMSGTEIGGYSLVVDEAKQR 601
           Y+DF+D DS  KALE+  TE+GGY+L VDEAK R
Sbjct: 623 YVDFSDVDSMGKALELHETELGGYTLTVDEAKPR 656

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357473911|ref|XP_003607240.1| RNA-binding protein [Medicago truncatula] gi|355508295|gb|AES89437.1| RNA-binding protein [Medicago truncatula]

 Score =  286 bits (732), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 135/222 (60%), Positives = 174/222 (78%), Gaps = 6/222 (2%)

Query: 383 SKTPKKNVTDVKMVDA-ESGKKAAQTPFTP-QSGGSKTLFVGNLPFSVEQADVQNFFSEV 440
           SKTP+K + DV+MVDA +SGKKA  TP TP ++ GSKTLFVGNL FSV+++D++ FF + 
Sbjct: 328 SKTPQKKIKDVEMVDAGKSGKKAPNTPATPIENSGSKTLFVGNLSFSVQRSDIEKFFQDC 387

Query: 441 AEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARERGAYTPY 500
            EVVDVR SSD +GRFKG+GHVEFAS E A  A+E+NGQ L  RA+RLD ARERGA+TP 
Sbjct: 388 GEVVDVRFSSDEEGRFKGFGHVEFASAEAAQSALEMNGQELLQRAVRLDLARERGAFTP- 446

Query: 501 SGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHF-GSCGEITRISVPKDYD 559
              N + S Q GGRGQ + T+F++GFD ++GED++RA L EHF G+CGE TR+S+PKD++
Sbjct: 447 -NNNSNYSAQSGGRGQ-SQTVFVRGFDKNLGEDEIRAKLMEHFGGTCGEPTRVSIPKDFE 504

Query: 560 TGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDEAKQR 601
           +G  KG AY+DF D+DSF+KALE+  +E+ GY L VDEAK R
Sbjct: 505 SGYSKGFAYMDFKDSDSFSKALELHESELDGYQLSVDEAKPR 546

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357473909|ref|XP_003607239.1| RNA-binding protein [Medicago truncatula] gi|355508294|gb|AES89436.1| RNA-binding protein [Medicago truncatula]

 Score =  286 bits (731), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 135/222 (60%), Positives = 174/222 (78%), Gaps = 6/222 (2%)

Query: 383 SKTPKKNVTDVKMVDA-ESGKKAAQTPFTP-QSGGSKTLFVGNLPFSVEQADVQNFFSEV 440
           SKTP+K + DV+MVDA +SGKKA  TP TP ++ GSKTLFVGNL FSV+++D++ FF + 
Sbjct: 340 SKTPQKKIKDVEMVDAGKSGKKAPNTPATPIENSGSKTLFVGNLSFSVQRSDIEKFFQDC 399

Query: 441 AEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARERGAYTPY 500
            EVVDVR SSD +GRFKG+GHVEFAS E A  A+E+NGQ L  RA+RLD ARERGA+TP 
Sbjct: 400 GEVVDVRFSSDEEGRFKGFGHVEFASAEAAQSALEMNGQELLQRAVRLDLARERGAFTP- 458

Query: 501 SGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHF-GSCGEITRISVPKDYD 559
              N + S Q GGRGQ + T+F++GFD ++GED++RA L EHF G+CGE TR+S+PKD++
Sbjct: 459 -NNNSNYSAQSGGRGQ-SQTVFVRGFDKNLGEDEIRAKLMEHFGGTCGEPTRVSIPKDFE 516

Query: 560 TGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDEAKQR 601
           +G  KG AY+DF D+DSF+KALE+  +E+ GY L VDEAK R
Sbjct: 517 SGYSKGFAYMDFKDSDSFSKALELHESELDGYQLSVDEAKPR 558

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118486193|gb|ABK94939.1| unknown [Populus trichocarpa]

 Score =  284 bits (727), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 134/226 (59%), Positives = 174/226 (76%), Gaps = 8/226 (3%)

Query: 383 SKTPKKNVTDVKMVDAE--SGKKAAQTPFTP---QSGGSKTLFVGNLPFSVEQADVQNFF 437
           +KTPKKN TDV+MVDA+  S  K  +TP TP   ++ GSKTLFVGNL F VE+ADV+NFF
Sbjct: 301 AKTPKKNDTDVEMVDADIKSDVKTPKTPVTPVAHENTGSKTLFVGNLSFQVERADVENFF 360

Query: 438 SEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARERGAY 497
               EV DVR + DAD RF+G+GHVEF + E A KA++L+G  L  R +RLD ARE+G+ 
Sbjct: 361 KGAGEVADVRFALDADERFRGFGHVEFTTAEAAQKALKLHGNTLLGRDVRLDLAREKGSN 420

Query: 498 TPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKD 557
           TPYS   +S+SF KGG GQ+  TIF++GFD S GED++R+SL+EHFGSCGEI R+S+P D
Sbjct: 421 TPYS--KDSSSFPKGGSGQS-QTIFVRGFDKSAGEDEIRSSLQEHFGSCGEIKRVSIPTD 477

Query: 558 YDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDEAKQRGD 603
           YDTG++KG+AYL+F DAD+ +KA E++G+++G Y L VDEAK R D
Sbjct: 478 YDTGAIKGMAYLEFNDADALSKAFELNGSQLGEYCLTVDEAKPRSD 523

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|1279563|emb|CAA61298.1| nuM1 [Medicago sativa]

 Score =  283 bits (724), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 134/221 (60%), Positives = 173/221 (78%), Gaps = 6/221 (2%)

Query: 384 KTPKKNVTDVKMVDA-ESGKKAAQTPFTP-QSGGSKTLFVGNLPFSVEQADVQNFFSEVA 441
           KTP+K + DV+MVDA +SGKKA  TP TP ++ GSKTLFVGNL F V+++D++NFF    
Sbjct: 341 KTPQKKIKDVEMVDAGKSGKKAPNTPATPNETSGSKTLFVGNLSFDVKRSDIENFFQGCV 400

Query: 442 EVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARERGAYTPYS 501
           EVVDVRL+SD DG FKG+GHVEFA+ E A  A+E+NGQ L +RA+RLD ARERGA+TP  
Sbjct: 401 EVVDVRLASDGDGVFKGFGHVEFATAEAAQSALEMNGQELLHRALRLDLARERGAFTP-- 458

Query: 502 GGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHF-GSCGEITRISVPKDYDT 560
             N + S Q GGRGQ + T+F++GFD ++GED++RA L EHF G+CGE TR+S+PKDY++
Sbjct: 459 NNNSNYSAQSGGRGQ-SQTVFVRGFDKNLGEDEIRAKLMEHFGGTCGEPTRVSIPKDYES 517

Query: 561 GSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDEAKQR 601
           G  KG AY+DF D+DSF+KALE+  +E+ GY L VDEAK R
Sbjct: 518 GYSKGFAYMDFKDSDSFSKALELHESELDGYQLSVDEAKPR 558

Source: Medicago sativa

Species: Medicago sativa

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224096554|ref|XP_002310655.1| predicted protein [Populus trichocarpa] gi|222853558|gb|EEE91105.1| predicted protein [Populus trichocarpa]

 Score =  282 bits (722), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 134/226 (59%), Positives = 174/226 (76%), Gaps = 8/226 (3%)

Query: 383 SKTPKKNVTDVKMVDAE--SGKKAAQTPFTP---QSGGSKTLFVGNLPFSVEQADVQNFF 437
           +KTPKKN TDV+MVDA+  S  K  +TP TP   ++ GSKTLFVGNL F VE+ADV+NFF
Sbjct: 259 AKTPKKNDTDVEMVDADIKSDVKTPKTPVTPVAHENTGSKTLFVGNLSFQVERADVENFF 318

Query: 438 SEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARERGAY 497
               EV DVR + DAD RF+G+GHVEF + E A KA++L+G  L  R +RLD ARE+G+ 
Sbjct: 319 KGAGEVADVRFALDADERFRGFGHVEFTTAEAAQKALKLHGNTLLGRDVRLDLAREKGSN 378

Query: 498 TPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKD 557
           TPYS   +S+SF KGG GQ+  TIF++GFD S GED++R+SL+EHFGSCGEI R+S+P D
Sbjct: 379 TPYS--KDSSSFPKGGSGQS-QTIFVRGFDKSAGEDEIRSSLQEHFGSCGEIKRVSIPTD 435

Query: 558 YDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDEAKQRGD 603
           YDTG++KG+AYL+F DAD+ +KA E++G+++G Y L VDEAK R D
Sbjct: 436 YDTGAIKGMAYLEFNDADALSKAFELNGSQLGEYRLTVDEAKPRSD 481

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	675
TAIR|locus:2028451	557	NUC-L1 "nucleolin like 1" [Ara	0.358	0.434	0.494	7.6e-70
TAIR|locus:2086884	636	NUC-L2 "nucleolin like 2" [Ara	0.305	0.323	0.516	4.3e-66
POMBASE|SPAC140.02	500	gar2 "nucleolar protein requir	0.282	0.382	0.315	1.3e-17
ASPGD|ASPL0000076731	524	AN4865 [Emericella nidulans (t	0.296	0.381	0.320	3.9e-17
UNIPROTKB|F1P336	689	NCL "Nucleolin" [Gallus gallus	0.274	0.268	0.333	2.4e-15
UNIPROTKB|F1NU40	691	NCL "Nucleolin" [Gallus gallus	0.274	0.267	0.333	2.4e-15
UNIPROTKB|P15771	694	NCL "Nucleolin" [Gallus gallus	0.274	0.266	0.333	2.4e-15
UNIPROTKB|G4MY43	486	MGG_01268 "Nuclear localizatio	0.148	0.205	0.485	8.3e-15
TAIR|locus:2160437	567	AT5G41690 [Arabidopsis thalian	0.269	0.320	0.323	3.9e-14
POMBASE|SPBC4F6.14	674	SPBC4F6.14 "RNA-binding protei	0.262	0.262	0.327	4.1e-14

TAIR|locus:2028451 NUC-L1 "nucleolin like 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 586 (211.3 bits), Expect = 7.6e-70, Sum P(4) = 7.6e-70
 Identities = 129/261 (49%), Positives = 170/261 (65%)

Query:   348 QKKKDVKPNTKALKKXXXXXXXXXXXXXXXXXXXXXKTPKKNVTDVKMVDAE-SGKKAAQ 406
             +K    K +TKA KK                     +TPKK  +DV+MVDAE S  K  +
Sbjct:   230 EKPAQKKADTKASKKSSSDESSESEEDESEDEE---ETPKKKSSDVEMVDAEKSSAKQPK 286

Query:   407 TPFTPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFA 465
             TP TP +GGSKTLF  NL F++E+ADV+NFF E  EVVDVR S++ D G F+G+GHVEFA
Sbjct:   287 TPSTPAAGGSKTLFAANLSFNIERADVENFFKEAGEVVDVRFSTNRDDGSFRGFGHVEFA 346

Query:   466 SVEDAHKAIELNGQMLGNRAIRLDFARERG------AYTPYSGGNESNSFQKGGRGQAAH 519
             S E+A KA+E +G+ L  R IRLD A+ERG      A+TP SG     +F+ GG G    
Sbjct:   347 SSEEAQKALEFHGRPLLGREIRLDIAQERGERGERPAFTPQSG-----NFRSGGDGGDEK 401

Query:   520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNK 579
              IF+KGFD+S+ ED ++ +L EHF SCGEI  +SVP D DTG+ KGIAYL+F++     K
Sbjct:   402 KIFVKGFDASLSEDDIKNTLREHFSSCGEIKNVSVPIDRDTGNSKGIAYLEFSEGKE--K 459

Query:   580 ALEMSGTEIGG-YSLVVDEAK 599
             ALE++G+++GG + LVVDE +
Sbjct:   460 ALELNGSDMGGGFYLVVDEPR 480

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA;ISS

GO:0005730 "nucleolus" evidence=IDA

GO:0006364 "rRNA processing" evidence=RCA;IMP

GO:0042254 "ribosome biogenesis" evidence=TAS

GO:0000478 "endonucleolytic cleavage involved in rRNA processing" evidence=RCA;IMP

GO:0010305 "leaf vascular tissue pattern formation" evidence=IMP

GO:0010588 "cotyledon vascular tissue pattern formation" evidence=IMP

GO:0048364 "root development" evidence=IMP

GO:0048366 "leaf development" evidence=IMP

GO:0048367 "shoot system development" evidence=IMP

GO:0080056 "petal vascular tissue pattern formation" evidence=IMP

GO:0080057 "sepal vascular tissue pattern formation" evidence=IMP

GO:0005829 "cytosol" evidence=RCA

GO:0001510 "RNA methylation" evidence=RCA

GO:0009220 "pyrimidine ribonucleotide biosynthetic process" evidence=RCA

GO:0005739 "mitochondrion" evidence=IDA

TAIR|locus:2086884 NUC-L2 "nucleolin like 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 565 (203.9 bits), Expect = 4.3e-66, Sum P(4) = 4.3e-66
 Identities = 112/217 (51%), Positives = 153/217 (70%)

Query:   385 TPKKNVTDVKMVDAE--SGKKAAQTPFTPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAE 442
             TPKK  +DV+MVDAE  S  K  +TP     GGSKTLF GNL + + ++D++NFF E  E
Sbjct:   350 TPKKKDSDVEMVDAEQKSNAKQPKTPTNQTQGGSKTLFAGNLSYQIARSDIENFFKEAGE 409

Query:   443 VVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARERGAYTPYSG 502
             VVDVRLSS  DG FKGYGH+EFAS E+A KA+E+NG++L  R +RLD A ERG  TP   
Sbjct:   410 VVDVRLSSFDDGSFKGYGHIEFASPEEAQKALEMNGKLLLGRDVRLDLANERG--TP--- 464

Query:   503 GNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGS 562
                SN  +KG  G  + TI+++GF SS+GED+++  L  HF  CGE+TR+ VP D +TG+
Sbjct:   465 -RNSNPGRKG-EGSQSRTIYVRGFSSSLGEDEIKKELRSHFSKCGEVTRVHVPTDRETGA 522

Query:   563 VKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDEAK 599
              +G AY+D T    F++AL++SG+EIGG ++ V+E++
Sbjct:   523 SRGFAYIDLTSG--FDEALQLSGSEIGGGNIHVEESR 557

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

GO:0005730 "nucleolus" evidence=IDA

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

POMBASE|SPAC140.02 gar2 "nucleolar protein required for rRNA processing" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 239 (89.2 bits), Expect = 1.3e-17, P = 1.3e-17
 Identities = 63/200 (31%), Positives = 98/200 (49%)

Query:   394 KMVDAESGKKAAQTPFTPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD 453
             K   A   + A  T  +  S  + T+FVG L ++V+   +   F E   +V  R+  D  
Sbjct:   240 KAEPASEERPAKITKPSQDSNETCTVFVGRLSWNVDDQWLGQEFEEYGTIVGARVIMDGQ 299

Query:   454 -GRFKGYGHVEFASVEDAHKAIELNG-QMLGNRAIRLDFARERGAYT-PYSGGNESNSFQ 510
              GR KGYG+V+F + E A  A+  NG + +  R + LD +  R A   PY+     N   
Sbjct:   300 SGRSKGYGYVDFETPEAAKAAVAANGTKEIDGRMVNLDLSNPRPANPQPYAQQRAGNFGD 359

Query:   511 KGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLD 570
             +    + + T+F+     +  ED +  +    FG CG+I  I +P D  +G +KG  Y+ 
Sbjct:   360 Q--LSEPSDTVFVGNLSFNATEDDLSTA----FGGCGDIQSIRLPTDPQSGRLKGFGYVT 413

Query:   571 FTDADSFNKALEMSGTEIGG 590
             F+D DS  K +EM+G  I G
Sbjct:   414 FSDIDSAKKCVEMNGHFIAG 433

GO:0003723 "RNA binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IDA

GO:0005732 "small nucleolar ribonucleoprotein complex" evidence=ISS

GO:0006364 "rRNA processing" evidence=IMP

GO:0007000 "nucleolus organization" evidence=IMP

GO:0042254 "ribosome biogenesis" evidence=IMP

ASPGD|ASPL0000076731 AN4865 [Emericella nidulans (taxid:162425)]

 Score = 237 (88.5 bits), Expect = 3.9e-17, Sum P(2) = 3.9e-17
 Identities = 68/212 (32%), Positives = 100/212 (47%)

Query:   392 DVKMVDAESGKKAAQTPFTPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD 451
             D K   AE    AA      + G S  LFVGNL ++V +  +   F +  E+   R+ ++
Sbjct:   252 DSKKRKAEEEPAAASKKSKTEEGASANLFVGNLSWNVTEEWLHQEFEQFGEL-SARIMTE 310

Query:   452 AD-GRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARERGAYTPYSGGNE--SN 507
              D GR +G+G+VEF +  DA KA E +    +  R I LD+A  R A     G  E   N
Sbjct:   311 RDTGRSRGFGYVEFTNAADAAKAYEAMKEHEIDGRKINLDYATGRPANKDQGGFKERAQN 370

Query:   508 SFQKGG--RGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKG 565
               +  G      + T+F+     S  ED    S+ E FG  G +  I +P D ++G  KG
Sbjct:   371 RARSFGDQTSPESDTLFVGNLPFSANED----SVHEVFGPQGNVLGIRLPTDMESGRPKG 426

Query:   566 IAYLDFTDADSFNKAL-EMSGTEIGGYSLVVD 596
               Y+ ++  D   KA  E+ G EI G  + +D
Sbjct:   427 FGYVQYSSVDEARKAYNELQGAEIDGRPIRLD 458

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F1P336 NCL "Nucleolin" [Gallus gallus (taxid:9031)]

 Score = 223 (83.6 bits), Expect = 2.4e-15, Sum P(2) = 2.4e-15
 Identities = 70/210 (33%), Positives = 105/210 (50%)

Query:   395 MVDAESGKKAAQTPFTPQSGG---SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD 451
             MV   +G+K+ Q   + + GG   SKTL V NL ++  +  +Q  F +   +   ++  +
Sbjct:   436 MVIDYTGEKSQQE--SQKGGGERESKTLIVNNLSYAASEETLQELFKKATSI---KMPQN 490

Query:   452 ADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQ 510
               GR KGY  VEF + EDA +A+   N   +  RAIRL+F+        +  GN  N+  
Sbjct:   491 NQGRPKGYAFVEFPTAEDAKEALNSCNNTEIEGRAIRLEFSSPS-----WQKGN-MNA-- 542

Query:   511 KGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLD 570
             +GG  Q + T+F++G      E+ +R S E   GS     RI    D DTGS KG  ++D
Sbjct:   543 RGGFNQQSKTLFVRGLSEDTTEETLRESFE---GSIS--ARIVT--DRDTGSSKGFGFVD 595

Query:   571 FTDADSFNKALE-MSGTEIGGYSLVVDEAK 599
             F+  +    A E M   EI G  + +D AK
Sbjct:   596 FSSPEDAKAAKEAMEDGEIDGNKVTLDFAK 625

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|F1NU40 NCL "Nucleolin" [Gallus gallus (taxid:9031)]

 Score = 223 (83.6 bits), Expect = 2.4e-15, Sum P(2) = 2.4e-15
 Identities = 70/210 (33%), Positives = 105/210 (50%)

Query:   395 MVDAESGKKAAQTPFTPQSGG---SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD 451
             MV   +G+K+ Q   + + GG   SKTL V NL ++  +  +Q  F +   +   ++  +
Sbjct:   438 MVIDYTGEKSQQE--SQKGGGERESKTLIVNNLSYAASEETLQELFKKATSI---KMPQN 492

Query:   452 ADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQ 510
               GR KGY  VEF + EDA +A+   N   +  RAIRL+F+        +  GN  N+  
Sbjct:   493 NQGRPKGYAFVEFPTAEDAKEALNSCNNTEIEGRAIRLEFSSPS-----WQKGN-MNA-- 544

Query:   511 KGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLD 570
             +GG  Q + T+F++G      E+ +R S E   GS     RI    D DTGS KG  ++D
Sbjct:   545 RGGFNQQSKTLFVRGLSEDTTEETLRESFE---GSIS--ARIVT--DRDTGSSKGFGFVD 597

Query:   571 FTDADSFNKALE-MSGTEIGGYSLVVDEAK 599
             F+  +    A E M   EI G  + +D AK
Sbjct:   598 FSSPEDAKAAKEAMEDGEIDGNKVTLDFAK 627

GO:0000166 "nucleotide binding" evidence=IEA

GO:0001525 "angiogenesis" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005654 "nucleoplasm" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005938 "cell cortex" evidence=IEA

GO:0008022 "protein C-terminus binding" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0042162 "telomeric DNA binding" evidence=IEA

UNIPROTKB|P15771 NCL "Nucleolin" [Gallus gallus (taxid:9031)]

 Score = 223 (83.6 bits), Expect = 2.4e-15, Sum P(2) = 2.4e-15
 Identities = 70/210 (33%), Positives = 105/210 (50%)

Query:   395 MVDAESGKKAAQTPFTPQSGG---SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD 451
             MV   +G+K+ Q   + + GG   SKTL V NL ++  +  +Q  F +   +   ++  +
Sbjct:   438 MVIDYTGEKSQQE--SQKGGGERESKTLIVNNLSYAASEETLQELFKKATSI---KMPQN 492

Query:   452 ADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQ 510
               GR KGY  VEF + EDA +A+   N   +  RAIRL+F+        +  GN  N+  
Sbjct:   493 NQGRPKGYAFVEFPTAEDAKEALNSCNNTEIEGRAIRLEFSSPS-----WQKGN-MNA-- 544

Query:   511 KGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLD 570
             +GG  Q + T+F++G      E+ +R S E   GS     RI    D DTGS KG  ++D
Sbjct:   545 RGGFNQQSKTLFVRGLSEDTTEETLRESFE---GSIS--ARIVT--DRDTGSSKGFGFVD 597

Query:   571 FTDADSFNKALE-MSGTEIGGYSLVVDEAK 599
             F+  +    A E M   EI G  + +D AK
Sbjct:   598 FSSPEDAKAAKEAMEDGEIDGNKVTLDFAK 627

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

UNIPROTKB|G4MY43 MGG_01268 "Nuclear localization sequence binding protein" [Magnaporthe oryzae 70-15 (taxid:242507)]

 Score = 215 (80.7 bits), Expect = 8.3e-15, Sum P(2) = 8.3e-15
 Identities = 52/107 (48%), Positives = 65/107 (60%)

Query:   416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAI 474
             S TLFVGNLPF  ++  V  FFSEVAEV  +RL ++ + GR KG+G+V F SVEDA  A 
Sbjct:   341 SDTLFVGNLPFDADEDSVGAFFSEVAEVKSLRLPTEQESGRRKGFGYVTFNSVEDAKSAF 400

Query:   475 E-LNGQMLGNRAIRLDFA-----RERGAYTPYSGGNESNSFQKGGRG 515
             E LNGQ +  R  RLD++     RE G +    GG      + GGRG
Sbjct:   401 EQLNGQSINGRNCRLDYSTPRPPREDGGFGGRGGGRGGFGGRGGGRG 447

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2160437 AT5G41690 [Arabidopsis thaliana (taxid:3702)]

 Score = 210 (79.0 bits), Expect = 3.9e-14, P = 3.9e-14
 Identities = 63/195 (32%), Positives = 100/195 (51%)

Query:   417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIEL 476
             KTLFV NLP+  +  ++ +FF +V EVV V+L  +  G+  G G VEFASV +A +A++ 
Sbjct:    68 KTLFVANLPYETKIPNIIDFFKKVGEVVRVQLIVNLKGKLVGCGFVEFASVNEAEEALQK 127

Query:   477 -NGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFI-KGFDSSVGE-- 532
              NG+ L N  I LD A ++  Y P     +   + K  R   +H I   +   +SV E  
Sbjct:   128 KNGECLDNNKIFLDVANKKATYLPPKYCIDHKVWDKDYRRLESHPIEEDERPPNSVEEVL 187

Query:   533 ------DQVRAS-LEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MS 584
                    Q + S + + F   GE+  I +  +++ G   G  +++F  AD   KALE  +
Sbjct:   188 FVANLSPQTKISDIFDFFNCVGEVVSIRLMVNHE-GKHVGYGFVEFASADETKKALENKN 246

Query:   585 GTEIGGYSLVVDEAK 599
             G  +  + + +D AK
Sbjct:   247 GEYLHDHKIFIDVAK 261

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

POMBASE|SPBC4F6.14 SPBC4F6.14 "RNA-binding protein (predicted)" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 211 (79.3 bits), Expect = 4.1e-14, P = 4.1e-14
 Identities = 61/186 (32%), Positives = 95/186 (51%)

Query:   416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVD-VRLSSDADGRFKGYGHVEFASVEDAHKAI 474
             + TLFV NL F  +Q D+ NFFS+V  +   V +++   G  +GYG V F+ +EDA +A 
Sbjct:     4 NSTLFVRNLAFQTKQDDLTNFFSDVGPIKHAVVVTNPETGENRGYGFVTFSMLEDAQRAA 63

Query:   475 -ELNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGED 533
              EL  + L  R +RLDFA  R      +  N++   +K  R      + I+    S+ + 
Sbjct:    64 KELKNKKLHGRILRLDFATPRKRSEVDTDQNKA--VKKTIRQDNRPRLIIRNLPWSIKKP 121

Query:   534 QVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYS 592
             Q    LE HF   G++  I +P     G + G A++   D  +  +A+  ++GTEI G  
Sbjct:   122 Q---HLEPHFSKFGKVREIKIPTK-GGGRMCGFAFVWMKDRKAAEEAMNSLNGTEIDGRP 177

Query:   593 LVVDEA 598
             + VD A
Sbjct:   178 IAVDWA 183

GO:0003723 "RNA binding" evidence=IEA

GO:0005730 "nucleolus" evidence=ISS;IDA

GO:0006364 "rRNA processing" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: fgenesh4_pm.C_LG_VII000277 hypothetical protein (548 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	675
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	1e-30
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	6e-29
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	1e-19
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	7e-19
smart00360	73	smart00360, RRM, RNA recognition motif	8e-19
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-18
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	8e-18
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	9e-18
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-16
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	5e-16
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	8e-16
PLN03237	1465	PLN03237, PLN03237, DNA topoisomerase 2; Provision	9e-16
cd12402	77	cd12402, RRM_eIF4B, RNA recognition motif in eukar	1e-15
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	1e-15
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	2e-15
smart00360	73	smart00360, RRM, RNA recognition motif	4e-15
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	3e-14
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	3e-14
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	7e-14
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	4e-13
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	6e-13
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	6e-13
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	7e-13
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	9e-13
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-12
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	2e-12
COG5271	4600	COG5271, MDN1, AAA ATPase containing von Willebran	4e-12
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	7e-12
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	7e-12
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	8e-12
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	3e-11
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	4e-11
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	4e-11
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	4e-11
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	7e-11
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	7e-11
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	7e-11
PLN03237	1465	PLN03237, PLN03237, DNA topoisomerase 2; Provision	1e-10
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	1e-10
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	1e-10
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	1e-10
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	1e-10
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	2e-10
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	2e-10
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	2e-10
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	2e-10
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	3e-10
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	4e-10
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	4e-10
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	5e-10
cd12508	80	cd12508, RRM2_ESRPs_Fusilli, RNA recognition motif	7e-10
cd12230	82	cd12230, RRM1_U2AF65, RNA recognition motif 1 foun	1e-09
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	1e-09
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	1e-09
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	2e-09
cd12514	73	cd12514, RRM4_RBM12_like, RNA recognition motif 4	2e-09
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	3e-09
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	4e-09
cd12511	73	cd12511, RRM2_RBM12_like, RNA recognition motif 2	4e-09
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	4e-09
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	7e-09
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	7e-09
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	7e-09
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	8e-09
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	9e-09
PLN03237	1465	PLN03237, PLN03237, DNA topoisomerase 2; Provision	1e-08
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	1e-08
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	1e-08
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	1e-08
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	1e-08
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	1e-08
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	2e-08
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-08
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-08
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	2e-08
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	3e-08
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	3e-08
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	3e-08
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	3e-08
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	4e-08
cd12746	78	cd12746, RRM2_RBM12B, RNA recognition motif 2 in R	5e-08
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	5e-08
cd12459	80	cd12459, RRM1_CID8_like, RNA recognition motif 1 i	5e-08
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	5e-08
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	5e-08
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	6e-08
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	8e-08
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	8e-08
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	9e-08
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	9e-08
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	9e-08
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	1e-07
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	1e-07
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	1e-07
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	1e-07
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	1e-07
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	1e-07
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-07
COG5271	4600	COG5271, MDN1, AAA ATPase containing von Willebran	2e-07
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-07
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	2e-07
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	2e-07
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	2e-07
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	2e-07
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	2e-07
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	2e-07
cd12291	72	cd12291, RRM1_La, RNA recognition motif 1 in La au	2e-07
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	3e-07
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	3e-07
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	3e-07
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	3e-07
cd12506	75	cd12506, RRM3_hnRNPH_CRSF1_like, RNA recognition m	3e-07
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	3e-07
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	3e-07
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	3e-07
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	3e-07
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	5e-07
cd12459	80	cd12459, RRM1_CID8_like, RNA recognition motif 1 i	6e-07
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	6e-07
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	6e-07
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	6e-07
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	6e-07
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	6e-07
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	6e-07
cd12550	76	cd12550, RRM_II_PABPN1, RNA recognition motif in t	7e-07
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	8e-07
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	8e-07
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	8e-07
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	9e-07
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	9e-07
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	1e-06
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	1e-06
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	1e-06
pfam04615	728	pfam04615, Utp14, Utp14 protein	1e-06
PLN03237	1465	PLN03237, PLN03237, DNA topoisomerase 2; Provision	2e-06
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	2e-06
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	2e-06
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	2e-06
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	2e-06
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	2e-06
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	2e-06
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	2e-06
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	3e-06
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	3e-06
cd12502	72	cd12502, RRM2_RMB19, RNA recognition motif 2 in RN	3e-06
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	3e-06
cd12555	87	cd12555, RRM2_RBM15, RNA recognition motif 2 in ve	3e-06
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	3e-06
cd12505	75	cd12505, RRM2_GRSF1, RNA recognition motif 2 in G-	3e-06
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	3e-06
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	3e-06
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	3e-06
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	4e-06
cd12513	81	cd12513, RRM3_RBM12B, RNA recognition motif 3 in R	4e-06
cd12537	85	cd12537, RRM1_RBM23, RNA recognition motif 1 in ve	4e-06
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	4e-06
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	4e-06
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	4e-06
cd12561	81	cd12561, RRM1_RBM5_like, RNA recognition motif 1 i	4e-06
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	4e-06
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	4e-06
PLN03237	1465	PLN03237, PLN03237, DNA topoisomerase 2; Provision	5e-06
pfam04615	728	pfam04615, Utp14, Utp14 protein	5e-06
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	5e-06
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	5e-06
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	5e-06
PRK05035	695	PRK05035, PRK05035, electron transport complex pro	5e-06
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	6e-06
PRK08581	619	PRK08581, PRK08581, N-acetylmuramoyl-L-alanine ami	6e-06
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	6e-06
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	7e-06
cd12403	75	cd12403, RRM1_NCL, RNA recognition motif 1 in vert	8e-06
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	8e-06
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	8e-06
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	8e-06
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	9e-06
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	1e-05
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	1e-05
cd12339	71	cd12339, RRM2_SRSF1_4_like, RNA recognition motif	1e-05
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	1e-05
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	1e-05
cd12747	75	cd12747, RRM2_RBM12, RNA recognition motif 2 in RN	1e-05
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	1e-05
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	1e-05
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	1e-05
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	1e-05
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	2e-05
PRK08581	619	PRK08581, PRK08581, N-acetylmuramoyl-L-alanine ami	2e-05
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	2e-05
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	2e-05
cd12503	77	cd12503, RRM1_hnRNPH_GRSF1_like, RNA recognition m	2e-05
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	2e-05
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	2e-05
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	2e-05
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	3e-05
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	3e-05
PRK05035	695	PRK05035, PRK05035, electron transport complex pro	3e-05
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	3e-05
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	3e-05
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	3e-05
cd12504	77	cd12504, RRM2_hnRNPH_like, RNA recognition motif 2	3e-05
pfam07172	91	pfam07172, GRP, Glycine rich protein family	3e-05
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	3e-05
PRK14949	944	PRK14949, PRK14949, DNA polymerase III subunits ga	3e-05
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	4e-05
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	4e-05
cd12463	80	cd12463, RRM_G3BP1, RNA recognition motif found in	4e-05
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	4e-05
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	4e-05
cd12485	78	cd12485, RRM1_RBM47, RNA recognition motif 1 found	4e-05
cd12659	76	cd12659, RRM2_hnRNPM, RNA recognition motif 2 in v	5e-05
cd12611	81	cd12611, RRM1_NGR1_NAM8_like, RNA recognition moti	5e-05
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	5e-05
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	5e-05
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	6e-05
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	6e-05
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	6e-05
cd12536	85	cd12536, RRM1_RBM39, RNA recognition motif 1 in ve	6e-05
cd12735	75	cd12735, RRM3_hnRNPH3, RNA recognition motif 3 in	6e-05
PRK06958	182	PRK06958, PRK06958, single-stranded DNA-binding pr	6e-05
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	7e-05
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	7e-05
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	7e-05
cd12556	85	cd12556, RRM2_RBM15B, RNA recognition motif 2 in p	7e-05
PTZ00441	576	PTZ00441, PTZ00441, sporozoite surface protein 2 (	8e-05
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	8e-05
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	9e-05
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	9e-05
cd12267	77	cd12267, RRM_YRA1_MLO3, RNA recognition motif in y	9e-05
cd12748	76	cd12748, RRM4_RBM12B, RNA recognition motif 4 in R	9e-05
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	9e-05
COG5271	4600	COG5271, MDN1, AAA ATPase containing von Willebran	1e-04
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	1e-04
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	1e-04
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	1e-04
cd12460	82	cd12460, RRM2_CID8_like, RNA recognition motif 2 i	1e-04
TIGR00600	1034	TIGR00600, rad2, DNA excision repair protein (rad2	1e-04
cd12275	71	cd12275, RRM1_MEI2_EAR1_like, RNA recognition moti	1e-04
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	1e-04
cd12253	79	cd12253, RRM_PIN4_like, RNA recognition motif in y	1e-04
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	1e-04
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	1e-04
COG5271	4600	COG5271, MDN1, AAA ATPase containing von Willebran	2e-04
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	2e-04
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	2e-04
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	2e-04
PRK08581	619	PRK08581, PRK08581, N-acetylmuramoyl-L-alanine ami	2e-04
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	2e-04
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	2e-04
cd12660	76	cd12660, RRM2_MYEF2, RNA recognition motif 2 in ve	2e-04
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	2e-04
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	2e-04
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	3e-04
PRK08581	619	PRK08581, PRK08581, N-acetylmuramoyl-L-alanine ami	3e-04
TIGR00600	1034	TIGR00600, rad2, DNA excision repair protein (rad2	3e-04
cd12426	79	cd12426, RRM4_PTBPH3, RNA recognition motif 4 in p	3e-04
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	3e-04
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	3e-04
pfam05268	261	pfam05268, GP38, Phage tail fibre adhesin Gp38	3e-04
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	3e-04
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	4e-04
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	4e-04
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	4e-04
cd12734	76	cd12734, RRM3_hnRNPH_hnRNPH2_hnRNPF, RNA recogniti	4e-04
PRK13108	460	PRK13108, PRK13108, prolipoprotein diacylglyceryl	4e-04
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	4e-04
PRK12678	672	PRK12678, PRK12678, transcription termination fact	4e-04
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	4e-04
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	5e-04
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	5e-04
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	5e-04
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	5e-04
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	5e-04
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	5e-04
PRK07735	430	PRK07735, PRK07735, NADH dehydrogenase subunit C;	5e-04
cd12441	73	cd12441, RRM_Nup53_like, RNA recognition motif in	5e-04
PRK13108	460	PRK13108, PRK13108, prolipoprotein diacylglyceryl	6e-04
PRK12678	672	PRK12678, PRK12678, transcription termination fact	6e-04
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	6e-04
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	6e-04
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	6e-04
pfam04615	728	pfam04615, Utp14, Utp14 protein	7e-04
pfam09073	424	pfam09073, BUD22, BUD22	7e-04
cd12730	79	cd12730, RRM1_GRSF1, RNA recognition motif 1 in G-	7e-04
cd12228	84	cd12228, RRM_ENOX, RNA recognition motif (RRM) in	7e-04
cd12536	85	cd12536, RRM1_RBM39, RNA recognition motif 1 in ve	8e-04
TIGR04260	119	TIGR04260, Cyano_gly_rpt, rSAM-associated Gly-rich	8e-04
cd12245	79	cd12245, RRM_scw1_like, RNA recognition motif in y	8e-04
cd12484	78	cd12484, RRM1_RBM46, RNA recognition motif 1 found	8e-04
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	9e-04
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	0.001
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	0.001
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	0.001
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	0.001
cd12475	88	cd12475, RRM2_RBMS3, RNA recognition motif 2 found	0.001
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	0.001
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	0.001
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	0.001
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	0.001
cd12250	82	cd12250, RRM2_hnRNPR_like, RNA recognition motif 2	0.001
COG1512	271	COG1512, COG1512, Beta-propeller domains of methan	0.001
COG1512	271	COG1512, COG1512, Beta-propeller domains of methan	0.001
cd12257	72	cd12257, RRM1_RBM26_like, RNA recognition motif 1	0.001
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	0.001
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	0.001
cd12396	85	cd12396, RRM1_Nop13p_fungi, RNA recognition motif	0.001
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	0.001
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	0.001
cd12658	76	cd12658, RRM1_MYEF2, RNA recognition motif 1 in ve	0.001
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	0.002
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	0.002
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	0.002
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	0.002
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	0.002
PRK13108	460	PRK13108, PRK13108, prolipoprotein diacylglyceryl	0.002
pfam05793	528	pfam05793, TFIIF_alpha, Transcription initiation f	0.002
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	0.002
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	0.002
pfam03344	715	pfam03344, Daxx, Daxx Family	0.002
cd12452	88	cd12452, RRM_ARP_like, RNA recognition motif in ye	0.002
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	0.002
pfam05505	717	pfam05505, Ebola_NP, Ebola nucleoprotein	0.002
cd12464	83	cd12464, RRM_G3BP2, RNA recognition motif in ras G	0.002
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	0.002
cd12595	70	cd12595, RRM1_SRSF5, RNA recognition motif 1 in ve	0.002
cd12657	76	cd12657, RRM1_hnRNPM, RNA recognition motif 1 in v	0.002
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	0.003
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	0.003
pfam05793	528	pfam05793, TFIIF_alpha, Transcription initiation f	0.003
cd12486	78	cd12486, RRM1_ACF, RNA recognition motif 1 found i	0.003
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	0.003
cd12360	78	cd12360, RRM_cwf2, RNA recognition motif in yeast	0.003
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	0.003
pfam03753	993	pfam03753, HHV6-IE, Human herpesvirus 6 immediate	0.003
cd12296	71	cd12296, RRM1_Prp24, RNA recognition motif 1 in fu	0.003
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	0.004
cd12537	85	cd12537, RRM1_RBM23, RNA recognition motif 1 in ve	0.004
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	0.004
TIGR00600	1034	TIGR00600, rad2, DNA excision repair protein (rad2	0.004
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	0.004
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	0.004
cd12667	92	cd12667, RRM3_RAVER1, RNA recognition motif 3 in v	0.004
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	0.004
cd12600	72	cd12600, RRM2_SRSF4_like, RNA recognition motif 2	0.004
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	0.004
cd12512	101	cd12512, RRM3_RBM12, RNA recognition motif 3 in RN	0.004
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	0.004
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	0.004
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	0.004
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	0.004

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

 Score =  114 bits (287), Expect = 1e-30
 Identities = 49/79 (62%), Positives = 63/79 (79%)

Query: 520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNK 579
           TIF+KGFDSS+GED +R SL EHF SCGEITR+S+P D +TG+ KG AY++F   D   K
Sbjct: 1   TIFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEK 60

Query: 580 ALEMSGTEIGGYSLVVDEA 598
           ALE+ G+++GG +LVVDEA
Sbjct: 61  ALELDGSDLGGGNLVVDEA 79

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

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

 Score =  109 bits (275), Expect = 6e-29
 Identities = 46/77 (59%), Positives = 57/77 (74%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELN 477
           TLFVGNL +S EQ D++ FF E  EVVDVR++ D DGR KG+GHVEFA+ E A KA+E +
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALEKS 60

Query: 478 GQMLGNRAIRLDFARER 494
           G+ L  R IR+D A ER
Sbjct: 61  GEELLGREIRVDLATER 77

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

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

 Score = 83.1 bits (206), Expect = 1e-19
 Identities = 33/72 (45%), Positives = 46/72 (63%), Gaps = 1/72 (1%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LN 477
           LFVGNLP    + D++  FS+  E+  VR+  D DG+ KG+  VEF S EDA KA+E LN
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 478 GQMLGNRAIRLD 489
           G+ L  R +++ 
Sbjct: 61  GKELDGRKLKVS 72

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

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

 Score = 89.6 bits (222), Expect = 7e-19
 Identities = 74/326 (22%), Positives = 123/326 (37%), Gaps = 28/326 (8%)

Query: 335 DSSSEEESSDEEPQKKKDVKPNTKALKKESSSDEEDSDDEDEGEEEEASKTP-----KKN 389
           D       +D     K   +   ++  ++ S    D D          S++P      + 
Sbjct: 4   DRERGRLRNDTRRSDKGRERSRRRSRSRDRSRRRRDRDYYRGRRGRSRSRSPNRYYRPRG 63

Query: 390 VTDVKMVDAESGKKAAQTPFTPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLS 449
               +  D  SG+   + P T      +T+FV  L     + D+  FFS+V +V DV+  
Sbjct: 64  DRSYRRDDRRSGRNTKE-PLTEAERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCI 122

Query: 450 SDAD-GRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFA---RERGAYTPYSGGNE 505
            D +  R KG  +VEF  VE   KA+ L GQML  R I +  +   + R A         
Sbjct: 123 KDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQSSQAEKNRAA--------- 173

Query: 506 SNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKG 565
             +  + G       +++     ++ E +    L + F   G+I  + + +D +TG  KG
Sbjct: 174 KAATHQPGDIPNFLKLYVGNLHFNITEQE----LRQIFEPFGDIEDVQLHRDPETGRSKG 229

Query: 566 IAYLDFTDADSFNKALE-MSGTEIGGYSLVVDEAKQRGDFGSGGGRSGGRGGRSGGRDFG 624
             ++ F DA+   +ALE M+G E+ G  + V  A+                     +   
Sbjct: 230 FGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQDSTYLLDAANTFED----IDKQQQM 285

Query: 625 RSGGRDGGRFGGRGRGGRDGGRGGRG 650
                   R     +  RD G GG  
Sbjct: 286 GKNLNTEEREQLMEKLDRDDGDGGLL 311

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|214636 smart00360, RRM, RNA recognition motif

 Score = 80.7 bits (200), Expect = 8e-19
 Identities = 33/73 (45%), Positives = 47/73 (64%), Gaps = 2/73 (2%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAIE- 475
           TLFVGNLP    + +++  FS+  +V  VRL  D + G+ KG+  VEF S EDA KA+E 
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 476 LNGQMLGNRAIRL 488
           LNG+ L  R +++
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 79.9 bits (198), Expect = 1e-18
 Identities = 32/70 (45%), Positives = 44/70 (62%), Gaps = 1/70 (1%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LN 477
           LFVGNLP    + D+++ FS+   +  +R+  D  GR KG+  VEF   EDA KA+E LN
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 478 GQMLGNRAIR 487
           G+ LG R +R
Sbjct: 61  GKELGGRELR 70

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

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

 Score = 78.0 bits (193), Expect = 8e-18
 Identities = 31/77 (40%), Positives = 50/77 (64%), Gaps = 2/77 (2%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAIE- 475
            L+VGNLP++V + D+++ F +  EV   R+ +D + GR +G+G VE  + E+A+ AIE 
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 476 LNGQMLGNRAIRLDFAR 492
           LNG   G R + ++ AR
Sbjct: 61  LNGTDFGGRTLTVNEAR 77

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

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

 Score = 77.8 bits (192), Expect = 9e-18
 Identities = 34/73 (46%), Positives = 45/73 (61%), Gaps = 2/73 (2%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAIE-L 476
           LFVGNL F  ++  +   F E  E+  VRL +D D GR KG+G+VEF+S E A  A++ L
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 477 NGQMLGNRAIRLD 489
            G  L  R +RLD
Sbjct: 61  GGTDLLGRPVRLD 73

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

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

 Score = 82.5 bits (204), Expect = 2e-16
 Identities = 52/178 (29%), Positives = 88/178 (49%), Gaps = 20/178 (11%)

Query: 415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI 474
           G   +FV NL  SV+   + + FS+   ++  ++++D +G+ +GYG V F   E A  AI
Sbjct: 87  GVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAI 146

Query: 475 E-LNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGED 533
           + +NG +L ++ +             Y G       ++    +    +++K  D SV ED
Sbjct: 147 QKVNGMLLNDKEV-------------YVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNED 193

Query: 534 QVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGG 590
                L E F   GEIT  +V KD  +G  +G A+++F   +   KA+E M+G +IG 
Sbjct: 194 ----KLRELFAKFGEITSAAVMKD-GSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGL 246

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|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic translation initiation factor 4H (eIF-4H) and similar proteins

 Score = 72.7 bits (179), Expect = 5e-16
 Identities = 31/75 (41%), Positives = 47/75 (62%), Gaps = 2/75 (2%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAIEL 476
           T FVGNLPF+  Q D+   F ++  V  VRL  D +  +FKG+ +VEF  VE   +A+E 
Sbjct: 3   TAFVGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVESLKEALEY 61

Query: 477 NGQMLGNRAIRLDFA 491
           +G +  +R++R+D A
Sbjct: 62  DGALFDDRSLRVDIA 76

This subfamily corresponds to the RRM of eIF-4H, also termed Williams-Beuren syndrome chromosomal region 1 protein, which, together with elf-4B/eIF-4G, serves as the accessory protein of RNA helicase eIF-4A. eIF-4H contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It stimulates protein synthesis by enhancing the helicase activity of eIF-4A in the initiation step of mRNA translation. . Length = 76

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

 Score = 72.3 bits (178), Expect = 8e-16
 Identities = 35/74 (47%), Positives = 44/74 (59%), Gaps = 2/74 (2%)

Query: 420 FVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAIE-LN 477
           FVGN+P+   +  +   FSEV  VV  RL +D D G+ KGYG  EF  +E A  AI  LN
Sbjct: 2   FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61

Query: 478 GQMLGNRAIRLDFA 491
           G     RA+R+DFA
Sbjct: 62  GYEFNGRALRVDFA 75

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

>gnl|CDD|215641 PLN03237, PLN03237, DNA topoisomerase 2; Provisional

 Score = 81.4 bits (201), Expect = 9e-16
 Identities = 68/321 (21%), Positives = 103/321 (32%), Gaps = 52/321 (16%)

Query: 21   EAEDAIEKLVSAKKQKGNDGVAQAVKKAKVEAKTQKKNKNDETSSSSSEEDSSDSEEEQK 80
            +AE+A EKL  A  +  +    +  ++A  +   +K  K    S ++ E   S + E + 
Sbjct: 1174 KAEEAREKLQRAAARGESGAAKKVSRQAPKKPAPKKTTKKASESETTEETYGSSAMETEN 1233

Query: 81   VKAVVTNKG--GKAAKPPVKESSSEEEDS-------------SSDEEPPKKQPVAAKNGA 125
            V  VV  KG  G   K P      EEED               S      K     K   
Sbjct: 1234 VAEVVKPKGRAGAKKKAPAAAKEKEEEDEILDLKDRLAAYNLDSAPAQSAKMEETVKAVP 1293

Query: 126  VAATAKKSKPDSSSSDSSDDDSDEDEVPTSIKKLPVAAAKNGPSAPQKKKDDSSDSSDEE 185
                A + KP +S S  SD D D+D+    +        K G                  
Sbjct: 1294 ARRAAARKKPLASVSVISDSDDDDDDFAVEVSLAERLKKKGGRKP--------------- 1338

Query: 186  SDESSDEDDKSTKAIPQPKKLPASTAKKGTVAATKKSTGSSDDDSSSSEDSSESEEDNGA 245
                         A  +  K PA+  K+G   AT +S           E    +E    +
Sbjct: 1339 -----------AAANKKAAKPPAAAKKRG--PATVQSGQKLLT-----EMLKPAEAIGIS 1380

Query: 246  PAKVTSEAKKLPAVKNVPAPAAKKKTESSDSSDEESEDSSDEDEEPTHVTKATPVKKLSA 305
            P K   + +  P  K   +   +  T     S E    SS  +++   V      K    
Sbjct: 1381 PEKKVRKMRASPFNKKSGSVLGRAATNKETESSENVSGSSSSEKDEIDV----SAKPRPQ 1436

Query: 306  VVTKNKVESSSSSDESESEEE 326
               + +     S  ESES ++
Sbjct: 1437 RANRKQTTYVLSDSESESADD 1457

Length = 1465

>gnl|CDD|240848 cd12402, RRM_eIF4B, RNA recognition motif in eukaryotic translation initiation factor 4B (eIF-4B) and similar proteins

 Score = 72.0 bits (177), Expect = 1e-15
 Identities = 29/76 (38%), Positives = 45/76 (59%), Gaps = 3/76 (3%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD--ADGRFKGYGHVEFASVEDAHKAIE 475
           T ++GNLP+ V + D++ FF  +  V  VRL  +    GR +G+G+ EF   +   +A+ 
Sbjct: 3   TAYLGNLPYDVTEEDIKEFFRGL-NVSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQALS 61

Query: 476 LNGQMLGNRAIRLDFA 491
           LN + L NR IR+D A
Sbjct: 62  LNDESLKNRRIRVDIA 77

This subfamily corresponds to the RRM of eIF-4B, a multi-domain RNA-binding protein that has been primarily implicated in promoting the binding of 40S ribosomal subunits to mRNA during translation initiation. It contains two RNA-binding domains; the N-terminal well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), binds the 18S rRNA of the 40S ribosomal subunit and the C-terminal basic domain (BD), including two arginine-rich motifs (ARMs), binds mRNA during initiation, and is primarily responsible for the stimulation of the helicase activity of eIF-4A. eIF-4B also contains a DRYG domain (a region rich in Asp, Arg, Tyr, and Gly amino acids) in the middle, which is responsible for both, self-association of eIF-4B and binding to the p170 subunit of eIF3. Additional research indicates that eIF-4B can interact with the poly(A) binding protein (PABP) in mammalian cells, which can stimulate both, the eIF-4B-mediated activation of the helicase activity of eIF-4A and binding of poly(A) by PABP. eIF-4B has also been shown to interact specifically with the internal ribosome entry sites (IRES) of several picornaviruses which facilitate cap-independent translation initiation. . Length = 77

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

 Score = 71.5 bits (176), Expect = 1e-15
 Identities = 27/70 (38%), Positives = 37/70 (52%), Gaps = 1/70 (1%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAIEL 476
           T+FV  L   V + D+  FFS+  +V DVR+  D +  R KG  +VEF   E    A+ L
Sbjct: 1   TVFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALGL 60

Query: 477 NGQMLGNRAI 486
            GQ L  + I
Sbjct: 61  TGQRLLGQPI 70

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

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

 Score = 70.7 bits (174), Expect = 2e-15
 Identities = 26/72 (36%), Positives = 41/72 (56%), Gaps = 1/72 (1%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVD-VRLSSDADGRFKGYGHVEFASVEDAHKAIEL 476
            + +  LPFS  + D+++FFS +    D + +  D DGR  G  +VEFAS EDA +A+  
Sbjct: 1   VVRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALRK 60

Query: 477 NGQMLGNRAIRL 488
           +   +G R I +
Sbjct: 61  HNNKMGGRYIEV 72

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

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

 Score = 70.3 bits (173), Expect = 4e-15
 Identities = 23/77 (29%), Positives = 40/77 (51%), Gaps = 5/77 (6%)

Query: 520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNK 579
           T+F+        E++    L E F   G++  + + +D +TG  KG A+++F   +   K
Sbjct: 1   TLFVGNLPPDTTEEE----LRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEK 56

Query: 580 ALE-MSGTEIGGYSLVV 595
           ALE ++G E+ G  L V
Sbjct: 57  ALEALNGKELDGRPLKV 73

Length = 73

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

 Score = 68.0 bits (167), Expect = 3e-14
 Identities = 27/72 (37%), Positives = 44/72 (61%), Gaps = 1/72 (1%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAIEL 476
           ++FVGNLPF +E+ +++  F +  +V  VR+  D   G  KG+G+V F + +    A++L
Sbjct: 1   SVFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKL 60

Query: 477 NGQMLGNRAIRL 488
           NG  L  R IR+
Sbjct: 61  NGIKLKGRKIRV 72

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

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

 Score = 67.7 bits (166), Expect = 3e-14
 Identities = 25/69 (36%), Positives = 45/69 (65%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELN 477
           T+FV NL +SV + +++  FS+  E+ DVRL  +  G+ KGY +VEF + E   +A++L+
Sbjct: 1   TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEALKLD 60

Query: 478 GQMLGNRAI 486
            +++  R +
Sbjct: 61  RELIKGRPM 69

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

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

 Score = 66.9 bits (164), Expect = 7e-14
 Identities = 29/74 (39%), Positives = 44/74 (59%), Gaps = 1/74 (1%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LN 477
           L V NLPF   +AD++  FS    V +V +    DG+ KG+  V+F S  DA KAI+ +N
Sbjct: 2   LIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVN 61

Query: 478 GQMLGNRAIRLDFA 491
           G+ +  R + +D+A
Sbjct: 62  GKKIKGRPVAVDWA 75

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

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

 Score = 64.5 bits (158), Expect = 4e-13
 Identities = 33/70 (47%), Positives = 45/70 (64%), Gaps = 2/70 (2%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LN 477
           L+V NLP SV + D++ FFS   +V  VRL  + D R +G+  VEFAS EDA  A++ LN
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD-RPRGFAFVEFASPEDAEAALKKLN 59

Query: 478 GQMLGNRAIR 487
           G +L  R +R
Sbjct: 60  GLVLDGRTLR 69

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

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

 Score = 64.0 bits (156), Expect = 6e-13
 Identities = 30/73 (41%), Positives = 48/73 (65%), Gaps = 2/73 (2%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAIEL 476
           T+++GNL + + + DV+ FF    E+  VRL++D + G FKG+GHV+FA  E    A++L
Sbjct: 1   TVYIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAALKL 59

Query: 477 NGQMLGNRAIRLD 489
           +G +L  R IR+ 
Sbjct: 60  DGTVLCGRPIRIA 72

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

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

 Score = 69.6 bits (169), Expect = 6e-13
 Identities = 62/289 (21%), Positives = 115/289 (39%), Gaps = 12/289 (4%)

Query: 304 SAVVTKNKVESSSSSDESESEEEKPPAKMDVDSSSEEESSDEEPQKKKDVKPNTKALKKE 363
           S  +        S   E     +     +  +    EE++ +E   + + +     +   
Sbjct: 3   SKNLKGPHSSFESVKPEDIESGKLTELLLKEEYGGLEEANSKELNLEVNSRKIESEISPP 62

Query: 364 SSSDEEDSDDEDEGEEEEASKTPKKNVTDVKMVDAESGKKAAQTPFTPQSGGSKTLFVGN 423
           S      S+ ++E E E   +   +     +  +       +          + TLFVGN
Sbjct: 63  SKKRLLSSERKEENEREMEEQNDGERGYTKEFEEELFRSSESPKSRQKSKEENNTLFVGN 122

Query: 424 LPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAIE-LNGQML 481
           LP+ V + D++  F +   V  VRL  D + G+ +G+  VEF S E A KAIE LNG+ L
Sbjct: 123 LPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKEL 182

Query: 482 GNRAIRLDFARER-GAYTPYSGGNESNSFQKGGRGQAAH-----TIFIKGFDSSVGEDQV 535
             R +R+  A+      +  S   +++  +K  RG+A        +++        E++ 
Sbjct: 183 EGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEE- 241

Query: 536 RASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMS 584
              L + F S G+I R S+P   D    K  +++    +    ++    
Sbjct: 242 ---LADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNEASKDALESNSRG 287

Length = 306

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

 Score = 63.8 bits (156), Expect = 7e-13
 Identities = 28/75 (37%), Positives = 40/75 (53%), Gaps = 4/75 (5%)

Query: 521 IFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKA 580
           IF+   D     ++    L+EHF SCG I RI++  D  TG  KG AY++F D  S   A
Sbjct: 2   IFVGNVDYGTTPEE----LQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENA 57

Query: 581 LEMSGTEIGGYSLVV 595
           L ++ +E  G  + V
Sbjct: 58  LLLNESEFRGRQIKV 72

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

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

 Score = 63.4 bits (155), Expect = 9e-13
 Identities = 32/69 (46%), Positives = 42/69 (60%), Gaps = 1/69 (1%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LN 477
           +FV NLPFSV   D+++ F E   V+   + +D DGR KG+G V F S EDA +AIE  N
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFN 60

Query: 478 GQMLGNRAI 486
           G  L  R +
Sbjct: 61  GYDLEGREL 69

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

 Score = 69.8 bits (171), Expect = 2e-12
 Identities = 52/196 (26%), Positives = 91/196 (46%), Gaps = 21/196 (10%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LN 477
           L+V NL  SV +  ++  F++  E+    +  D  GR +G+  V F   EDA KA+E +N
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMN 240

Query: 478 GQMLGNRAI---------RLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDS 528
           G+ +G             +    RE      +    +    +  G       +++K  D 
Sbjct: 241 GKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQG-----VNLYVKNLDD 295

Query: 529 SVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKAL-EMSGTE 587
           +V ++++R    E F  CGEIT   V  D + G  +G  ++ F++ +  N+A+ EM G  
Sbjct: 296 TVTDEKLR----ELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEANRAVTEMHGRM 350

Query: 588 IGGYSLVVDEAKQRGD 603
           +GG  L V  A+++  
Sbjct: 351 LGGKPLYVALAQRKEQ 366

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|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional

 Score = 70.5 bits (173), Expect = 2e-12
 Identities = 48/274 (17%), Positives = 95/274 (34%), Gaps = 31/274 (11%)

Query: 20   REAEDAIEKLVSAKKQKGNDGVAQAVKKAKVEAKTQKKNKNDETSS--SSSEEDSSDSEE 77
             EA +  E++   +  K         K     +K +K     +      SS + S  +  
Sbjct: 1138 EEALEEQEEVEEKEIAKEQ---RLKSKTKGKASKLRKPKLKKKEKKKKKSSADKSKKASV 1194

Query: 78   EQKVKAVVTNKGGKAAKPPVKESSSEEEDSSSDEEPPKKQPVAAKNGAVAATAKKSKPDS 137
                K V +++  K    P  + S+       D+E  K +P  +    + +    S   S
Sbjct: 1195 VGNSKRVDSDEKRKLDDKPDNKKSNSSGSDQEDDEEQKTKPKKSSVKRLKSKKNNSSKSS 1254

Query: 138  SSSDSSDDDSDEDEVPTSIKKLPVAAAKNGPSAPQKKKDDSSDSSDEESDESSDEDDKST 197
              +D    D    E         V+A +  P  P K+ D  S+   + S  +  +  K  
Sbjct: 1255 EDNDEFSSDDLSKEGKPKNAPKRVSAVQYSPPPPSKRPDGESNGGSKPSSPTKKKVKKR- 1313

Query: 198  KAIPQPKKLPASTAKKGTVAATKKSTGSSDDDSSSSEDSSESEEDNGAPAKVTSEAKKLP 257
                           +G++AA KK   S  +  ++ +  S++     + ++ +       
Sbjct: 1314 --------------LEGSLAALKKKKKS--EKKTARKKKSKTRVKQASASQSSRLL---- 1353

Query: 258  AVKNVPAPAAKKKTESSDSSDEESEDSSDEDEEP 291
                   P  KK   SS+  D+   D S+++++ 
Sbjct: 1354 -----RRPRKKKSDSSSEDDDDSEVDDSEDEDDE 1382

Length = 1388

>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

 Score = 69.6 bits (170), Expect = 4e-12
 Identities = 47/291 (16%), Positives = 109/291 (37%), Gaps = 35/291 (12%)

Query: 138  SSSDSSDDDSDEDEVPTSIKKLPVAAAKNGPSAPQKKKDDSSDSSDEESDESSDEDDKST 197
            S +++SD + +  ++   +  +P              +D S+  +++  DE ++ED   T
Sbjct: 3874 SENENSDSEEENQDLDEEVNDIP--------------EDLSNSLNEKLWDEPNEEDLLET 3919

Query: 198  KAIPQPKKLPASTAKKGTVAATKKSTGSSDDDSSSSEDSSESEEDNGAPAKVTSE----- 252
            +     +   A+  +   V+    +    D D    ED  E  +D G   ++  +     
Sbjct: 3920 EQKSNEQS--AANNESDLVSKEDDNKALEDKDRQEKEDEEEMSDDVGIDDEIQPDIQENN 3977

Query: 253  AKKLPAVKNVPAPAAKKKTESSDSSDEESE------DSSDEDEEPTHVTKATPVKKLSAV 306
            ++  P  +++  P   K  E      ++S+      +++DE++E     K  P++    +
Sbjct: 3978 SQPPPENEDLDLPEDLKLDEKEGDVSKDSDLEDMDMEAADENKEEADAEKDEPMQDEDPL 4037

Query: 307  VTKNKVE--------SSSSSDESESEEEKPPAKMDVDSSSEEESSDEEPQKKKDVKPNTK 358
               N ++        S  + D+ +  E+     +  +  S E+    + + ++   P  +
Sbjct: 4038 EENNTLDEDIQQDDFSDLAEDDEKMNEDGFEENVQENEESTEDGVKSDEELEQGEVPEDQ 4097

Query: 359  ALKKESSSDEEDSDDEDEGEEEEASKTPKKNVTDVKMVDAESGKKAAQTPF 409
            A+      D + +    E +EE   K       ++   D   G   A   F
Sbjct: 4098 AIDNHPKMDAKSTFASAEADEENTDKGIVGENEELGEEDGVRGNGTADGEF 4148

Length = 4600

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

 Score = 61.0 bits (149), Expect = 7e-12
 Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 2/72 (2%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAI-EL 476
           L+VG+L   V +A +   FS    V+ +R+  D    R  GY +V F +  DA +A+  L
Sbjct: 2   LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTL 61

Query: 477 NGQMLGNRAIRL 488
           N  ++  + IR+
Sbjct: 62  NFDVIKGKPIRI 73

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

>gnl|CDD|240671 cd12225, RRM1_2_CID8_like, RNA recognition motif 1 and 2 (RRM1, RRM2) in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 60.8 bits (148), Expect = 7e-12
 Identities = 28/73 (38%), Positives = 39/73 (53%), Gaps = 5/73 (6%)

Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD--ADGRFKGYGHVEFASVEDAHKAI 474
           +T+ VG +  S+ + D++ FFS   EV  VRL  D     RF     VEFA  E A  A+
Sbjct: 1   RTIHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSARF---AFVEFADAESALSAL 57

Query: 475 ELNGQMLGNRAIR 487
            L+G +LG   +R
Sbjct: 58  NLSGTLLGGHPLR 70

This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 77

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

 Score = 60.8 bits (148), Expect = 8e-12
 Identities = 26/70 (37%), Positives = 35/70 (50%), Gaps = 1/70 (1%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAIEL 476
            LFVGNLP+     D+   F        VRL +D   G+ KG   VEF + E   KA++L
Sbjct: 2   ILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKL 61

Query: 477 NGQMLGNRAI 486
           +  +L  R I
Sbjct: 62  HHTLLKGRKI 71

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

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

 Score = 59.3 bits (144), Expect = 3e-11
 Identities = 30/71 (42%), Positives = 41/71 (57%), Gaps = 2/71 (2%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAI-EL 476
           +FVG+L   ++   ++  F+   E+ D R+  D   G+ KGYG V F   EDA  AI  +
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 477 NGQMLGNRAIR 487
           NGQ LG RAIR
Sbjct: 62  NGQWLGGRAIR 72

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

>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional

 Score = 66.2 bits (162), Expect = 4e-11
 Identities = 44/238 (18%), Positives = 89/238 (37%), Gaps = 13/238 (5%)

Query: 7    VATPTKSAKKGGKREAEDAIEKLVSAKKQKGNDGVAQAVKKAKVEAKTQKKNKNDETSSS 66
              T  K++K    +  +   +K  S+  +     V    K+   + K +  +K D   S+
Sbjct: 1160 SKTKGKASKLRKPKLKKKEKKKKKSSADKSKKASVVGNSKRVDSDEKRKLDDKPDNKKSN 1219

Query: 67   SSEEDSSDSEEEQKVKAVVTNKGGKAAKPPVKESSSEEEDSSSDEEPPKKQPVAAKNGAV 126
            SS  D  D EE++      + K  K+ K    +SS + ++ SSD+   + +P  A     
Sbjct: 1220 SSGSDQEDDEEQKTKPKKSSVKRLKSKKNNSSKSSEDNDEFSSDDLSKEGKPKNAPKRVS 1279

Query: 127  AATAKKSKPDSSSSDSSDDDSDEDEVPTSIKKLPVAAAKNGPSAPQKKKDDSSDSSDEES 186
            A       P       S+  S          K  +  +       +K +  ++     ++
Sbjct: 1280 AVQYSPPPPSKRPDGESNGGSKPSSPTKKKVKKRLEGSLAALKKKKKSEKKTARKKKSKT 1339

Query: 187  DESSDEDDKSTKAIPQPKKLPASTAKKGTVAATKKSTGSSDDDSSSSEDSSESEEDNG 244
                    +S++ + +P+K              K  + S DDD S  +DS + ++++ 
Sbjct: 1340 RVKQASASQSSRLLRRPRK-------------KKSDSSSEDDDDSEVDDSEDEDDEDD 1384

Length = 1388

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

 Score = 58.9 bits (143), Expect = 4e-11
 Identities = 34/76 (44%), Positives = 51/76 (67%), Gaps = 2/76 (2%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAIE- 475
           TLFVGNL +SV+   ++  F +   VV  R+ +D + GR +G+G+V+F S EDA KAIE 
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 476 LNGQMLGNRAIRLDFA 491
           ++G+ L  R I +DF+
Sbjct: 61  MDGKELDGRPINVDFS 76

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

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

 Score = 59.1 bits (143), Expect = 4e-11
 Identities = 36/79 (45%), Positives = 50/79 (63%), Gaps = 2/79 (2%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAI-E 475
           TLFV NL FSV Q D+ +FFS+VA +    + +D + G  +GYG V FA +EDA +A+ +
Sbjct: 1   TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK 60

Query: 476 LNGQMLGNRAIRLDFARER 494
           L  + L  R +RLD A  R
Sbjct: 61  LKNKKLHGRILRLDIAERR 79

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

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

 Score = 58.1 bits (141), Expect = 7e-11
 Identities = 23/77 (29%), Positives = 36/77 (46%), Gaps = 6/77 (7%)

Query: 521 IFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKA 580
           +F+        E+     L E F   GEI  + + +D   G  KG A+++F   +   KA
Sbjct: 1   LFVGNLPPDTTEED----LRELFSKFGEIESVRIVRD-KDGKSKGFAFVEFESPEDAEKA 55

Query: 581 LE-MSGTEIGGYSLVVD 596
           LE ++G E+ G  L V 
Sbjct: 56  LEALNGKELDGRKLKVS 72

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

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

 Score = 58.0 bits (141), Expect = 7e-11
 Identities = 24/74 (32%), Positives = 39/74 (52%), Gaps = 6/74 (8%)

Query: 521 IFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKA 580
           +F+        E+     L++ F   G I  I + +D +TG  KG A+++F D +   KA
Sbjct: 1   LFVGNLPPDTTEED----LKDLFSKFGPIESIRIVRD-ETGRSKGFAFVEFEDEEDAEKA 55

Query: 581 LE-MSGTEIGGYSL 593
           LE ++G E+GG  L
Sbjct: 56  LEALNGKELGGREL 69

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

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

 Score = 64.8 bits (158), Expect = 7e-11
 Identities = 49/176 (27%), Positives = 82/176 (46%), Gaps = 26/176 (14%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE- 475
           +L+VG+L   V +A + + F     V+ VR+  D+   R  GYG+V F +  DA +A+E 
Sbjct: 2   SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALET 61

Query: 476 LNGQMLGNRAIRLDFARERGAYTPYSG-GNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQ 534
           +N + LG + IR+ ++ +R      SG GN                IF+K  D SV    
Sbjct: 62  MNFKRLGGKPIRIMWS-QRDPSLRRSGVGN----------------IFVKNLDKSVDN-- 102

Query: 535 VRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIG 589
              +L + F   G I    V  D + G  +G  ++ F   +S   A++ ++G  + 
Sbjct: 103 --KALFDTFSKFGNILSCKVATD-ENGKSRGYGFVHFEKEESAKAAIQKVNGMLLN 155

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|215641 PLN03237, PLN03237, DNA topoisomerase 2; Provisional

 Score = 64.5 bits (157), Expect = 1e-10
 Identities = 61/298 (20%), Positives = 113/298 (37%), Gaps = 23/298 (7%)

Query: 103  EEEDSSSDEEPPKKQPVAAKNGAVAA------TAKKSKPDSSSSDSSDDDSDEDEVPTSI 156
            ++ED+ ++E   K Q  AA+  + AA        KK  P  ++  +S+ ++ E+   +S 
Sbjct: 1169 DKEDAKAEEAREKLQRAAARGESGAAKKVSRQAPKKPAPKKTTKKASESETTEETYGSSA 1228

Query: 157  KKLPVAAAKNGPSAPQKKKDDSSDSSDEESDESSDEDDKSTKAIPQPKKLPASTAKKGT- 215
             +    A    P      K  +  ++ E+ +E    D K   A       PA +AK    
Sbjct: 1229 METENVAEVVKPKGRAGAKKKAPAAAKEKEEEDEILDLKDRLAAYNLDSAPAQSAKMEET 1288

Query: 216  ---VAATKKSTGSSDDDSSSSEDSSESEEDNGAPAKVTSE------AKKLPAVKNVPAPA 266
               V A + +       S S    S+ ++D+ A     +E       +K  A     A  
Sbjct: 1289 VKAVPARRAAARKKPLASVSVISDSDDDDDDFAVEVSLAERLKKKGGRKPAAANKKAAKP 1348

Query: 267  AKKKTESSDSSDEESEDSSDEDEEPTHVTKATPVKKLSAVVTK--NKVESSSSSDESESE 324
                 +   ++ +  +    E  +P      +P KK+  +     NK   S     + ++
Sbjct: 1349 PAAAKKRGPATVQSGQKLLTEMLKPAEAIGISPEKKVRKMRASPFNKKSGSVLGRAATNK 1408

Query: 325  EEKPPAKMDVDSSSEEESSDEEPQKKKDVKPN----TKALKKESSSDEEDSDDEDEGE 378
            E +    +   SSSE++  D    K +  + N    T  L    S   +DSD +D+ +
Sbjct: 1409 ETESSENVSGSSSSEKDEID-VSAKPRPQRANRKQTTYVLSDSESESADDSDFDDDED 1465

Length = 1465

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

 Score = 57.6 bits (140), Expect = 1e-10
 Identities = 20/71 (28%), Positives = 39/71 (54%), Gaps = 4/71 (5%)

Query: 520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNK 579
           ++F+      + E+++R    +HF  CG++  + + +D  TG  KG  Y+ F   DS   
Sbjct: 1   SVFVGNLPFDIEEEELR----KHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVAL 56

Query: 580 ALEMSGTEIGG 590
           AL+++G ++ G
Sbjct: 57  ALKLNGIKLKG 67

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

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

 Score = 58.0 bits (141), Expect = 1e-10
 Identities = 23/69 (33%), Positives = 37/69 (53%), Gaps = 6/69 (8%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVR---LSSDADGRFKGYGHVEFASVEDAHKAI 474
           TL+V N P S +Q+D+++ F +  E++ +R   L  +   RF    +V+F S E A  A+
Sbjct: 2   TLWVTNFPPSFDQSDIRDLFEQYGEILSIRFPSLRFNKTRRF---CYVQFTSPESAAAAV 58

Query: 475 ELNGQMLGN 483
            L    LG 
Sbjct: 59  ALLNGKLGE 67

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

 Score = 57.6 bits (140), Expect = 1e-10
 Identities = 28/79 (35%), Positives = 44/79 (55%), Gaps = 2/79 (2%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAIE- 475
           TLFV NLP+      ++ FFSEV  +    +  D    + +G+G+V FA  EDA +A+E 
Sbjct: 1   TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60

Query: 476 LNGQMLGNRAIRLDFARER 494
                 G R I ++FA+++
Sbjct: 61  KKKTKFGGRKIHVEFAKKK 79

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

>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 62.4 bits (152), Expect = 1e-10
 Identities = 28/54 (51%), Positives = 28/54 (51%)

Query: 601 RGDFGSGGGRSGGRGGRSGGRDFGRSGGRDGGRFGGRGRGGRDGGRGGRGRGRG 654
               G GGGR GGRGG  GG   G   G   G   GRGRGG  GGRGG G G  
Sbjct: 1   GMGGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGGRGGGGGGGP 54

Length = 293

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

 Score = 56.9 bits (138), Expect = 2e-10
 Identities = 29/82 (35%), Positives = 43/82 (52%), Gaps = 5/82 (6%)

Query: 520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNK 579
           T+F+     S  +D     LEE F  CGE+  + + +D D G  KG  +++F   +   K
Sbjct: 1   TLFVGNLSWSAEQD----DLEEFFKECGEVVDVRIAQDDD-GRSKGFGHVEFATEEGAQK 55

Query: 580 ALEMSGTEIGGYSLVVDEAKQR 601
           ALE SG E+ G  + VD A +R
Sbjct: 56  ALEKSGEELLGREIRVDLATER 77

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

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

 Score = 56.9 bits (138), Expect = 2e-10
 Identities = 32/72 (44%), Positives = 46/72 (63%), Gaps = 2/72 (2%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAIE-L 476
           L+VGNL F++ + D++  F    E+  V+L  D + GR KGYG ++FA  EDA KA+E L
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 477 NGQMLGNRAIRL 488
           NG  L  R I++
Sbjct: 61  NGFELAGRPIKV 72

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

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

 Score = 56.9 bits (138), Expect = 2e-10
 Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE- 475
             L V N+PF   + +++  FS   +V  VRL    DG  +G+  VEF + ++A  A+E 
Sbjct: 1   TKLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEA 60

Query: 476 LNGQMLGNRAIRLDFA 491
           L    L  R + L++A
Sbjct: 61  LKSTHLYGRHLVLEYA 76

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

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

 Score = 56.9 bits (138), Expect = 2e-10
 Identities = 24/77 (31%), Positives = 41/77 (53%), Gaps = 6/77 (7%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI-EL 476
           T++VGNLP  + + ++Q  FS    + +VR+  D     KGY  V F + E A  AI  +
Sbjct: 2   TVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD-----KGYAFVRFDTHEAAATAIVAV 56

Query: 477 NGQMLGNRAIRLDFARE 493
           NG  +  + ++  + +E
Sbjct: 57  NGTSINGQTVKCSWGKE 73

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

>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional

 Score = 63.5 bits (155), Expect = 3e-10
 Identities = 59/286 (20%), Positives = 92/286 (32%), Gaps = 43/286 (15%)

Query: 99   ESSSEEEDSSSDEE--PPKKQPVAAKNGAVAATAKKSKPDSSSSDSSDDDSDEDEVPTSI 156
            E   E E+    +E     K    A         KK K    SS      +         
Sbjct: 1142 EEQEEVEEKEIAKEQRLKSKTKGKASKLRKPKLKKKEKKKKKSSADKSKKASVVGNS--- 1198

Query: 157  KKLPVAAAKNGPSAPQKKKDDSSDSSDEESDESSDEDDKSTKAIPQPKKLPASTAKKGTV 216
                    K   S  ++K DD  D+    S  S  EDD+      Q  K   S+ K+   
Sbjct: 1199 --------KRVDSDEKRKLDDKPDNKKSNSSGSDQEDDE-----EQKTKPKKSSVKRLKS 1245

Query: 217  AATKKSTGSSDDDSSSSEDSSESEEDNGAPAKVTSEAKKLPAVKNVPAPAAKKKTESSDS 276
                 S  S D+D  SS+D S+  +   AP +V++           P+     ++     
Sbjct: 1246 KKNNSSKSSEDNDEFSSDDLSKEGKPKNAPKRVSAV----QYSPPPPSKRPDGESNGGSK 1301

Query: 277  SDEESEDSSDEDEEPTHVTKATPVKKLSAVVTKNKVESS--SSSDESESEEEKPPAKMDV 334
                ++    +  E +        K       K K ++    +S    S   + P K   
Sbjct: 1302 PSSPTKKKVKKRLEGSLAALKKKKKSEKKTARKKKSKTRVKQASASQSSRLLRRPRKKKS 1361

Query: 335  DSSSEEESSDEEPQKKKDVKPNTKALKKESSSDEEDSDDEDEGEEE 380
            DSSSE++   E                     D ED DDED+ +++
Sbjct: 1362 DSSSEDDDDSEV-------------------DDSEDEDDEDDEDDD 1388

Length = 1388

>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional

 Score = 63.1 bits (154), Expect = 4e-10
 Identities = 55/290 (18%), Positives = 107/290 (36%), Gaps = 40/290 (13%)

Query: 58   NKNDETSSSSSEEDSSDSEEEQKVKAVVTNKGGKAAKPPVK-ESSSEEEDSSSDEEPPKK 116
            +K +E      E +  +  +EQ++K+    K  K  KP +K +   +++ S+   +    
Sbjct: 1135 DKFEEALEEQEEVEEKEIAKEQRLKSKTKGKASKLRKPKLKKKEKKKKKSSADKSKKASV 1194

Query: 117  QPVAAKNGAVAATAKKSKPDSSSSDSSDDDSDEDEVPTSIKKLPVAAAKNGPSAPQKKKD 176
               + +  +        KPD+  S+SS  D ++DE   +             S  + K  
Sbjct: 1195 VGNSKRVDSDEKRKLDDKPDNKKSNSSGSDQEDDEEQKT--------KPKKSSVKRLKSK 1246

Query: 177  DSSDSSDEESDESSDEDDKSTKAIPQPKKLPASTAKKGTVAATKKSTGSSDDDSSSSEDS 236
             ++ S   E ++    DD S +  P+      S  +      +K+  G S+  S  S  +
Sbjct: 1247 KNNSSKSSEDNDEFSSDDLSKEGKPKNAPKRVSAVQYSPPPPSKRPDGESNGGSKPSSPT 1306

Query: 237  SESEEDNGAPAKVTSEAKKLPAVKNVPAPAAKKKTESSDSSDEESEDSSDEDEEPTHVTK 296
             +  +     +    + KK    +   A   K KT    +S  +S               
Sbjct: 1307 KKKVKKRLEGSLAALKKKKKS--EKKTARKKKSKTRVKQASASQS--------------- 1349

Query: 297  ATPVKKLSAVVTKNKVESSSSSDESESEEEKPPAKMDVDSSSEEESSDEE 346
                   S ++ + + + S SS E + + E       VD S +E+  D+E
Sbjct: 1350 -------SRLLRRPRKKKSDSSSEDDDDSE-------VDDSEDEDDEDDE 1385

Length = 1388

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

 Score = 56.1 bits (136), Expect = 4e-10
 Identities = 22/71 (30%), Positives = 38/71 (53%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELN 477
            +FVG +P    + ++++FFS    V DV++ +D  G  KGYG V F + EDA K + + 
Sbjct: 4   RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEKILAMG 63

Query: 478 GQMLGNRAIRL 488
                 + + +
Sbjct: 64  NLNFRGKKLNI 74

This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. Invertebrates contain a single DAZ homolog, BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. The family members encode closely related RNA-binding proteins that are required for fertility in numerous organisms. These proteins contain an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a varying number of copies of a DAZ motif, believed to mediate protein-protein interactions. DAZL and BOULE contain a single copy of the DAZ motif, while DAZ proteins can contain 8-24 copies of this repeat. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 80

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

 Score = 55.6 bits (134), Expect = 5e-10
 Identities = 31/75 (41%), Positives = 44/75 (58%), Gaps = 2/75 (2%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAIE-L 476
           +FVGN+P+   +  +++ FSEV  VV  RL  D + G+ KGYG  E+   E A  A+  L
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 477 NGQMLGNRAIRLDFA 491
           NG  L  R +R+D A
Sbjct: 61  NGYELNGRQLRVDNA 75

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

>gnl|CDD|240952 cd12508, RRM2_ESRPs_Fusilli, RNA recognition motif 2 in epithelial splicing regulatory protein ESRP1, ESRP2, Drosophila RNA-binding protein Fusilli and similar proteins

 Score = 55.4 bits (134), Expect = 7e-10
 Identities = 24/69 (34%), Positives = 34/69 (49%), Gaps = 4/69 (5%)

Query: 424 LPFSVEQADVQNFFSEVAEVVDVR----LSSDADGRFKGYGHVEFASVEDAHKAIELNGQ 479
           LP+S   AD+  FF  +  VV         +  DGR  G   V F + EDA +A+  + +
Sbjct: 9   LPYSATAADILAFFGGLCPVVGGPDGILFVTGPDGRPTGDAFVLFETEEDAQRALGKHKE 68

Query: 480 MLGNRAIRL 488
            LG+R I L
Sbjct: 69  NLGSRYIEL 77

This subfamily corresponds to the RRM2 of ESRPs and Fusilli. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of the fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. They are highly conserved paralogs and specifically bind to GU-rich binding site. ESRP1 and ESRP2 contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes Drosophila fusilli (fus) gene encoding RNA-binding protein Fusilli.Loss of fusilli activity causes lethality during embryogenesis in flies. Drosophila Fusilli can regulate endogenous FGFR2 splicing and functions as a splicing factor. It shows high sequence homology to ESRPs and contains three RRMs as well. It also has an N-terminal domain with unknown function and a C-terminal domain particularly rich in alanine, glutamine, and serine. . Length = 80

>gnl|CDD|240676 cd12230, RRM1_U2AF65, RNA recognition motif 1 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 54.9 bits (133), Expect = 1e-09
 Identities = 20/81 (24%), Positives = 43/81 (53%), Gaps = 16/81 (19%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAE-----------VVDVRLSSDADGRFKGYGHVEFASV 467
           L+VGNLP  + + ++ +FF++              V+ V+++ +     K +  VEF +V
Sbjct: 4   LYVGNLPPGITEEELVDFFNQAMLAAGLNQAPGNPVLSVQINPE-----KNFAFVEFRTV 58

Query: 468 EDAHKAIELNGQMLGNRAIRL 488
           E+A  A+ L+G +   + +++
Sbjct: 59  EEATAALALDGIIFKGQPLKI 79

The subfamily corresponds to the RRM1 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 82

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

 Score = 55.0 bits (133), Expect = 1e-09
 Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 8/80 (10%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAI--- 474
           +++G LP+ + + D+   FS+  E+VD+ L  D   G+ KG+  + +   ED    I   
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAY---EDQRSTILAV 68

Query: 475 -ELNGQMLGNRAIRLDFARE 493
             LNG  L  R IR+D  R 
Sbjct: 69  DNLNGIKLLGRTIRVDHVRN 88

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

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

 Score = 54.6 bits (132), Expect = 1e-09
 Identities = 25/75 (33%), Positives = 38/75 (50%), Gaps = 7/75 (9%)

Query: 519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVK---GIAYLDFTDAD 575
             I+++  D  + ED     L   F   GE+  I +PK  D    +   G A++ F DA 
Sbjct: 1   REIYVRNLDFKLDEDD----LRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDAS 56

Query: 576 SFNKALEMSGTEIGG 590
           S   AL+++GTE+GG
Sbjct: 57  SAENALQLNGTELGG 71

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

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

 Score = 54.1 bits (131), Expect = 2e-09
 Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 2/72 (2%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLS-SDADGRFKGYGHVEFASVEDAHKAIE- 475
            +++G+LP    + +++ +FS+   V  +RLS S   G+ KGY  VEF S E A    E 
Sbjct: 1   VVYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAET 60

Query: 476 LNGQMLGNRAIR 487
           +N  +L  R ++
Sbjct: 61  MNNYLLFERLLK 72

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

>gnl|CDD|240958 cd12514, RRM4_RBM12_like, RNA recognition motif 4 in RNA-binding protein RBM12, RBM12B and similar proteins

 Score = 53.9 bits (130), Expect = 2e-09
 Identities = 24/67 (35%), Positives = 36/67 (53%), Gaps = 1/67 (1%)

Query: 423 NLPFSVEQADVQNFFSEVAEVVD-VRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQML 481
           N+PF V + +V  FF+ +A     + +  D  G+  G  +VEF S EDA +A  L+ + L
Sbjct: 6   NIPFDVTKGEVLAFFAGIAIAEQGIHILYDKTGKTLGEAYVEFVSEEDAMRAERLHRKKL 65

Query: 482 GNRAIRL 488
             R I L
Sbjct: 66  KGREILL 72

This subfamily corresponds to the RRM4 of RBM12 and RBM12B. RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two proline-rich regions, and several putative transmembrane domains. RBM12B show high sequence semilarity with RBM12. It contains five distinct RRMs as well. The biological roles of both RBM12 and RBM12B remain unclear. . Length = 73

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

 Score = 53.8 bits (130), Expect = 3e-09
 Identities = 28/78 (35%), Positives = 40/78 (51%), Gaps = 6/78 (7%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVD---VRLSSDADGRFKGYGHVEFASVEDAHKA- 473
            L VGNLP        +   S    V     V   S++ G  KGYG VE+AS   A KA 
Sbjct: 1   LLCVGNLPLEFTDEQFRELVSPFGAVERCFLVY--SESTGESKGYGFVEYASKASALKAK 58

Query: 474 IELNGQMLGNRAIRLDFA 491
            +L+G+ +G R +++D+A
Sbjct: 59  NQLDGKQIGGRKLQVDWA 76

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

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

 Score = 53.4 bits (129), Expect = 4e-09
 Identities = 28/78 (35%), Positives = 50/78 (64%), Gaps = 4/78 (5%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAIE- 475
           TL++G+L   +++A + + F+E  EV  V++  +   G+  GYG VEFA+ E A +A++ 
Sbjct: 1   TLWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQS 60

Query: 476 LNGQMLGN--RAIRLDFA 491
           LNG+ + N  +  RL++A
Sbjct: 61  LNGKPIPNTQQRFRLNWA 78

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

>gnl|CDD|240955 cd12511, RRM2_RBM12_like, RNA recognition motif 2 in RNA-binding protein RBM12, RBM12B and similar proteins

 Score = 52.9 bits (127), Expect = 4e-09
 Identities = 23/70 (32%), Positives = 44/70 (62%), Gaps = 1/70 (1%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNG 478
           +F+  LP++ ++ DV+ FF  + +V DV      +GR  G   V+FA+ +DA +A++ + 
Sbjct: 2   VFLHGLPYTADEHDVKEFFHGL-DVEDVIFLKRHNGRNNGNAIVKFATFQDAKEALKRHR 60

Query: 479 QMLGNRAIRL 488
           +++G+R I L
Sbjct: 61  ELMGSRYIEL 70

This subfamily corresponds to the RRM2 of RBM12 and RBM12B. RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two proline-rich regions, and several putative transmembrane domains. RBM12B shows high sequence semilarity with RBM12. It contains five distinct RRMs as well. The biological roles of both RBM12 and RBM12B remain unclear. . Length = 73

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 59.8 bits (144), Expect = 4e-09
 Identities = 101/414 (24%), Positives = 169/414 (40%), Gaps = 34/414 (8%)

Query: 2    DAAPVVATPTKSAKKGGKREAEDAIEKLVSAKKQKGNDGVAQAVKKAKVEA---KTQKKN 58
            DAA   A   K A +  K EAE A ++  +A+++       +   K K +A   K ++K 
Sbjct: 1332 DAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKK 1391

Query: 59   KNDETSSSSSEEDSSDSEEEQKVKAVVTNKGGKAAKPPVKESSSEEEDSSSDEEPPKKQP 118
            K DE +   +EED   ++E +K  A    K    AK   +E    +E     EE  K   
Sbjct: 1392 KADE-AKKKAEEDKKKADELKKAAA--AKKKADEAKKKAEEKKKADEAKKKAEEAKKADE 1448

Query: 119  VA--AKNGAVAATAKKSKPDSSSSDSSDDDSDEDEVPTSIKKLPVAAAKNGPSAPQKKKD 176
                A+    A  AKK   ++  +D +   ++E +     KK    A K    A  KK  
Sbjct: 1449 AKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEA--KKAA 1506

Query: 177  DSSDSSDE----ESDESSDEDDKSTKAIPQPKKLPASTAKKGTVAATKKSTGSSDDDSSS 232
            ++   +DE    E  + +DE  K+ +A  +  +   +  KK      K       ++   
Sbjct: 1507 EAKKKADEAKKAEEAKKADEAKKAEEA-KKADEAKKAEEKKKADELKKAEELKKAEEKKK 1565

Query: 233  SEDSSESEEDNGAPAKVTSEAKKLPAVKNVPAPAAKKKTESSDSSDEESEDSSDEDEEPT 292
            +E++ ++EED     +   EAKK  A +       K   E      EE++ + +   +  
Sbjct: 1566 AEEAKKAEEDKNMALRKAEEAKK--AEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAE 1623

Query: 293  HVTKATPVKKLSAVVTKNKVESSSSSDESESEEEKPPAKMDVDSSSEEESSDEEPQKKKD 352
             + KA   KK    + K + E    ++E +  EE+   K      + EE+   E  KKK 
Sbjct: 1624 ELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIK------AAEEAKKAEEDKKK- 1676

Query: 353  VKPNTKALKKESSSDEEDSDDEDEGEEEEASKTPKKNVTDVKMVDAESGKKAAQ 406
                     +E+   EED     E  ++EA +   K   ++K  +AE  KKA +
Sbjct: 1677 --------AEEAKKAEEDEKKAAEALKKEAEE--AKKAEELKKKEAEEKKKAEE 1720

Length = 2084

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

 Score = 52.2 bits (126), Expect = 7e-09
 Identities = 16/74 (21%), Positives = 36/74 (48%), Gaps = 7/74 (9%)

Query: 521 IFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKA 580
           ++++    SV E+ +R    E F   G++  + + ++ D    +G A+++F   +    A
Sbjct: 1   LYVRNLPPSVTEEDLR----EFFSPYGKVEGVRLVRNKDRP--RGFAFVEFASPEDAEAA 54

Query: 581 LEMS-GTEIGGYSL 593
           L+   G  + G +L
Sbjct: 55  LKKLNGLVLDGRTL 68

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

>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 = 52.6 bits (127), Expect = 7e-09
 Identities = 29/77 (37%), Positives = 43/77 (55%), Gaps = 2/77 (2%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAI-E 475
            LFV  L     + +++  FS+   V +V L  D   G  +G+G V F SVEDA  AI +
Sbjct: 3   KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRD 62

Query: 476 LNGQMLGNRAIRLDFAR 492
           LNG+ L  R I+++ A+
Sbjct: 63  LNGKELEGRVIKVEKAK 79

This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has been implicated in the splicing control of several pre-mRNAs. Moreover, hnRNP G may function as a regulator of transcription for SREBP-1c and GnRH1. Research has shown that hnRNP G may also act as a tumor-suppressor since it upregulates the Txnip gene and promotes the fidelity of DNA end-joining activity. In addition, hnRNP G appears to play a critical role in proper neural development of zebrafish and frog embryos. The family also includes several paralogs of hnRNP G, such as hRBMY and hnRNP G-T (also termed RNA-binding motif protein, X-linked-like-2). Both, hRBMY and hnRNP G-T, are exclusively expressed in testis and critical for male fertility. Like hnRNP G, hRBMY and hnRNP G-T interact with factors implicated in the regulation of pre-mRNA splicing, such as hTra2-beta1 and T-STAR. Although members in this family share a high conserved N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), they appear to recognize different RNA targets. For instance, hRBMY interacts specifically with a stem-loop structure in which the loop is formed by the sequence CA/UCAA. In contrast, hnRNP G associates with single stranded RNA sequences containing a CCA/C motif. In addition to the RRM, hnRNP G contains a nascent transcripts targeting domain (NTD) in the middle region and a novel auxiliary RNA-binding domain (RBD) in its C-terminal region. The C-terminal RBD exhibits distinct RNA binding specificity, and would play a critical role in the regulation of alternative splicing by hnRNP G. . Length = 80

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

 Score = 52.8 bits (127), Expect = 7e-09
 Identities = 22/71 (30%), Positives = 40/71 (56%), Gaps = 1/71 (1%)

Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI-E 475
             LFV  LPFSV + +++  F +   V  VRL ++  G+ KG  +VE+ +   A +A+ +
Sbjct: 3   HKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLK 62

Query: 476 LNGQMLGNRAI 486
           ++G  +  + I
Sbjct: 63  MDGTEIKEKTI 73

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

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

 Score = 53.0 bits (128), Expect = 8e-09
 Identities = 26/77 (33%), Positives = 44/77 (57%), Gaps = 2/77 (2%)

Query: 416 SKTLFVGNLPFS-VEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKA- 473
           S+ LFV  LP +  + + ++  FS+V +    +L+   +G+ +G+  VE+A+ EDA +A 
Sbjct: 2   SRCLFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQ 61

Query: 474 IELNGQMLGNRAIRLDF 490
             LNG  L    IR+ F
Sbjct: 62  QALNGHSLQGSPIRVSF 78

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

>gnl|CDD|240671 cd12225, RRM1_2_CID8_like, RNA recognition motif 1 and 2 (RRM1, RRM2) in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 52.4 bits (126), Expect = 9e-09
 Identities = 31/80 (38%), Positives = 45/80 (56%), Gaps = 6/80 (7%)

Query: 520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNK 579
           TI + G D S+ ED ++    E F +CGE+TR  V    D       A+++F DA+S   
Sbjct: 2   TIHVGGIDGSLSEDDLK----EFFSNCGEVTR--VRLCGDRQHSARFAFVEFADAESALS 55

Query: 580 ALEMSGTEIGGYSLVVDEAK 599
           AL +SGT +GG+ L V  +K
Sbjct: 56  ALNLSGTLLGGHPLRVSPSK 75

This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 77

>gnl|CDD|215641 PLN03237, PLN03237, DNA topoisomerase 2; Provisional

 Score = 58.3 bits (141), Expect = 1e-08
 Identities = 47/251 (18%), Positives = 81/251 (32%), Gaps = 7/251 (2%)

Query: 158  KLPVAAAKNGPSAPQKKKDDSSDSSDEESDESSDEDDKSTKAIPQPKKLPASTAKKGTVA 217
                  ++  P  P  KK     S  E ++E+       T+ + +  K P   A     A
Sbjct: 1192 GAAKKVSRQAPKKPAPKKTTKKASESETTEETYGSSAMETENVAEVVK-PKGRAGAKKKA 1250

Query: 218  ATKKSTGSSDDDSSSSEDSSESEEDNGAPAKVTSEAKKLPAVKNVPAPAAKKKTESSDSS 277
                     +D+    +D   +   + APA+    AK    VK VPA  A  + +   S 
Sbjct: 1251 PAAAKEKEEEDEILDLKDRLAAYNLDSAPAQ---SAKMEETVKAVPARRAAARKKPLASV 1307

Query: 278  DEESEDSSDEDEEPTHVTKATPVKKL---SAVVTKNKVESSSSSDESESEEEKPPAKMDV 334
               S+   D+D+    V+ A  +KK           K     ++ +          +  +
Sbjct: 1308 SVISDSDDDDDDFAVEVSLAERLKKKGGRKPAAANKKAAKPPAAAKKRGPATVQSGQKLL 1367

Query: 335  DSSSEEESSDEEPQKKKDVKPNTKALKKESSSDEEDSDDEDEGEEEEASKTPKKNVTDVK 394
                +   +     +KK  K       K+S S    +    E E  E       +  D  
Sbjct: 1368 TEMLKPAEAIGISPEKKVRKMRASPFNKKSGSVLGRAATNKETESSENVSGSSSSEKDEI 1427

Query: 395  MVDAESGKKAA 405
             V A+   + A
Sbjct: 1428 DVSAKPRPQRA 1438

Length = 1465

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

 Score = 51.9 bits (125), Expect = 1e-08
 Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 4/72 (5%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRF----KGYGHVEFASVEDAHKAI 474
           ++V NL F +++ D++  FS+  EV  +R+    D +      G+  V F     A  A+
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62

Query: 475 ELNGQMLGNRAI 486
           +LNG  LG R I
Sbjct: 63  QLNGTELGGRKI 74

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

>gnl|CDD|240706 cd12260, RRM2_SREK1, RNA recognition motif 2 in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins

 Score = 52.3 bits (126), Expect = 1e-08
 Identities = 25/70 (35%), Positives = 38/70 (54%), Gaps = 1/70 (1%)

Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIEL 476
           +T++VGNL  +     +  FFS+  EV  VR++ D + +   Y  VEFA       A++L
Sbjct: 5   RTIYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGD-ETQPTRYAFVEFAEQTSVINALKL 63

Query: 477 NGQMLGNRAI 486
           NG M G R +
Sbjct: 64  NGAMFGGRPL 73

This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site. . Length = 85

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

 Score = 52.2 bits (126), Expect = 1e-08
 Identities = 28/75 (37%), Positives = 41/75 (54%), Gaps = 2/75 (2%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-L 476
           L V  L     + D++  FS    +  V++  D   GR +G+G V F SVEDA +A E L
Sbjct: 2   LGVFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERL 61

Query: 477 NGQMLGNRAIRLDFA 491
           NG  +  R IR+D++
Sbjct: 62  NGMEIDGRRIRVDYS 76

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

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

 Score = 52.0 bits (125), Expect = 1e-08
 Identities = 22/78 (28%), Positives = 45/78 (57%), Gaps = 1/78 (1%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKA-I 474
           ++TLFVGNL  ++ + +++  F     V DV +     G+   Y  V+F +++ AH+A +
Sbjct: 2   TRTLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAKV 61

Query: 475 ELNGQMLGNRAIRLDFAR 492
            ++GQ +G   I++ + +
Sbjct: 62  AMSGQYIGRNQIKIGYGK 79

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

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

 Score = 51.8 bits (125), Expect = 1e-08
 Identities = 25/74 (33%), Positives = 41/74 (55%), Gaps = 1/74 (1%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-L 476
            L V NL + V + D++  F  V EV  V+++ D  GR +G   V F   EDA +AI+  
Sbjct: 2   RLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQF 61

Query: 477 NGQMLGNRAIRLDF 490
           NG +L  + ++++ 
Sbjct: 62  NGVLLDGQPMQVEL 75

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

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

 Score = 50.7 bits (122), Expect = 2e-08
 Identities = 27/71 (38%), Positives = 42/71 (59%), Gaps = 5/71 (7%)

Query: 520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNK 579
           T+F+   D SV ED++R    + F  CGEIT + + K+Y  G  KG AY++F + +S  +
Sbjct: 1   TVFVSNLDYSVPEDELR----KLFSKCGEITDVRLVKNY-KGKSKGYAYVEFENEESVQE 55

Query: 580 ALEMSGTEIGG 590
           AL++    I G
Sbjct: 56  ALKLDRELIKG 66

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

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 57.8 bits (139), Expect = 2e-08
 Identities = 93/406 (22%), Positives = 175/406 (43%), Gaps = 22/406 (5%)

Query: 3    AAPVVATPTKSAKKGGKREAEDAIEKLVSAKKQKGNDGVAQAVKKAKVEAKTQKKNKNDE 62
            A    A   + A+K  + +  +  +K   AKK +      +A KKA+   K  +  K  E
Sbjct: 1266 ARRQAAIKAEEARKADELKKAEEKKKADEAKKAEEKKKADEAKKKAEEAKKADEAKKKAE 1325

Query: 63   TSSSSSEEDSSDSEEEQKVKAVVTNKGGKAAKPPVKESSSEEEDSSSDEEPPKKQPVAAK 122
             +   ++     +EE +K  A       +AA    + +  + E +   +E  KK+  AAK
Sbjct: 1326 EAKKKADAAKKKAEEAKK-AAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAK 1384

Query: 123  NGAVAATAKKSKPDSSSSDSSDDDSDEDEVPTSIKKLPVAAAKNGPSAPQKKKDDSSDSS 182
              A     +K K D +   + +D    DE+  +      A      +  +KK D++   +
Sbjct: 1385 KKA----EEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKA 1440

Query: 183  DE--ESDESSDEDDKSTKAIPQPKKLPASTAKKGTVAATKKSTGSSDDDSSSSEDSSESE 240
            +E  ++DE+  + +++ KA    KK  A  AKK   A  K       D++    + ++ +
Sbjct: 1441 EEAKKADEAKKKAEEAKKAEEAKKK--AEEAKKADEAKKKAEEAKKADEAKKKAEEAKKK 1498

Query: 241  EDNGAPAKVTSEAKKLPAVKNVPAPAAKKKTESSDSSDEESEDSSDEDEEPTHVTKATPV 300
             D    AK  +EAKK    K   A  A++  ++ ++   E    +DE ++     KA  +
Sbjct: 1499 ADE---AKKAAEAKK----KADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADEL 1551

Query: 301  KKLSAVVTKNKVESSSSSDESESEEEKPPAKMDVDSSSEEESSDEEPQKKKDVKPNTKAL 360
            KK   +    K E    ++E++  EE    K      +EE    EE + ++ +K   +  
Sbjct: 1552 KKAEEL---KKAEEKKKAEEAKKAEED---KNMALRKAEEAKKAEEARIEEVMKLYEEEK 1605

Query: 361  KKESSSDEEDSDDEDEGEEEEASKTPKKNVTDVKMVDAESGKKAAQ 406
            K ++   ++  + + + EE + ++  KK V  +K  +AE  KKA +
Sbjct: 1606 KMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEE 1651

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 57.5 bits (138), Expect = 2e-08
 Identities = 90/394 (22%), Positives = 162/394 (41%), Gaps = 32/394 (8%)

Query: 20   REAEDAIEKLVSAKKQKGNDGVAQAVKKAKVEAKTQKKNKNDETSSSSSE---EDSSDSE 76
            R+AEDA +K  +A+K       A+ V+KA+   K +   K +    +  E   E++  +E
Sbjct: 1170 RKAEDA-KKAEAARK-------AEEVRKAEELRKAEDARKAEAARKAEEERKAEEARKAE 1221

Query: 77   EEQKVKAVVTNKGGKAAKPPVKESSSEEEDSSSDEEPPKKQPVAAKNGAVAATAKKSKPD 136
            + +K +AV   +  K      K++  E  +    +    +    A+  A     +  K D
Sbjct: 1222 DAKKAEAVKKAEEAKKDAEEAKKAEEERNNEEIRKFEEARMAHFARRQAAIKAEEARKAD 1281

Query: 137  SSSSDSSDDDSDEDEVPTSIKKLPVAAAKNGPSAPQKKKDDSSDSSDEESDESSDEDDKS 196
                      +DE +     KK   A  K    A + KK D +    EE+ + +D   K 
Sbjct: 1282 ELKKAEEKKKADEAKKAEEKKKADEAKKK----AEEAKKADEAKKKAEEAKKKADAAKKK 1337

Query: 197  TKAIPQPKKLPASTAKKGTVAATKKSTGSSDDDSSSSEDSSESEEDNGAPAKVTSEAKKL 256
                       A  AKK   AA  ++  ++D+ + ++E+ +E+ E     AK  ++A K 
Sbjct: 1338 -----------AEEAKKAAEAAKAEAEAAADE-AEAAEEKAEAAEKKKEEAKKKADAAKK 1385

Query: 257  PAVKNVPAPAAKKKTESSDSSDEESEDSSDEDEEPTHVTKATPVKKLSAVVTKNKVESSS 316
             A +   A  AKKK E      +E + ++   ++     K    KK  A   K K E + 
Sbjct: 1386 KAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKK-KADEAKKKAEEAK 1444

Query: 317  SSDESESEEEKPPAKMDVDSSSEEESSDEEPQKKKDVKPNTKALKKESSSDEEDSDDEDE 376
             +DE++ + E+     +    +EE    +E +KK +        KK++   ++ +D+  +
Sbjct: 1445 KADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKK 1504

Query: 377  GEEEEASKTPKKNVTDVKMVD----AESGKKAAQ 406
              E +      K   + K  D    AE  KKA +
Sbjct: 1505 AAEAKKKADEAKKAEEAKKADEAKKAEEAKKADE 1538

Length = 2084

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

 Score = 51.2 bits (123), Expect = 2e-08
 Identities = 19/70 (27%), Positives = 43/70 (61%), Gaps = 1/70 (1%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSS-DADGRFKGYGHVEFASVEDAHKAIELN 477
           ++VG +P+   + +++++FS   E+ ++ L +    GRF+G   + F + E A +A+ L+
Sbjct: 1   VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRALALD 60

Query: 478 GQMLGNRAIR 487
           G+ +G R ++
Sbjct: 61  GEDMGGRFLK 70

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

>gnl|CDD|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 = 51.0 bits (123), Expect = 3e-08
 Identities = 27/63 (42%), Positives = 39/63 (61%), Gaps = 2/63 (3%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAIE-L 476
           LFVG LP +  + DV+  F E   + +V +  D D G+ KG   V+F+S E+A KAIE L
Sbjct: 2   LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEAL 61

Query: 477 NGQ 479
           +G+
Sbjct: 62  HGK 64

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

 Score = 50.6 bits (121), Expect = 3e-08
 Identities = 31/74 (41%), Positives = 42/74 (56%), Gaps = 2/74 (2%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAI-EL 476
           +FVG+L   V  A +   FS      D R+  D   GR +GYG V F S +DA  AI E+
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61

Query: 477 NGQMLGNRAIRLDF 490
           NG+ LG+R IR ++
Sbjct: 62  NGKWLGSRPIRCNW 75

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

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

 Score = 50.5 bits (121), Expect = 3e-08
 Identities = 26/76 (34%), Positives = 42/76 (55%), Gaps = 2/76 (2%)

Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE- 475
           K L V N+PF     D++  F +   ++DV +  +  G  KG+G V FA+  DA +A E 
Sbjct: 1   KRLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERGS-KGFGFVTFANSADADRAREK 59

Query: 476 LNGQMLGNRAIRLDFA 491
           L+G ++  R I ++ A
Sbjct: 60  LHGTVVEGRKIEVNNA 75

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

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

 Score = 50.8 bits (122), Expect = 3e-08
 Identities = 26/79 (32%), Positives = 44/79 (55%), Gaps = 3/79 (3%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVD-VRLSSDAD-GRFKGYGHVEFASVEDAHKAIE- 475
           LF+GNL   V++  + + FS    ++   ++  D D G  KG+  + + S E +  AIE 
Sbjct: 4   LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63

Query: 476 LNGQMLGNRAIRLDFARER 494
           +NGQ L NR I + +A ++
Sbjct: 64  MNGQYLCNRPITVSYAFKK 82

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

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

 Score = 50.7 bits (122), Expect = 4e-08
 Identities = 25/82 (30%), Positives = 40/82 (48%), Gaps = 7/82 (8%)

Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAIE 475
           +T+F+ NLPF   + +++  FS+  EV   R+  D   G  KG   V+F + E A K +E
Sbjct: 1   RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLE 60

Query: 476 ------LNGQMLGNRAIRLDFA 491
                  +G  L  R + +  A
Sbjct: 61  AADNAEDSGLSLDGRRLIVTLA 82

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

>gnl|CDD|241190 cd12746, RRM2_RBM12B, RNA recognition motif 2 in RNA-binding protein 12B (RBM12B) and similar proteins

 Score = 50.2 bits (120), Expect = 5e-08
 Identities = 25/70 (35%), Positives = 41/70 (58%), Gaps = 1/70 (1%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNG 478
           LF+  LPFSV + +V++FFS +  V  V    +  G   G   V+FA+ EDA + ++ + 
Sbjct: 2   LFLRGLPFSVTEDNVRDFFSGLK-VDGVIFLKNRRGLNNGNSMVKFATKEDAIEGLKRDR 60

Query: 479 QMLGNRAIRL 488
           Q +G+R I +
Sbjct: 61  QYMGSRYIEI 70

This subgroup corresponds to the RRM2 of RBM12B which contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Its biological role remains unclear. . Length = 78

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

 Score = 50.0 bits (120), Expect = 5e-08
 Identities = 26/73 (35%), Positives = 41/73 (56%), Gaps = 6/73 (8%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI-ELN 477
           LFVGNLP  + + + +  FS+  EV +V L+ +     KG+G +   +  +A KA  EL+
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE-----KGFGFIRLDTRTNAEKAKAELD 58

Query: 478 GQMLGNRAIRLDF 490
           G M   R +R+ F
Sbjct: 59  GIMRKGRQLRVRF 71

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

>gnl|CDD|240905 cd12459, RRM1_CID8_like, RNA recognition motif 1 in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 50.1 bits (120), Expect = 5e-08
 Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 5/74 (6%)

Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADG--RFKGYGHVEFASVEDAHKAI 474
           +T++V ++   V +  +   FS   +VVD R+  D +   RF     +EF   E A  A+
Sbjct: 3   RTVYVSDIDQQVTEEQLAALFSNCGQVVDCRVCGDPNSVLRF---AFIEFTDEEGARAAL 59

Query: 475 ELNGQMLGNRAIRL 488
            L+G MLG   +R+
Sbjct: 60  SLSGTMLGFYPVRV 73

This subgroup corresponds to the RRM1 domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 80

>gnl|CDD|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 50.0 bits (120), Expect = 5e-08
 Identities = 24/77 (31%), Positives = 37/77 (48%), Gaps = 3/77 (3%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEV-AEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKA-I 474
           ++FVG+L   V    +Q  F      V   ++  D   GR KGYG V F   ++  +A  
Sbjct: 3   SIFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALT 62

Query: 475 ELNGQMLGNRAIRLDFA 491
           E+NG    +R +R+  A
Sbjct: 63  EMNGVYCSSRPMRVSPA 79

This subfamily corresponds to the RRM2 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs. . Length = 80

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

 Score = 50.0 bits (120), Expect = 5e-08
 Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 6/72 (8%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI-EL 476
           T+FVG L  +V + ++++ F    E+V V++        KG G V+F     A  AI +L
Sbjct: 3   TVFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPG-----KGCGFVQFVHRAAAEAAIQQL 57

Query: 477 NGQMLGNRAIRL 488
            G ++G   IRL
Sbjct: 58  QGTIIGGSRIRL 69

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

>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 55.3 bits (133), Expect = 6e-08
 Identities = 67/346 (19%), Positives = 126/346 (36%), Gaps = 46/346 (13%)

Query: 282 EDSSDEDEEPTHVTKATPVKKLSAVVTKNKVESSSSSDESESEEEKPPAKMDVDSSSEEE 341
           EDS   D           ++  S   ++++    S S  S  +  +        S S + 
Sbjct: 48  EDSRPRDRRRYDSRSPRSLRYSSVRRSRDRPRRRSRSVRSIEQHRRRLRDR---SPSNQW 104

Query: 342 SSDEEPQKKKDVKPNTKALKKESSSDEEDSDDEDEGEEEEASKT-PKKNVTDVKMVDAES 400
             D++ +   D+KP           +   +D     +      T P+  +TD + + AE 
Sbjct: 105 RKDDKKRSLWDIKP--------PGYELVTADQAKASQVFSVPGTAPRPAMTDPEKLLAEG 156

Query: 401 GKKAAQTPFTPQSGGSKT---LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD---- 453
                      Q   ++    L+VG +P    +  V +FF+++        + D      
Sbjct: 157 SIITPLPVLPYQQQATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSS 216

Query: 454 ---GRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARERGAYTP----------- 499
               + K +  +EF +VE+A  A+ L+  +  N  +++   R    Y P           
Sbjct: 217 VNINKEKNFAFLEFRTVEEATFAMALDSIIYSNVFLKI---RRPHDYIPVPQITPEVSQK 273

Query: 500 ----YSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVP 555
                +   E           +   I+I      +GEDQ++  LE    S G++   ++ 
Sbjct: 274 NPDDNAKNVEKLVNSTTVL-DSKDRIYIGNLPLYLGEDQIKELLE----SFGDLKAFNLI 328

Query: 556 KDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVDEAKQ 600
           KD  TG  KG A+ ++ D    + A+  ++G + G   L V  A  
Sbjct: 329 KDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACV 374

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

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

 Score = 49.7 bits (119), Expect = 8e-08
 Identities = 17/54 (31%), Positives = 28/54 (51%)

Query: 537 ASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGG 590
             L  HF + G    + +  D  TG  KG A+++F  A++  KAL++  T + G
Sbjct: 15  EDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLHHTLLKG 68

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

>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 54.0 bits (130), Expect = 8e-08
 Identities = 31/57 (54%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 612 GGRGGRSGGRDFGRSGGRDGGRFGGRGRGGRDGGRGGRGRGRGTPNRPSLAAAGTGK 668
           G  GG  GGR  GR GG  GGR GG GRGG  GG  GRGRG G   R      G GK
Sbjct: 1   GMGGGFGGGRGGGRGGGGGGGRGGG-GRGGGRGGGRGRGRGGGGGGRGGGGGGGPGK 56

Length = 293

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

 Score = 49.3 bits (118), Expect = 9e-08
 Identities = 21/60 (35%), Positives = 36/60 (60%), Gaps = 1/60 (1%)

Query: 538 SLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEM-SGTEIGGYSLVVD 596
           S+ E FG  GEI+ + +P D D+G  KG  Y++F+  ++   AL+   GT++ G  + +D
Sbjct: 14  SIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDALGGTDLLGRPVRLD 73

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

>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional

 Score = 55.4 bits (134), Expect = 9e-08
 Identities = 45/202 (22%), Positives = 79/202 (39%), Gaps = 14/202 (6%)

Query: 1    VDAAPVVATPTKSAKKGGKREAEDAIEKLVSAKKQKGNDGVAQAVKKAKVEAKTQKKNKN 60
              A+ V  +    + +  K + +   +K  S+   + +D   +   K     + + K  N
Sbjct: 1190 KKASVVGNSKRVDSDEKRKLDDKPDNKKSNSSGSDQEDDEEQKTKPKKSSVKRLKSKKNN 1249

Query: 61   DETSSSSSEEDSSD---SEEEQKVKAVVTNKGGKAAKPPVKESSSEEEDSSSDEEPPKKQ 117
               SS  ++E SSD    E + K      +    +  PP K    E    S    P KK+
Sbjct: 1250 SSKSSEDNDEFSSDDLSKEGKPKNAPKRVSAVQYSPPPPSKRPDGESNGGSKPSSPTKKK 1309

Query: 118  PVAAKNGAVAATAKKSKPDSSSSDSSDDDSDEDEVPTSIKKLPVAAAKNGPSAPQKKKDD 177
                  G++AA  KK K +  ++          +  T +K+   + +      P+KKK D
Sbjct: 1310 VKKRLEGSLAALKKKKKSEKKTARK-------KKSKTRVKQASASQSSRLLRRPRKKKSD 1362

Query: 178  SSDSSDEES----DESSDEDDK 195
            SS   D++S     E  D++D 
Sbjct: 1363 SSSEDDDDSEVDDSEDEDDEDD 1384

Length = 1388

>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 = 49.2 bits (118), Expect = 9e-08
 Identities = 25/72 (34%), Positives = 37/72 (51%), Gaps = 2/72 (2%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAI-EL 476
           LFV NLPF+  + +++  F    E+ +V L  D    R KG+  V F   E A KA  EL
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 477 NGQMLGNRAIRL 488
           +G +   R + +
Sbjct: 62  DGSIFQGRLLHV 73

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

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

 Score = 48.8 bits (117), Expect = 1e-07
 Identities = 17/68 (25%), Positives = 29/68 (42%), Gaps = 1/68 (1%)

Query: 420 FVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNG 478
           FVGN+ +     ++Q  F     +  + +  D   G+ KG+ ++EF        A+ LN 
Sbjct: 3   FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALLLNE 62

Query: 479 QMLGNRAI 486
                R I
Sbjct: 63  SEFRGRQI 70

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

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

 Score = 49.1 bits (118), Expect = 1e-07
 Identities = 26/77 (33%), Positives = 41/77 (53%), Gaps = 8/77 (10%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFK----GYGHVEFASVEDAHKAI 474
           L+VGNL F   +  +   FS   ++  + +  D   RF     G+  VE+ + EDA  A+
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLD---RFTKTPCGFCFVEYYTREDAENAV 57

Query: 475 E-LNGQMLGNRAIRLDF 490
           + LNG  L +R IR+D+
Sbjct: 58  KYLNGTKLDDRIIRVDW 74

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

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

 Score = 49.2 bits (118), Expect = 1e-07
 Identities = 23/75 (30%), Positives = 41/75 (54%), Gaps = 2/75 (2%)

Query: 419 LFVGNLPFSVEQADVQNFFSE-VAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-L 476
           L V NLP S+ +A+++  FS+   E+ DV+L    DG+ +    + + + E+A KA +  
Sbjct: 3   LIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAKDYF 62

Query: 477 NGQMLGNRAIRLDFA 491
           N   +    I ++FA
Sbjct: 63  NNTYINTSKISVEFA 77

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

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

 Score = 49.0 bits (117), Expect = 1e-07
 Identities = 25/74 (33%), Positives = 43/74 (58%), Gaps = 3/74 (4%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAIELN 477
           LFVGNL F   + +++  F  V  +  VR+ +  D G+ KG+  V+F  +E A  A++  
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALK-- 58

Query: 478 GQMLGNRAIRLDFA 491
           G+ L  RA+R+++ 
Sbjct: 59  GKHLNGRALRVEYG 72

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

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

 Score = 49.3 bits (118), Expect = 1e-07
 Identities = 28/75 (37%), Positives = 43/75 (57%), Gaps = 2/75 (2%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAI-EL 476
           L V  LP ++ Q ++++ FS + E+   +L  D   G+  GYG V +   EDA KAI  L
Sbjct: 4   LIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTL 63

Query: 477 NGQMLGNRAIRLDFA 491
           NG  L N+ I++ +A
Sbjct: 64  NGLRLQNKTIKVSYA 78

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

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

 Score = 51.2 bits (122), Expect = 1e-07
 Identities = 34/102 (33%), Positives = 54/102 (52%), Gaps = 2/102 (1%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAI 474
           S  LF+G L +  + A +++ F+   +VVD ++  D + GR +G+G V F     A  AI
Sbjct: 34  STKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAI 93

Query: 475 -ELNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRG 515
            E++G+ L  R IR++ A +R +     GG    S   GG G
Sbjct: 94  SEMDGKELNGRHIRVNPANDRPSAPRAYGGGGGYSGGGGGYG 135

Length = 144

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

 Score = 48.4 bits (116), Expect = 2e-07
 Identities = 22/81 (27%), Positives = 44/81 (54%), Gaps = 5/81 (6%)

Query: 520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNK 579
            +++     +V E+ ++    +     GE+T   V  D +TG  +G  +++   A+  N 
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQF----GEVTSARVITDRETGRSRGFGFVEMETAEEANA 56

Query: 580 ALE-MSGTEIGGYSLVVDEAK 599
           A+E ++GT+ GG +L V+EA+
Sbjct: 57  AIEKLNGTDFGGRTLTVNEAR 77

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

>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

 Score = 54.6 bits (131), Expect = 2e-07
 Identities = 62/341 (18%), Positives = 129/341 (37%), Gaps = 50/341 (14%)

Query: 85   VTNKGGKAAKPPVKESSSEEEDSSSDEEPPKKQPVAAKNGAVAATAKKSKPDSSSSDSSD 144
            V N G  +   P ++S+S E +S +         + +  GA   T   ++ D     +++
Sbjct: 3792 VANNGFCSPDLPQEKSNSGELESGTG--------LGSGVGAEDITNTLNEDDDLEELANE 3843

Query: 145  DDSDEDEVPTSIKKLPVAAAKNGPSAPQKKKDDSSDSSDEESDESSDEDDKSTKAIPQPK 204
            +D+         +   + +  NG +       DS  S +E SD   +  D   +    P+
Sbjct: 3844 EDTANQSDLDESEARELESDMNGVT------KDSVVSENENSDSEEENQDLDEEVNDIPE 3897

Query: 205  KLPASTAKKGTVAATKKSTGSSDDDSSSSEDSSESEEDNGAPAKVTSEAKKLPAVKNVPA 264
             L  S  +K               D  + ED  E+E+ +   +   +E+  +    +  A
Sbjct: 3898 DLSNSLNEKLW-------------DEPNEEDLLETEQKSNEQSAANNESDLVSKEDDNKA 3944

Query: 265  PAAKKKTESSDSSDEESEDSSDEDEEPTHVTKATPVKKLSAVVTKNKV-----ESSSSSD 319
               K + E  D   E S+D   +DE      +    +  S    +N+      +      
Sbjct: 3945 LEDKDRQEKEDEE-EMSDDVGIDDE-----IQPDIQENNSQPPPENEDLDLPEDLKLDEK 3998

Query: 320  ESESEEEKPPAKMDVDSSSE-EESSDEEPQKKKDVKPNTKALKKESSSDEEDSDDED--- 375
            E +  ++     MD++++ E +E +D E   K +   +   L++ ++ DE+   D+    
Sbjct: 3999 EGDVSKDSDLEDMDMEAADENKEEADAE---KDEPMQDEDPLEENNTLDEDIQQDDFSDL 4055

Query: 376  -EGEEEEASKTPKKNVTDVKMVDAESGKKAAQTPFTPQSGG 415
             E +E+      ++NV      + ES +   ++    + G 
Sbjct: 4056 AEDDEKMNEDGFEENV----QENEESTEDGVKSDEELEQGE 4092

Length = 4600

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 54.8 bits (131), Expect = 2e-07
 Identities = 81/401 (20%), Positives = 162/401 (40%), Gaps = 16/401 (3%)

Query: 20   REAEDAIEKLVSAKKQKGNDGVAQAVKKAKVEAKTQKKNKNDETSSSSSEEDSSDSEEEQ 79
            R+AE+A  K   AKK +      +A K A+   K +++  N+E         +  +  + 
Sbjct: 1212 RKAEEA-RKAEDAKKAEAVKKAEEAKKDAEEAKKAEEERNNEEIRKFEEARMAHFARRQA 1270

Query: 80   KVKAVVTNKGGKAAKPPVKESSSEEEDSSSDEEPPKKQPVAAKNGAVAATAKKSKPDSSS 139
             +KA    K  +  K   K+ + E + +   ++  + +  A +        KK++     
Sbjct: 1271 AIKAEEARKADELKKAEEKKKADEAKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKK 1330

Query: 140  SDSSDDDSDEDEVPTSIKKLPVAAAKNGPSAPQKKKDDSSDSSDEE---SDESSDEDDKS 196
            +D++   ++E +      K    AA +   A ++K + +    +E    +D +  + ++ 
Sbjct: 1331 ADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEK 1390

Query: 197  TKAIPQPKKLPASTAKKGTVAATKKSTGSSDDDSSSSEDSSESEE-DNGAPAKVTSEAKK 255
             KA    KK      K   +     +   +D+    +E+  +++E    A     ++  K
Sbjct: 1391 KKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAK 1450

Query: 256  LPAVKNVPAPAAKKKTESSDSSDEESEDSSDEDEEPTHVTKATPVKKLSAVVTKNKVESS 315
              A +   A  AKKK E +  +DE  + + +  +      KA   KK  A   K   E+ 
Sbjct: 1451 KKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKK-KADEAKKAAEAK 1509

Query: 316  SSSDESESEEEKPPA----------KMDVDSSSEEESSDEEPQKKKDVKPNTKALKKESS 365
              +DE++  EE   A          K D    +EE+   +E +K +++K   +  K E +
Sbjct: 1510 KKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEA 1569

Query: 366  SDEEDSDDEDEGEEEEASKTPKKNVTDVKMVDAESGKKAAQ 406
               E+  +    + EEA K  +  + +V  +  E  K  A+
Sbjct: 1570 KKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAE 1610

Length = 2084

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

 Score = 50.4 bits (120), Expect = 2e-07
 Identities = 34/93 (36%), Positives = 48/93 (51%), Gaps = 5/93 (5%)

Query: 537 ASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKAL-EMSGTEIGGYSLVV 595
           ASL + F   G++    V  D +TG  +G  +++F D  +   A+ EM G E+ G  + V
Sbjct: 49  ASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRV 108

Query: 596 DEAKQRGD----FGSGGGRSGGRGGRSGGRDFG 624
           + A  R      +G GGG SGG GG  GG D G
Sbjct: 109 NPANDRPSAPRAYGGGGGYSGGGGGYGGGGDGG 141

Length = 144

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

 Score = 48.7 bits (116), Expect = 2e-07
 Identities = 27/76 (35%), Positives = 46/76 (60%), Gaps = 4/76 (5%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE 475
           ++TLFV NLP+++   +++  F +    VD+RL S  DG  KG  ++EF +  +A KA+E
Sbjct: 3   ARTLFVKNLPYNITVDELKEVFEDA---VDIRLPSGKDGSSKGIAYIEFKTEAEAEKALE 59

Query: 476 -LNGQMLGNRAIRLDF 490
              G  +  R+I +D+
Sbjct: 60  EKQGAEVDGRSIVVDY 75

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

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 54.6 bits (131), Expect = 2e-07
 Identities = 47/267 (17%), Positives = 102/267 (38%), Gaps = 12/267 (4%)

Query: 116 KQPVAAKNGAVAATAKKSKPDSSSSDSSDDDSDEDEVPTSIKKLPVAAAKNGPSAPQKKK 175
           ++PVA     V A    SK D + ++ + + + E+    +  +        G +  + + 
Sbjct: 618 RRPVAK----VMALGDLSKGDVAEAEHTGERTGEEGERPTEAEGENGEESGGEAEQEGET 673

Query: 176 DDSSDSSDEESDESSDEDDKSTKAIPQPKKLPASTAKKGTVAATKKSTGSSDDDSSSSED 235
           +   ++  E    +  + ++  +   + K+   +  K  T A   +  G ++ + +  E 
Sbjct: 674 ETKGENESEGEIPAERKGEQEGEGEIEAKE---ADHKGETEAEEVEHEGETEAEGTEDEG 730

Query: 236 SSESEEDNGAPAKVTSEAKKLPAVKNVPAPAAKKKTESSDSSDEESEDSSDEDEEPTHVT 295
             E+ E+     +   +  +  A           + E+    + E+E   DEDE      
Sbjct: 731 EIETGEE----GEEVEDEGEGEAEGKHEVETEGDRKETEHEGETEAEGKEDEDEGEIQAG 786

Query: 296 KATPVKKLSAVVTKNKVESSSSSDES-ESEEEKPPAKMDVDSSSEEESSDEEPQKKKDVK 354
           +   +K       K + E  + + E  E E +      D +   E    +   + + + K
Sbjct: 787 EDGEMKGDEGAEGKVEHEGETEAGEKDEHEGQSETQADDTEVKDETGEQELNAENQGEAK 846

Query: 355 PNTKALKKESSSDEEDSDDEDEGEEEE 381
            + K +     SD  DS++E+E EEEE
Sbjct: 847 QDEKGVDGGGGSDGGDSEEEEEEEEEE 873

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

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

 Score = 48.6 bits (116), Expect = 2e-07
 Identities = 24/69 (34%), Positives = 39/69 (56%), Gaps = 2/69 (2%)

Query: 420 FVGNLPFSVEQADVQNFF-SEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LN 477
           F+ N+P+ ++  D+++ F  +V EV  V L  D +G+ +G G VEF   E   KA+E +N
Sbjct: 3   FISNIPYDLKWQDLKDLFREKVGEVTYVELFKDEEGKSRGCGVVEFKDKESVQKALETMN 62

Query: 478 GQMLGNRAI 486
              L  R +
Sbjct: 63  RYELKGRKL 71

This subfamily corresponds to the RRM1 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 76

>gnl|CDD|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 48.5 bits (116), Expect = 2e-07
 Identities = 24/71 (33%), Positives = 39/71 (54%), Gaps = 1/71 (1%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LN 477
           +FV NL + V    ++  F    +VV   +  D +G+ +G G V+F    +A +AI   N
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKEGKSRGMGVVQFEHPIEAVQAISMFN 60

Query: 478 GQMLGNRAIRL 488
           GQML +R +R+
Sbjct: 61  GQMLFDRPMRV 71

This subfamily corresponds to the RRM2 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 74

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

 Score = 48.3 bits (116), Expect = 2e-07
 Identities = 22/69 (31%), Positives = 42/69 (60%), Gaps = 1/69 (1%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LN 477
           +F+ NL  S++   + + FS    ++  ++++D +G  KGYG V F + E A +AIE +N
Sbjct: 5   IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRAIEKVN 64

Query: 478 GQMLGNRAI 486
           G +L ++ +
Sbjct: 65  GMLLNDKKV 73

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|240737 cd12291, RRM1_La, RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins

 Score = 48.0 bits (115), Expect = 2e-07
 Identities = 22/59 (37%), Positives = 33/59 (55%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIEL 476
           T++V   P      D+Q FF +  +V ++R+  D D +FKG   VEF + EDA K +E 
Sbjct: 1   TVYVKGFPKDATLDDIQEFFEKFGKVNNIRMRRDLDKKFKGSVFVEFKTEEDAKKFLEK 59

This subfamily corresponds to the RRM1 of La autoantigen, also termed Lupus La protein, or La ribonucleoprotein, or Sjoegren syndrome type B antigen (SS-B), a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. La contains an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus. . Length = 72

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

 Score = 47.6 bits (114), Expect = 3e-07
 Identities = 17/57 (29%), Positives = 33/57 (57%)

Query: 539 LEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVV 595
           L E F   G++  + + +D ++   KG+AY++F D +S   AL ++G  + G  ++V
Sbjct: 16  LYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALGLTGQRLLGQPIMV 72

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

>gnl|CDD|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end) protein family

 Score = 48.0 bits (115), Expect = 3e-07
 Identities = 22/77 (28%), Positives = 35/77 (45%), Gaps = 8/77 (10%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LN 477
           L+VG L      A+++  F     +  +          + Y ++E+ S+E A  A E L 
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAIRRIDYDPG-----RNYAYIEYESIEAAQAAKEALR 55

Query: 478 GQMLG--NRAIRLDFAR 492
           G  LG   R +R+DFA 
Sbjct: 56  GFPLGGPGRRLRVDFAD 72

This subfamily corresponds to the RRM3 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B) and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and is a novel component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 72

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

 Score = 48.0 bits (115), Expect = 3e-07
 Identities = 18/60 (30%), Positives = 32/60 (53%), Gaps = 1/60 (1%)

Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAIE 475
             +FVG LP+      ++ +FS+  E+ +  + +D   G+ +GYG V F   E A +A +
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60

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

 Score = 48.1 bits (115), Expect = 3e-07
 Identities = 26/75 (34%), Positives = 41/75 (54%), Gaps = 2/75 (2%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAI-E 475
            +FV NLP   +++ +   FS    V +V++  D    + KGYG V   + E+A+ AI  
Sbjct: 3   CIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIAS 62

Query: 476 LNGQMLGNRAIRLDF 490
           LNG  LG R +++ F
Sbjct: 63  LNGYRLGGRVLQVSF 77

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|240950 cd12506, RRM3_hnRNPH_CRSF1_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein hnRNP H protein family, G-rich sequence factor 1 (GRSF-1) and similar proteins

 Score = 47.7 bits (114), Expect = 3e-07
 Identities = 26/65 (40%), Positives = 39/65 (60%), Gaps = 1/65 (1%)

Query: 424 LPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGN 483
           LP+   + D+  FFS +   V+VR+  +ADGR  G   VEFA+ EDA  A+  + + +G+
Sbjct: 8   LPYRATENDIFEFFSPL-NPVNVRIEYNADGRATGEADVEFATHEDAVAAMSKDREHMGH 66

Query: 484 RAIRL 488
           R I L
Sbjct: 67  RYIEL 71

This subfamily corresponds to the RRM3 of hnRNP H proteins and GRSF-1. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. These proteins have similar RNA binding affinities and specifically recognize the sequence GGGA. They can either stimulate or repress splicing upon binding to a GGG motif. hnRNP H binds to the RNA substrate in the presence or absence of these proteins, whereas hnRNP F binds to the nuclear mRNA only in the presence of cap-binding proteins. hnRNP H and hnRNP H2 are almost identical; both have been found to bind nuclear-matrix proteins. hnRNP H activates exon inclusion by binding G-rich intronic elements downstream of the 5' splice site in the transcripts of c-src, human immunodeficiency virus type 1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons when bound to exonic elements in the transcripts of beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2 has been implicated in pre-mRNA 3' end formation. hnRNP H3 may be involved in the splicing arrest induced by heat shock. Most family members contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), except for hnRNP H3, in which the RRM1 is absent. RRM1 and RRM2 are responsible for the binding to the RNA at DGGGD motifs, and they play an important role in efficiently silencing the exon. For instance, members in this family can regulate the alternative splicing of the fibroblast growth factor receptor 2 (FGFR2) transcripts, and function as silencers of FGFR2 exon IIIc through an interaction with the exonic GGG motifs. The lack of RRM1 could account for the reduced silencing activity within hnRNP H3. In addition, the family members have an extensive glycine-rich region near the C-terminus, which may allow them to homo- or heterodimerize. The family also includes a cytoplasmic poly(A)+ mRNA binding protein, GRSF-1, which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. GRSF-1 also contains three potential RRMs responsible for the RNA binding, and two auxiliary domains (an acidic alpha-helical domain and an N-terminal alanine-rich region) that may play a role in protein-protein interactions and provide binding specificity. . Length = 75

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

 Score = 48.2 bits (115), Expect = 3e-07
 Identities = 26/80 (32%), Positives = 43/80 (53%), Gaps = 2/80 (2%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAIE- 475
            L +  LP ++   + ++ F  V  V + ++  D   G   G+G V++ S EDA +AI  
Sbjct: 2   NLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRT 61

Query: 476 LNGQMLGNRAIRLDFARERG 495
           LNG  L N+ I++ +AR  G
Sbjct: 62  LNGLQLQNKRIKVAYARPGG 81

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

 Score = 47.9 bits (115), Expect = 3e-07
 Identities = 29/84 (34%), Positives = 41/84 (48%), Gaps = 10/84 (11%)

Query: 416 SKTLFVGNLPFSVEQAD-------VQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVE 468
           SK L+V NL   V + D         +  SE   + D+RL ++  GR KG   V F S E
Sbjct: 1   SKRLYVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLMTE--GRMKGQAFVTFPSEE 58

Query: 469 DAHKAIEL-NGQMLGNRAIRLDFA 491
            A KA+ L NG +L  + + + F 
Sbjct: 59  IATKALNLVNGYVLKGKPMVIQFG 82

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

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

 Score = 48.2 bits (114), Expect = 3e-07
 Identities = 29/75 (38%), Positives = 43/75 (57%), Gaps = 2/75 (2%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAI-EL 476
           +FVG+L   +   D++  F+    + D R+  D A G+ KGYG V F +  DA  AI ++
Sbjct: 4   VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63

Query: 477 NGQMLGNRAIRLDFA 491
            GQ LG R IR ++A
Sbjct: 64  GGQWLGGRQIRTNWA 78

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

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

 Score = 47.7 bits (114), Expect = 3e-07
 Identities = 23/74 (31%), Positives = 36/74 (48%), Gaps = 1/74 (1%)

Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIEL 476
           +TLFVGNL   V +  +   F +   +  V++  D +G+ K +  V F        AI+L
Sbjct: 2   RTLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAIQL 61

Query: 477 -NGQMLGNRAIRLD 489
            NG  L  R +R+ 
Sbjct: 62  LNGIRLFGRELRIK 75

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

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

 Score = 47.3 bits (113), Expect = 5e-07
 Identities = 18/74 (24%), Positives = 38/74 (51%), Gaps = 2/74 (2%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-L 476
           ++FVG L   V + ++   FS   ++++V L   A+     +  ++F   + A +A+E  
Sbjct: 5   SIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHT-NAFAFIKFEREQAAARAVESE 63

Query: 477 NGQMLGNRAIRLDF 490
           N  ML N+ + + +
Sbjct: 64  NHSMLKNKTMHVQY 77

This subfamily corresponds to the RRM2 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 80

>gnl|CDD|240905 cd12459, RRM1_CID8_like, RNA recognition motif 1 in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 47.4 bits (113), Expect = 6e-07
 Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 6/76 (7%)

Query: 520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNK 579
           T+++   D  V E+Q    L   F +CG++    V  D +  SV   A+++FTD +    
Sbjct: 4   TVYVSDIDQQVTEEQ----LAALFSNCGQVVDCRVCGDPN--SVLRFAFIEFTDEEGARA 57

Query: 580 ALEMSGTEIGGYSLVV 595
           AL +SGT +G Y + V
Sbjct: 58  ALSLSGTMLGFYPVRV 73

This subgroup corresponds to the RRM1 domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 80

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

 Score = 46.9 bits (112), Expect = 6e-07
 Identities = 20/74 (27%), Positives = 38/74 (51%), Gaps = 1/74 (1%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LN 477
           L V NLP  +++  ++  F     + DV+L    DG+F+ +G V + + E+A KA++  N
Sbjct: 3   LIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHFN 62

Query: 478 GQMLGNRAIRLDFA 491
              +    I ++  
Sbjct: 63  NSFIDTSKITVEIC 76

This subgroup corresponds to the RRM1 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

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

 Score = 47.6 bits (114), Expect = 6e-07
 Identities = 26/80 (32%), Positives = 38/80 (47%), Gaps = 2/80 (2%)

Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAIE 475
            TLFVG L     +  ++  FS   ++  +RL  D   G  KGY  VE+    DA +A  
Sbjct: 4   LTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYR 63

Query: 476 L-NGQMLGNRAIRLDFARER 494
             +  ++    I +DF RER
Sbjct: 64  DAHKLVIDGSEIFVDFERER 83

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

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

 Score = 47.2 bits (113), Expect = 6e-07
 Identities = 28/79 (35%), Positives = 38/79 (48%), Gaps = 7/79 (8%)

Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD----GRFK--GYGHVEFASVEDA 470
            TLFV NL F   +  ++  F +   V  V ++   D    G+    GYG VEF S E A
Sbjct: 1   TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAA 60

Query: 471 HKAI-ELNGQMLGNRAIRL 488
            KA+  L G +L   A+ L
Sbjct: 61  QKALKRLQGTVLDGHALEL 79

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

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

 Score = 47.2 bits (113), Expect = 6e-07
 Identities = 26/79 (32%), Positives = 46/79 (58%), Gaps = 2/79 (2%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAIE-L 476
           +FV  +    ++ DV + F+E  E+ ++ L+ D   G  KGY  +E+ + ++A  AIE L
Sbjct: 9   IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 477 NGQMLGNRAIRLDFARERG 495
           NG+ L  + I +D+A  +G
Sbjct: 69  NGKELLGQTISVDWAFVKG 87

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

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

 Score = 46.9 bits (112), Expect = 6e-07
 Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 8/75 (10%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI-ELN 477
           +++G LP+   + DV+ FF     + ++ L +       G+G VEF    DA  A+ ELN
Sbjct: 2   VYIGRLPYRARERDVERFFKGYGRIREINLKN-------GFGFVEFEDPRDADDAVYELN 54

Query: 478 GQMLGNRAIRLDFAR 492
           G+ L    + ++ AR
Sbjct: 55  GKELCGERVIVEHAR 69

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

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

 Score = 51.5 bits (123), Expect = 6e-07
 Identities = 49/175 (28%), Positives = 84/175 (48%), Gaps = 26/175 (14%)

Query: 416 SKT-LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKA 473
           SKT L V  LP ++ Q ++++ F+ + E+   +L  D   G+  GYG V +   EDA KA
Sbjct: 2   SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKA 61

Query: 474 IE-LNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGE 532
           +  LNG  L N+ I++ +AR             S+   KG        +++ G   ++ +
Sbjct: 62  VNSLNGLRLQNKTIKVSYAR------------PSSDSIKGA------NLYVSGLPKTMTQ 103

Query: 533 DQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKAL-EMSGT 586
            +    LE  F   G+I    +  D  TG  KG+ ++ F   D  ++A+  ++GT
Sbjct: 104 HE----LESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGT 154

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

 Score = 47.1 bits (112), Expect = 7e-07
 Identities = 18/48 (37%), Positives = 29/48 (60%)

Query: 539 LEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGT 586
           LE HF  CG + R+++  D  +G  KG AY++F+D +S   AL +  +
Sbjct: 16  LEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTALALDES 63

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

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

 Score = 46.6 bits (111), Expect = 8e-07
 Identities = 22/75 (29%), Positives = 40/75 (53%), Gaps = 2/75 (2%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAIE-L 476
           L V  LP  + Q ++++ F  +  +   ++  D   G+  GYG V++    DA KAI  L
Sbjct: 3   LIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTL 62

Query: 477 NGQMLGNRAIRLDFA 491
           NG  + N+ +++ +A
Sbjct: 63  NGFEIRNKRLKVSYA 77

This subfamily corresponds to the RRM1 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. This family also includes the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds to its own pre-mRNA and promotes female-specific alternative splicing. It contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 77

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 51.9 bits (125), Expect = 8e-07
 Identities = 40/192 (20%), Positives = 73/192 (38%), Gaps = 14/192 (7%)

Query: 8   ATPTKSAKKGGKREAEDAIEKLVSAKKQKGN---DGVAQAVKKAKVEAKTQKKNKNDETS 64
            T +  A+   + EA+  ++KL +  K KG    + + +A++  K   +   +     + 
Sbjct: 2   TTASTKAELAAEEEAKKKLKKLAAKSKSKGFITKEEIKEALESKKKTPEQIDQVLIFLSG 61

Query: 65  SSSSEEDSSDSEEEQKVKAVVTNKGGKAAKPPVKESSSEEEDSSSDEEPPKKQPVAAKNG 124
                +D+++S+  +K           AAK P K+   +E DSS   E            
Sbjct: 62  MVKDTDDATESDIPKKKTKTAAKA--AAAKAPAKKKLKDELDSSKKAEKKNALDKDDDLN 119

Query: 125 AVAATAKKSKPDSSSSDSSDDDSDEDEVPTSIKKLPVAAAKNGPSAPQKKKDDSSDSSDE 184
            V      ++ D    D  DDD D+D++             +     +   DD  D  DE
Sbjct: 120 YVKDIDVLNQADDDDDDDDDDDLDDDDI---------DDDDDDEDDDEDDDDDDVDDEDE 170

Query: 185 ESDESSDEDDKS 196
           E  E+ + +  S
Sbjct: 171 EKKEAKELEKLS 182

Length = 509

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 51.5 bits (124), Expect = 8e-07
 Identities = 30/204 (14%), Positives = 69/204 (33%), Gaps = 13/204 (6%)

Query: 215 TVAATKKSTGSSDDDSSSSEDSSESEEDNGAPAKVTSEAKKLPAVKNVPAPAAKKKTESS 274
           T A+TK    + ++     +  +   +  G   K   E K+    K        +     
Sbjct: 2   TTASTKAELAAEEEAKKKLKKLAAKSKSKGFITK--EEIKEALESKKKTPEQIDQVLIFL 59

Query: 275 DSSDEESEDSSDEDEEPTHVTKATPVKKLSAVVTKNKVESSSSSDESESEEEKPPAK--- 331
               ++++D+++ D        A       A   K   +   SS ++E +          
Sbjct: 60  SGMVKDTDDATESDIPKKKTKTAAKAAAAKAPAKKKLKDELDSSKKAEKKNALDKDDDLN 119

Query: 332 --------MDVDSSSEEESSDEEPQKKKDVKPNTKALKKESSSDEEDSDDEDEGEEEEAS 383
                      D   +++  D+      D   + +   ++   D+ D +DE++ E +E  
Sbjct: 120 YVKDIDVLNQADDDDDDDDDDDLDDDDIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKELE 179

Query: 384 KTPKKNVTDVKMVDAESGKKAAQT 407
           K    +       D+E+ ++A + 
Sbjct: 180 KLSDDDDFVWDEDDSEALRQARKD 203

Length = 509

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

 Score = 46.7 bits (111), Expect = 9e-07
 Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 1/74 (1%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LN 477
           + V NLPF   + DV+  FS   ++  VR+    D   +G+  VEF++ ++A  A+  L 
Sbjct: 3   ILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNALK 62

Query: 478 GQMLGNRAIRLDFA 491
              L  R + L +A
Sbjct: 63  DTHLLGRRLVLQYA 76

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

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

 Score = 46.3 bits (110), Expect = 9e-07
 Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 6/78 (7%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI-EL 476
           T++VGN+P    QAD+   F     +++ R   D     +G+  V+  + E A  AI +L
Sbjct: 2   TVYVGNIPPYTTQADLIPLFQNFGYILEFRHQPD-----RGFAFVKLDTHEQAAMAIVQL 56

Query: 477 NGQMLGNRAIRLDFARER 494
            G  +  R +R  + ++R
Sbjct: 57  QGFPVHGRPLRCGWGKDR 74

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

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

 Score = 46.6 bits (111), Expect = 1e-06
 Identities = 22/61 (36%), Positives = 32/61 (52%), Gaps = 1/61 (1%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRL-SSDADGRFKGYGHVEFASVEDAHKAI 474
           S  LFVGNLP  + + +++ FF E   V++VR+ S    GR   +G V F   E   K +
Sbjct: 3   SHQLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKIL 62

Query: 475 E 475
            
Sbjct: 63  A 63

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

 Score = 46.5 bits (111), Expect = 1e-06
 Identities = 28/76 (36%), Positives = 42/76 (55%), Gaps = 2/76 (2%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGR-FKGYGHVEFASVEDAHKAIE- 475
           T++V NLPFS+   D+   FS+  +VV V +  D + R  KG   + F   EDAHK ++ 
Sbjct: 3   TVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKA 62

Query: 476 LNGQMLGNRAIRLDFA 491
           LN + L  R ++   A
Sbjct: 63  LNNKELFGRTLKCSIA 78

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

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

 Score = 46.4 bits (111), Expect = 1e-06
 Identities = 17/55 (30%), Positives = 30/55 (54%)

Query: 528 SSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE 582
           +++ ED     L E F   G I+R+ + KD +TG  +G A++ F   +   +A+E
Sbjct: 5   TNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIE 59

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|218177 pfam04615, Utp14, Utp14 protein

 Score = 51.2 bits (123), Expect = 1e-06
 Identities = 37/184 (20%), Positives = 61/184 (33%), Gaps = 8/184 (4%)

Query: 19  KREAEDAIEKLVSAKKQKGNDGVAQAVKKAKVEAKTQKKNKNDETSSSSSEEDSSDSEEE 78
             E  D  E    +KK  G         + + E+K  KK   +E       ++  + E+E
Sbjct: 403 GEEESDEEENEEPSKKNVGRRKFGPENGEKEAESKKLKKENKNEFKEKKESDEEEELEDE 462

Query: 79  QKVKAVVTNKGGKAAKPPVKESSSEEEDSSSDEEPPKKQPVAAKNGAVAATAKKSKPDSS 138
           ++ K        K  K   K    EEE+   +E P  K    +  G  A      K  SS
Sbjct: 463 EEAKVEKVAN--KLLKRSEKAQKEEEEEELDEENPWLKTT--SSVGKSAKKQDSKKKSSS 518

Query: 139 SSDSSDDDSDEDEVPTSIKKLPVAAAKNGPSAPQKKKDDSSDSSDEESDESSDEDDKSTK 198
             D + +   +  V    KK      +          D+      +  DE  ++D++   
Sbjct: 519 KLDKAANKISKAAVKVKKKKK----KEKSIDLDDDLIDEEDSIKLDVDDEEDEDDEELPF 574

Query: 199 AIPQ 202
              Q
Sbjct: 575 LFKQ 578

This protein is found to be part of a large ribonucleoprotein complex containing the U3 snoRNA. Depletion of the Utp proteins impedes production of the 18S rRNA, indicating that they are part of the active pre-rRNA processing complex. This large RNP complex has been termed the small subunit (SSU) processome. Length = 728

>gnl|CDD|215641 PLN03237, PLN03237, DNA topoisomerase 2; Provisional

 Score = 51.4 bits (123), Expect = 2e-06
 Identities = 49/227 (21%), Positives = 80/227 (35%), Gaps = 42/227 (18%)

Query: 3    AAPVVATPTKSAKKGGKREAEDAIEKLVSAKKQKGNDGVAQAVKKAKVEAKTQKKNKNDE 62
            A      P  + +K  + E  D  ++L +          A+  +  K     +   +   
Sbjct: 1244 AGAKKKAPAAAKEKEEEDEILDLKDRLAAYNLDSAPAQSAKMEETVKAVPARRAAARKKP 1303

Query: 63   TSSSSSEEDSSDSEEEQKVKAV----VTNKGG--------KAAKPPVKE----------- 99
             +S S   DS D +++  V+      +  KGG        KAAKPP              
Sbjct: 1304 LASVSVISDSDDDDDDFAVEVSLAERLKKKGGRKPAAANKKAAKPPAAAKKRGPATVQSG 1363

Query: 100  --------SSSEEEDSSSDEEPPK--KQPVAAKNGAVAATAKKSKPDSSSSDSSDDDSDE 149
                      +E    S +++  K    P   K+G+V   A  +K   SS + S   S E
Sbjct: 1364 QKLLTEMLKPAEAIGISPEKKVRKMRASPFNKKSGSVLGRAATNKETESSENVSGSSSSE 1423

Query: 150  DEVPTSIKKLPVAAAKNGPSAPQKKKDDS--SDSSDEESDESSDEDD 194
             +           +AK  P    +K+     SDS  E +D+S  +DD
Sbjct: 1424 KDE-------IDVSAKPRPQRANRKQTTYVLSDSESESADDSDFDDD 1463

Length = 1465

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

 Score = 46.0 bits (110), Expect = 2e-06
 Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 2/77 (2%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAIE- 475
           T+ V NL    ++ D++  F     +  V L+ D + G+ +G+  V F + EDA +AIE 
Sbjct: 1   TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60

Query: 476 LNGQMLGNRAIRLDFAR 492
           LNG    N  + +++A+
Sbjct: 61  LNGFGYDNLILSVEWAK 77

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

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

 Score = 46.2 bits (109), Expect = 2e-06
 Identities = 29/75 (38%), Positives = 44/75 (58%), Gaps = 2/75 (2%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAI-EL 476
           +FVG+L   +   D+++ F+   ++ D R+  D A G+ KGYG V F +  DA  AI  +
Sbjct: 4   VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 477 NGQMLGNRAIRLDFA 491
            GQ LG R IR ++A
Sbjct: 64  GGQWLGGRQIRTNWA 78

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

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

 Score = 45.7 bits (109), Expect = 2e-06
 Identities = 26/72 (36%), Positives = 38/72 (52%), Gaps = 2/72 (2%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAIE-L 476
           ++VGNL   V +  +   F +   VV+V +  D      +GYG VEF S EDA  AI+ +
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 477 NGQMLGNRAIRL 488
           N   L  + IR+
Sbjct: 61  NMIKLYGKPIRV 72

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

>gnl|CDD|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 50.4 bits (120), Expect = 2e-06
 Identities = 54/251 (21%), Positives = 96/251 (38%), Gaps = 46/251 (18%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAIE-L 476
           L V  LP  +   ++   F  +  +   R+  D   G   GY  V+F S  D+ +AI+ L
Sbjct: 110 LIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNL 169

Query: 477 NGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVR 536
           NG  + N+ +++ +AR                   GG       +++     ++ +DQ  
Sbjct: 170 NGITVRNKRLKVSYAR------------------PGGESIKDTNLYVTNLPRTITDDQ-- 209

Query: 537 ASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEI---GGYSL 593
             L+  FG  G+I + ++ +D  TG+ +G+A++ F   +   +A+      I   G   L
Sbjct: 210 --LDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPL 267

Query: 594 VVDEAKQRGDFGSGGGRSGGRGGRSGGRDFGRSGGRDGGRFGGRGRGGRDGGRGGRGRGR 653
            V  A++               G++    +    G       G G  G  GG G      
Sbjct: 268 TVRLAEEH--------------GKAKAHHYMSQMGHGNMGNMGHGNMGMAGGSGM----- 308

Query: 654 GTPNRPSLAAA 664
             PN P+    
Sbjct: 309 NPPNPPAFMGM 319

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661). Length = 346

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

 Score = 45.8 bits (109), Expect = 2e-06
 Identities = 28/73 (38%), Positives = 45/73 (61%), Gaps = 2/73 (2%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKA- 473
           +  LFV NLP+S ++ D++  FS+  E+ +V ++ D   G+ KG+ +V F   EDA KA 
Sbjct: 2   TGRLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAY 61

Query: 474 IELNGQMLGNRAI 486
            EL+G++   R I
Sbjct: 62  KELDGKVFQGRLI 74

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|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins

 Score = 45.8 bits (109), Expect = 2e-06
 Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 9/79 (11%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFK-------GYGHVEFASVEDA 470
            +++ NL +S  + D++ F  +  E V V + S     F+       G  + EF+S E A
Sbjct: 1   RVYISNLSYSSSEEDLEEFLKDF-EPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQA 59

Query: 471 HKAI-ELNGQMLGNRAIRL 488
            K + +LNG++  NR + +
Sbjct: 60  EKVVKDLNGKVFKNRKLFV 78

This subfamily corresponds to the RRM1 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 84

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

 Score = 45.6 bits (109), Expect = 2e-06
 Identities = 27/68 (39%), Positives = 35/68 (51%), Gaps = 3/68 (4%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAIEL- 476
           L VG L  +V +  ++  FS    V DV L  D      +GY +VEF S EDA KAI+  
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 477 -NGQMLGN 483
             GQ+ G 
Sbjct: 61  DGGQIDGQ 68

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

>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 49.0 bits (117), Expect = 3e-06
 Identities = 24/48 (50%), Positives = 24/48 (50%), Gaps = 6/48 (12%)

Query: 605 GSGGGRSGGRGGRSGGRDFGRSGGRDGGRFGGRGRGGRDGGRGGRGRG 652
           G GGG   G GGR GGR  GR  GR      G G GGR GG GG    
Sbjct: 15  GGGGGGGRGGGGRGGGRGGGRGRGR------GGGGGGRGGGGGGGPGK 56

Length = 293

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

 Score = 44.9 bits (107), Expect = 3e-06
 Identities = 23/65 (35%), Positives = 35/65 (53%), Gaps = 5/65 (7%)

Query: 532 EDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGG 590
           ED +R   E      GEI  + + +D +TG  KG  ++ F DA+   KALE ++G E+ G
Sbjct: 12  EDDLRGIFE----PFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLNGFELAG 67

Query: 591 YSLVV 595
             + V
Sbjct: 68  RPIKV 72

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

>gnl|CDD|240946 cd12502, RRM2_RMB19, RNA recognition motif 2 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 45.0 bits (107), Expect = 3e-06
 Identities = 22/65 (33%), Positives = 37/65 (56%), Gaps = 1/65 (1%)

Query: 424 LPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGN 483
            PF+V++  ++ FFS + + V +R+  +  GR  G+  V+  S ED  KA++ N   +G 
Sbjct: 8   APFNVKEKHIREFFSPL-KPVAIRIVKNDHGRKTGFAFVDLKSEEDLKKALKRNKDYMGG 66

Query: 484 RAIRL 488
           R I L
Sbjct: 67  RYIEL 71

This subfamily corresponds to the RRM2 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is also essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 72

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

 Score = 44.4 bits (106), Expect = 3e-06
 Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 5/60 (8%)

Query: 433 VQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA 491
           +   FS    V  ++L         G+  VEF++ E A KA++ LNG + G R +R+D++
Sbjct: 1   LYKLFSPFGNVEKIKLLKKK----PGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56

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

>gnl|CDD|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA binding motif protein 15 (RBM15)

 Score = 45.7 bits (108), Expect = 3e-06
 Identities = 20/78 (25%), Positives = 46/78 (58%), Gaps = 1/78 (1%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKA-I 474
           ++TLF+GNL  +V + D++  F     + +V +     G+   YG ++F +++ AH+A +
Sbjct: 7   NRTLFLGNLDITVTETDLRRAFDRFGVITEVDIKRPGRGQTSTYGFLKFENLDMAHRAKL 66

Query: 475 ELNGQMLGNRAIRLDFAR 492
            ++G++L    I++ + +
Sbjct: 67  AMSGKVLRRNPIKIGYGK 84

This subgroup corresponds to the RRM2 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties. . Length = 87

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

 Score = 45.3 bits (108), Expect = 3e-06
 Identities = 21/80 (26%), Positives = 40/80 (50%), Gaps = 5/80 (6%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEV--VDVRL--SSDADGRFKGYGHVEFASVEDAHKA 473
            L++GNL   + +  +   FS+  ++   D     S    G+ +GY  V F + E+A KA
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 474 IE-LNGQMLGNRAIRLDFAR 492
           ++ LNG+    + + + +A 
Sbjct: 61  LKSLNGKTALGKKLVVRWAH 80

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

>gnl|CDD|240949 cd12505, RRM2_GRSF1, RNA recognition motif 2 in G-rich sequence factor 1 (GRSF-1) and similar proteins

 Score = 45.1 bits (107), Expect = 3e-06
 Identities = 23/65 (35%), Positives = 40/65 (61%), Gaps = 3/65 (4%)

Query: 424 LPFSVEQADVQNFFSEVAEVVD--VRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQML 481
           LP+S  + D+ +FF  + ++VD  V +  +  GR  G  +V+FA+ E A+KA+  + + +
Sbjct: 9   LPYSCTEDDIIDFFRGL-DIVDDGVVIVLNRRGRKTGEAYVQFATPEMANKALLKHREEI 67

Query: 482 GNRAI 486
           GNR I
Sbjct: 68  GNRYI 72

This subfamily corresponds to the RRM2 of GRSF-1, a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. GRSF-1 contains three potential RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for the RNA binding. In addition, GRSF-1 has two auxiliary domains, an acidic alpha-helical domain and an N-terminal alanine-rich region, that may play a role in protein-protein interactions and provide binding specificity. . Length = 75

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

 Score = 44.9 bits (107), Expect = 3e-06
 Identities = 24/65 (36%), Positives = 41/65 (63%), Gaps = 1/65 (1%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI-ELN 477
           L+V NL  S++   ++  FS    +   ++ +D  GR KG+G V F+S E+A KA+ E+N
Sbjct: 4   LYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVTEMN 63

Query: 478 GQMLG 482
           G+++G
Sbjct: 64  GRIIG 68

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

 Score = 44.9 bits (107), Expect = 3e-06
 Identities = 19/66 (28%), Positives = 33/66 (50%), Gaps = 2/66 (3%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAI-EL 476
           LF+ +LP      D+   F+    V+  ++  D + G+ K +G V + + E A  AI  +
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 477 NGQMLG 482
           NG  +G
Sbjct: 61  NGFQVG 66

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

 Score = 44.9 bits (106), Expect = 3e-06
 Identities = 29/76 (38%), Positives = 42/76 (55%), Gaps = 5/76 (6%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE 475
           SK L V NL +S  +  +Q  F +      +R+  + +GR KGY  VEF S EDA +A+ 
Sbjct: 1   SKVLVVNNLSYSASEDSLQEVFEKA---TSIRIPQN-NGRPKGYAFVEFESAEDAKEALN 56

Query: 476 -LNGQMLGNRAIRLDF 490
             N   +  R+IRL+F
Sbjct: 57  SCNNTEIEGRSIRLEF 72

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

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

 Score = 44.7 bits (106), Expect = 4e-06
 Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 5/77 (6%)

Query: 520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNK 579
           T++I      + ED VR      F    EIT + +  D +TG  KG  ++DF D +S + 
Sbjct: 1   TVYIGNLAWDITEDDVRE-----FFKGCEITSVRLATDKETGEFKGFGHVDFADEESLDA 55

Query: 580 ALEMSGTEIGGYSLVVD 596
           AL++ GT + G  + + 
Sbjct: 56  ALKLDGTVLCGRPIRIA 72

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

>gnl|CDD|240957 cd12513, RRM3_RBM12B, RNA recognition motif 3 in RNA-binding protein 12B (RBM12B) and similar proteins

 Score = 45.0 bits (107), Expect = 4e-06
 Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 1/68 (1%)

Query: 423 NLPFSVEQADVQNFFSEVAEVVD-VRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQML 481
           NLPFSVE+ D++ FF ++      +   SD  G+      V F S+ D   A+  + ++L
Sbjct: 7   NLPFSVEKRDIRAFFGDLDLPDSQITFLSDKKGKRTRSAFVMFKSLRDYCAALAHHKRVL 66

Query: 482 GNRAIRLD 489
            NR + + 
Sbjct: 67  YNREVYVF 74

This subgroup corresponds to the RRM3 of RBM12B which contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Its biological role remains unclear. . Length = 81

>gnl|CDD|240981 cd12537, RRM1_RBM23, RNA recognition motif 1 in vertebrate probable RNA-binding protein 23 (RBM23)

 Score = 45.0 bits (106), Expect = 4e-06
 Identities = 26/67 (38%), Positives = 39/67 (58%), Gaps = 1/67 (1%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADG-RFKGYGHVEFASVEDAHKAI 474
           ++T+F   L   +   D+++FFS V +V DVR+ SD +  R KG  +VEF  ++    AI
Sbjct: 1   ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI 60

Query: 475 ELNGQML 481
            L GQ L
Sbjct: 61  GLTGQRL 67

This subgroup corresponds to the RRM1 of RBM23, also termed RNA-binding region-containing protein 4, or splicing factor SF2, which may function as a pre-mRNA splicing factor. It shows high sequence homology to RNA-binding protein 39 (RBM39 or 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). In contrast to RBM39, RBM23 contains only two RRMs. . Length = 85

>gnl|CDD|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic activator RIM4 and similar proteins

 Score = 45.1 bits (107), Expect = 4e-06
 Identities = 26/82 (31%), Positives = 40/82 (48%), Gaps = 7/82 (8%)

Query: 416 SKTLFVGNLPFSVE----QADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAH 471
           S  +FV +LP S      +A V   FS+   +V V++  D   R   Y  V+F + +DA 
Sbjct: 2   SACVFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRDWRQR--PYAFVQFTNDDDAK 59

Query: 472 KAIEL-NGQMLGNRAIRLDFAR 492
            A+    G +L  R IR + A+
Sbjct: 60  NALAKGQGTILDGRHIRCERAK 81

This subfamily corresponds to the RRM1 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 86

>gnl|CDD|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding protein 25 and similar proteins

 Score = 44.9 bits (107), Expect = 4e-06
 Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 1/61 (1%)

Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVD-VRLSSDADGRFKGYGHVEFASVEDAHKAIE 475
            T+FVGN+P  V    ++    +  +V+   R+   + G+ K +G  EF   E A +A+ 
Sbjct: 1   TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALR 60

Query: 476 L 476
           L
Sbjct: 61  L 61

This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor. . Length = 84

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

 Score = 44.5 bits (106), Expect = 4e-06
 Identities = 27/77 (35%), Positives = 38/77 (49%), Gaps = 8/77 (10%)

Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE- 475
           K L+V NLP S  +  ++  FSE  EV  V+   D       Y  V F   +DA KA+E 
Sbjct: 2   KVLYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD-------YAFVHFEERDDAVKAMEE 54

Query: 476 LNGQMLGNRAIRLDFAR 492
           +NG+ L    I +  A+
Sbjct: 55  MNGKELEGSPIEVSLAK 71

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

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

 Score = 44.7 bits (106), Expect = 4e-06
 Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 6/80 (7%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVA-EVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKA 473
           + T+ +  LP SV + D++N       E  DVRL      G  +G+  VEF S+E+A + 
Sbjct: 2   NNTIMLRGLPLSVTEEDIRNALVSHGVEPKDVRLMRRKTTGASRGFAFVEFMSLEEATRW 61

Query: 474 IELNG---QMLGNRAIRLDF 490
           +ELN    Q+   + I L +
Sbjct: 62  MELNQGKLQLQDYK-ITLHY 80

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

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

 Score = 44.7 bits (106), Expect = 4e-06
 Identities = 13/45 (28%), Positives = 24/45 (53%)

Query: 539 LEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEM 583
           L+  F   G +  +S+P+   TG +KG A+++F   +   KA + 
Sbjct: 16  LKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKH 60

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

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

 Score = 44.5 bits (106), Expect = 4e-06
 Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 2/71 (2%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAIE-L 476
           L+VG L   V++  +   F    ++ D+++  D    + +G+  VEF   EDA  AI+ +
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 477 NGQMLGNRAIR 487
           N   L  R IR
Sbjct: 61  NESELFGRTIR 71

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

>gnl|CDD|215641 PLN03237, PLN03237, DNA topoisomerase 2; Provisional

 Score = 49.5 bits (118), Expect = 5e-06
 Identities = 47/182 (25%), Positives = 64/182 (35%), Gaps = 36/182 (19%)

Query: 3    AAPVVATPTKSAKKGGKREA------------EDAIEKLVSA---KKQKGNDGVAQAVKK 47
               V A P + A    K  A            +D   ++  A   KK+ G    A   K 
Sbjct: 1286 EETVKAVPARRAAARKKPLASVSVISDSDDDDDDFAVEVSLAERLKKKGGRKPAAANKKA 1345

Query: 48   AKVEAKTQKKNKNDETSSSS------SEEDSSDSEEEQKVKAVVT---NKG-----GKAA 93
            AK  A  +K+      S            ++     E+KV+ +     NK      G+AA
Sbjct: 1346 AKPPAAAKKRGPATVQSGQKLLTEMLKPAEAIGISPEKKVRKMRASPFNKKSGSVLGRAA 1405

Query: 94   KPPVKESSSEEEDSSSDEE-----PPKKQPVAAKNGAVAATAKKSKPDSSSSDSSDDDSD 148
                 ESS     SSS E+       K +P  A       T   S  +S S+D SD D D
Sbjct: 1406 TNKETESSENVSGSSSSEKDEIDVSAKPRPQRANRKQ--TTYVLSDSESESADDSDFDDD 1463

Query: 149  ED 150
            ED
Sbjct: 1464 ED 1465

Length = 1465

>gnl|CDD|218177 pfam04615, Utp14, Utp14 protein

 Score = 49.3 bits (118), Expect = 5e-06
 Identities = 39/278 (14%), Positives = 101/278 (36%), Gaps = 31/278 (11%)

Query: 43  QAVKKAKVEAKTQKKNKNDETSSSSSEEDSSDSEEEQKVKAVVTNKGGKAAKPPVKESSS 102
           Q  +  ++  K + K+ ++E     S+ +  D ++++       +         +++   
Sbjct: 307 QLRQGEELRRKIEGKSVSEEDEDEDSDSEEEDEDDDE-------DDDDGENPWMLRKKLG 359

Query: 103 EEEDSSSDEEPPK-------KQPVAAKNGAVAATAKKSKPDSSSSDSSDDDSDEDEVPTS 155
           + ++   DEE          ++  A K     A  ++ + +    + SD++ +E+    +
Sbjct: 360 KLKEGEDDEENSGLLSMKFMQRAEARKKEENDAEIEELRRELEGEEESDEEENEEPSKKN 419

Query: 156 IKKLPVAAAKNGPSAPQKKKDDSSDSSDEESDESSDEDDKSTKAIPQPKKLPASTAKKGT 215
           + +           A  KK    + +  +E  ES +E++   +   + +K+     K+  
Sbjct: 420 VGRRKFGPENGEKEAESKKLKKENKNEFKEKKESDEEEELEDEEEAKVEKVANKLLKRSE 479

Query: 216 VAATKKSTGSSDDD-------SSSSEDSSESEEDNGAPAKVTSEAKKLPAVKNVPAPAAK 268
            A  ++     D++       SS  + + + +    + +K+   A K+           K
Sbjct: 480 KAQKEEEEEELDEENPWLKTTSSVGKSAKKQDSKKKSSSKLDKAANKISKAAVKVKKKKK 539

Query: 269 KKTESSDSSDEESED----------SSDEDEEPTHVTK 296
           K+       D   E+            ++DEE   + K
Sbjct: 540 KEKSIDLDDDLIDEEDSIKLDVDDEEDEDDEELPFLFK 577

This protein is found to be part of a large ribonucleoprotein complex containing the U3 snoRNA. Depletion of the Utp proteins impedes production of the 18S rRNA, indicating that they are part of the active pre-rRNA processing complex. This large RNP complex has been termed the small subunit (SSU) processome. Length = 728

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

 Score = 44.5 bits (106), Expect = 5e-06
 Identities = 26/81 (32%), Positives = 39/81 (48%), Gaps = 6/81 (7%)

Query: 521 IFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDF-TDADSFNK 579
           +F+ G   SV E      LEE F   G ++ + + K  D G  +G AY+D  T      K
Sbjct: 2   LFVGGLSPSVTESD----LEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKK 57

Query: 580 ALE-MSGTEIGGYSLVVDEAK 599
               ++GT+  G  L ++EAK
Sbjct: 58  CKSTLNGTKWKGSVLKIEEAK 78

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

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

 Score = 44.9 bits (107), Expect = 5e-06
 Identities = 23/80 (28%), Positives = 39/80 (48%), Gaps = 2/80 (2%)

Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE 475
           KTLFV  L +   ++ ++  F E   +  +RL  D   G+ +GY  +EF    D   A +
Sbjct: 2   KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYK 61

Query: 476 L-NGQMLGNRAIRLDFARER 494
             +G+ +  R + +D  R R
Sbjct: 62  YADGKKIDGRRVLVDVERGR 81

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

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

 Score = 44.7 bits (106), Expect = 5e-06
 Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 2/78 (2%)

Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAI- 474
            +L+V N+  +    D++  F +   +VDV +  D    R +G+ +V+F  V DA  A+ 
Sbjct: 1   TSLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALY 60

Query: 475 ELNGQMLGNRAIRLDFAR 492
            L+      R I + FA+
Sbjct: 61  YLDRTRFLGREIEIQFAQ 78

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

>gnl|CDD|235334 PRK05035, PRK05035, electron transport complex protein RnfC; Provisional

 Score = 49.6 bits (119), Expect = 5e-06
 Identities = 57/266 (21%), Positives = 97/266 (36%), Gaps = 58/266 (21%)

Query: 19  KREAEDAIEKLVSAKKQKGNDGVAQAVKKAKVEAKTQKKNKNDETSSSSSEEDSSDSEEE 78
           K   E   +K   A+  K  D VA A+  A+V+AK +          + +  D+S     
Sbjct: 466 KAAREARHKKAAEARAAKDKDAVAAAL--ARVKAK-KAAATQPIVIKAGARPDNSAVIAA 522

Query: 79  QKVKAVVTNKGGKAAKPPVKESSSEEEDSSSDEEPPKKQPVAAKNGAVA-ATAKKSKPDS 137
           +           +A K   +   +E++ +++ +  PKK  VAA   A+A A AKK+    
Sbjct: 523 R-----------EARKAQARARQAEKQAAAAAD--PKKAAVAA---AIARAKAKKAA--- 563

Query: 138 SSSDSSDDDSDEDEVPTSIKKLPVAAAKNGPSAPQKKKDDSSDSSDEESDESSDEDDKST 197
                    + E E     KK  VAAA    +  + KK     +S E  ++ ++ D K  
Sbjct: 564 -----QQAANAEAEEEVDPKKAAVAAAI---ARAKAKKAAQQAASAEPEEQVAEVDPKKA 615

Query: 198 KAIPQPKKLPASTAKKGTVAATKKSTGSSDDDSSSSEDSSESEEDNGAPAKVTSEAKKLP 257
                  +  A  A++                   +    E   D    A   + A+   
Sbjct: 616 AVAAAIARAKAKKAEQ------------------QANAEPEEPVDPRKAAVAAAIAR--- 654

Query: 258 AVKNVPAPAAKKKTESSDSSDEESED 283
                 A A K   + +++  EE+ED
Sbjct: 655 ------AKARKAAQQQANAEPEEAED 674

Length = 695

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

 Score = 43.9 bits (104), Expect = 6e-06
 Identities = 19/60 (31%), Positives = 32/60 (53%)

Query: 536 RASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVV 595
              +  +F  CGEI  + +    DTG  +GIA++ F   ++  +AL + G ++GG  L V
Sbjct: 12  EDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRALALDGEDMGGRFLKV 71

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

>gnl|CDD|236304 PRK08581, PRK08581, N-acetylmuramoyl-L-alanine amidase; Validated

 Score = 49.0 bits (117), Expect = 6e-06
 Identities = 40/296 (13%), Positives = 95/296 (32%), Gaps = 24/296 (8%)

Query: 30  VSAKKQKGNDGVAQAVKKAKVEAKTQKKNKNDETSSSSSEEDSSDSEEEQKVKAVVTNKG 89
            S   +   D  ++   KA     + + N + + S+  S    S++  +   K +     
Sbjct: 45  KSNDDETSKDTSSKDTDKADNNNTSNQDNNDKKFSTIDSSTSDSNNIIDFIYKNLPQTNI 104

Query: 90  GKAAKPPVKESSSEEEDSSSDEEPPKKQPVAAKNGAVAATAKKSKPDSSSSDSSDDDSDE 149
            +       + +     ++  +         +       + K +   + +SDSS  +  +
Sbjct: 105 NQLLTKNKYDDNYSL--TTLIQNLFNLNSDISDYEQPRNSEKSTNDSNKNSDSSIKNDTD 162

Query: 150 DEVPTSIKKLPVAAAKNGPSAPQKKKDDSSDSSDEESDESSDEDDKSTKAIPQPKKLPAS 209
            +            +     A  +K   S+++    S++  +    +       +  PAS
Sbjct: 163 TQ------------SSKQDKADNQKAPSSNNTKPSTSNKQPNSPKPTQPNQSNSQ--PAS 208

Query: 210 TAKKGTVAATKKSTGSSDDDSSS-----SEDSSESEEDNGAPAKVTSEAKKLPAVKNVPA 264
                  +++K +   SD    S     SED+ ++++D  + +K             +P 
Sbjct: 209 DDTANQKSSSKDNQSMSDSALDSILDQYSEDAKKTQKDYASQSKKDKTETSNTKNPQLPT 268

Query: 265 PAAKKKTESSDSSDEESEDSSDEDEEPTHVTKATPV-KKLSAVVTKNKVESSSSSD 319
               K       S E   + S+     T + +  P         + N V+S  +  
Sbjct: 269 QDELKHKSKPAQSFENDVNQSNTRS--TSLFETGPSLSNNDDSGSFNVVDSKDTRQ 322

Length = 619

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

 Score = 44.5 bits (105), Expect = 6e-06
 Identities = 20/57 (35%), Positives = 30/57 (52%)

Query: 539 LEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVV 595
           LE HF  CG I R+++  D  +G  KG AY++F   DS   A+ +  +   G  + V
Sbjct: 16  LEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAAVALDESSFRGRVIKV 72

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

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

 Score = 44.1 bits (105), Expect = 7e-06
 Identities = 25/83 (30%), Positives = 40/83 (48%), Gaps = 5/83 (6%)

Query: 520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNK 579
           T+F++       ++Q    LEE F   G I R  V KD  +   +G  Y+ F   +   +
Sbjct: 1   TLFVRNLPYDTTDEQ----LEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKR 56

Query: 580 ALEMS-GTEIGGYSLVVDEAKQR 601
           ALE    T+ GG  + V+ AK++
Sbjct: 57  ALEEKKKTKFGGRKIHVEFAKKK 79

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

>gnl|CDD|240849 cd12403, RRM1_NCL, RNA recognition motif 1 in vertebrate nucleolin

 Score = 44.0 bits (104), Expect = 8e-06
 Identities = 29/79 (36%), Positives = 43/79 (54%), Gaps = 10/79 (12%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEV-----AEVVDVRLSSDADGRFKGYGHVEFASVEDAHK 472
           +LFVGNL  + +  +++   SE        V DVR+     G  K +G+V+F S ED  K
Sbjct: 2   SLFVGNLNPNKDFDELKTAISEFFSKKNLAVQDVRI-----GSSKKFGYVDFESAEDLEK 56

Query: 473 AIELNGQMLGNRAIRLDFA 491
           A+EL G+ L    I+L+ A
Sbjct: 57  ALELTGKKLLGNEIKLEKA 75

This subfamily corresponds to the RRM1 of ubiquitously expressed protein nucleolin, also termed protein C23. Nucleolin is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. RRM1, together with RRM2, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 75

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

 Score = 43.9 bits (104), Expect = 8e-06
 Identities = 18/59 (30%), Positives = 31/59 (52%), Gaps = 2/59 (3%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA--DGRFKGYGHVEFASVEDAHKAIE 475
           + V N+PF     +++  FS   E+  VRL       G  +G+G V+F + +DA +A +
Sbjct: 3   ILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFK 61

This subgroup corresponds to the RRM6 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 43.9 bits (104), Expect = 8e-06
 Identities = 22/81 (27%), Positives = 43/81 (53%), Gaps = 6/81 (7%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI- 474
           S TL++G+L   V + D++N F E  E+  + +        +G  +V   + +DAH+A+ 
Sbjct: 2   STTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIPP-----RGCAYVCMETRQDAHRALQ 56

Query: 475 ELNGQMLGNRAIRLDFARERG 495
           +L    L  + I++ +A  +G
Sbjct: 57  KLRNVKLAGKKIKVAWAPNKG 77

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

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

 Score = 44.0 bits (104), Expect = 8e-06
 Identities = 22/54 (40%), Positives = 33/54 (61%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHK 472
           +FVG + F   + D++ FFS+   V +V++ +D  G  KGYG V F + EDA K
Sbjct: 5   IFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAGVSKGYGFVTFETQEDAQK 58

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

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

 Score = 43.8 bits (104), Expect = 9e-06
 Identities = 20/76 (26%), Positives = 40/76 (52%), Gaps = 5/76 (6%)

Query: 521 IFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKA 580
           +++ G    V E  + A     F   G+I  I +P DY+T   +G A+++F + +    A
Sbjct: 1   LYVGGLAEEVDEKVLHA----AFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAA 56

Query: 581 LE-MSGTEIGGYSLVV 595
           ++ M+ +E+ G ++ V
Sbjct: 57  IDNMNESELFGRTIRV 72

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

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

 Score = 43.8 bits (104), Expect = 1e-05
 Identities = 26/72 (36%), Positives = 39/72 (54%), Gaps = 2/72 (2%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAI-EL 476
           +FVG+L   V    +   FS+       ++  D   G+ KGYG V F+   D  KA+ E+
Sbjct: 9   IFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKEM 68

Query: 477 NGQMLGNRAIRL 488
           NG+ +GNR I+L
Sbjct: 69  NGKYVGNRPIKL 80

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

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

 Score = 43.3 bits (103), Expect = 1e-05
 Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 4/72 (5%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNG 478
           +FVG +P  + + ++   F +   + ++RL  D  G  +GY  V + + E A +A+    
Sbjct: 4   VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGLNRGYAFVTYTNKEAAQRAV---- 59

Query: 479 QMLGNRAIRLDF 490
           + L N  IR   
Sbjct: 60  KQLHNYEIRPGK 71

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

>gnl|CDD|240785 cd12339, RRM2_SRSF1_4_like, RNA recognition motif 2 in serine/arginine-rich splicing factor SRSF1, SRSF4 and similar proteins

 Score = 43.4 bits (103), Expect = 1e-05
 Identities = 21/69 (30%), Positives = 33/69 (47%), Gaps = 5/69 (7%)

Query: 421 VGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQ 479
           V  LP      D+++F  +  +V      +D D   +G G VEF S ED  +A+  L+G 
Sbjct: 5   VSGLPEGASWQDLKDFGRQAGDVT----YADVDRDQEGEGVVEFTSQEDMERALRKLDGT 60

Query: 480 MLGNRAIRL 488
               R +R+
Sbjct: 61  EFRGRRVRV 69

This subfamily corresponds to the RRM2 of several serine/arginine (SR) proteins that have been classified into two subgroups. The first subgroup consists of serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). The second subgroup is composed of serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C) and plant pre-mRNA-splicing factor SF2 (SR1). These SR proteins are mainly involved in regulating constitutive and alternative pre-mRNA splicing. They also have been implicated in transcription, genomic stability, mRNA export and translation. All SR proteins in this family, except SRSF5, undergo nucleocytoplasmic shuttling, suggesting their widespread roles in gene expression. These SR proteins share a common domain architecture comprising two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. Both domains can directly contact with RNA. The RRMs appear to determine the binding specificity and the SR domain also mediates protein-protein interactions. In addition, this subfamily includes the yeast nucleolar protein 3 (Npl3p), also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. It is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein with two RRMs, separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. . Length = 71

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

 Score = 43.3 bits (103), Expect = 1e-05
 Identities = 19/69 (27%), Positives = 39/69 (56%), Gaps = 1/69 (1%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LN 477
           ++V NL   ++   ++  F +  ++   ++  D +G+ KG+G V F + E A KA+E LN
Sbjct: 4   VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEELN 63

Query: 478 GQMLGNRAI 486
           G+ +  + +
Sbjct: 64  GKEVNGKKL 72

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|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional

 Score = 47.9 bits (114), Expect = 1e-05
 Identities = 26/88 (29%), Positives = 31/88 (35%), Gaps = 10/88 (11%)

Query: 571 FTDADSFNKALEMSGTEIGGYSLVVDEAKQRGDFGSGGGRSGGRGGRSGGRDFGRSGGRD 630
           FT     NK + M         L+ D     G    GGGR  G   R GGR+F   G R 
Sbjct: 545 FTRTRILNKPMNMQ--------LLGDAQPHTGGERRGGGRGFGGERREGGRNFS--GERR 594

Query: 631 GGRFGGRGRGGRDGGRGGRGRGRGTPNR 658
            G  G   R   +   G   R   +  R
Sbjct: 595 EGGRGDGRRFSGERREGRAPRRDDSTGR 622

Length = 629

>gnl|CDD|241191 cd12747, RRM2_RBM12, RNA recognition motif 2 in RNA-binding protein 12 (RBM12) and similar proteins

 Score = 43.2 bits (102), Expect = 1e-05
 Identities = 22/63 (34%), Positives = 35/63 (55%), Gaps = 1/63 (1%)

Query: 424 LPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGN 483
           LPFSV + D+++FF  +  +  + L  D  GR  G   V+F S  D  +A++ N  ++G 
Sbjct: 9   LPFSVLEHDIRDFFHGL-RIDAIHLLKDHVGRNNGNALVKFYSPHDTFEALKRNRMLMGQ 67

Query: 484 RAI 486
           R I
Sbjct: 68  RYI 70

This subgroup corresponds to the RRM2 of RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), which is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two proline-rich regions, and several putative transmembrane domains. The biological role of RBM12 remains unclear. . Length = 75

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

 Score = 43.2 bits (102), Expect = 1e-05
 Identities = 19/66 (28%), Positives = 38/66 (57%), Gaps = 2/66 (3%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLS-SDADGRFKGYGHVEFASVEDAHKAIE- 475
            +++G+LP    + +++ +FS+   V +VR++ S   G  K YG ++F + E A  A + 
Sbjct: 1   VIYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKS 60

Query: 476 LNGQML 481
           +N  +L
Sbjct: 61  MNNYLL 66

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

 Score = 43.1 bits (102), Expect = 1e-05
 Identities = 22/59 (37%), Positives = 36/59 (61%), Gaps = 4/59 (6%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFAS---VEDAHK 472
            LFVGNLP++V   +++ +FS+  +V    +  D + G  KGYG V F+S   +E+A +
Sbjct: 1   KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQ 59

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

 Score = 43.5 bits (102), Expect = 1e-05
 Identities = 27/76 (35%), Positives = 44/76 (57%), Gaps = 2/76 (2%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAIE-L 476
           L V  LP ++ Q ++++ FS + EV   +L  D   G   GYG V + + +DA +AI  L
Sbjct: 4   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTL 63

Query: 477 NGQMLGNRAIRLDFAR 492
           NG  L ++ I++ +AR
Sbjct: 64  NGLRLQSKTIKVSYAR 79

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

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

 Score = 43.1 bits (102), Expect = 1e-05
 Identities = 22/71 (30%), Positives = 40/71 (56%), Gaps = 9/71 (12%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVD--VRLSSDADGRFKGYGHVEFASVEDAHKAI-- 474
           L+V  L  + + AD++  FS+  +VV   +  ++ + G  + +G V  ASVE+A K I  
Sbjct: 2   LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGA-RCFGFVTMASVEEAAKCIQH 60

Query: 475 ----ELNGQML 481
               EL+G+++
Sbjct: 61  LHRTELHGRVI 71

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|240706 cd12260, RRM2_SREK1, RNA recognition motif 2 in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins

 Score = 43.4 bits (103), Expect = 2e-05
 Identities = 21/81 (25%), Positives = 36/81 (44%), Gaps = 6/81 (7%)

Query: 520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNK 579
           TI++   D +   DQ    L E F   GE+  + +  D         A+++F +  S   
Sbjct: 6   TIYVGNLDPTTTADQ----LLEFFSQAGEVKYVRMAGD--ETQPTRYAFVEFAEQTSVIN 59

Query: 580 ALEMSGTEIGGYSLVVDEAKQ 600
           AL+++G   GG  L V+ +  
Sbjct: 60  ALKLNGAMFGGRPLKVNHSNN 80

This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site. . Length = 85

>gnl|CDD|236304 PRK08581, PRK08581, N-acetylmuramoyl-L-alanine amidase; Validated

 Score = 47.9 bits (114), Expect = 2e-05
 Identities = 44/258 (17%), Positives = 90/258 (34%), Gaps = 16/258 (6%)

Query: 126 VAATAKKSKPDSSSSDSSDDDSDEDEVPTSIKKLPVAAAKNGPSAPQKKKDDSSDSSDEE 185
                K S   ++S DS   + DE    TS K      A N  ++ Q   D    + D  
Sbjct: 27  ADDPQKDSTAKTTSHDSKKSNDDETSKDTSSKD--TDKADNNNTSNQDNNDKKFSTIDSS 84

Query: 186 SDESSDEDDKSTKAIPQPK----KLPASTAKKGTVAATKKSTGSSDDDSSSSEDS-SESE 240
           + +S++  D   K +PQ                ++    ++  + + D S  E   +  +
Sbjct: 85  TSDSNNIIDFIYKNLPQTNINQLLTKNKYDDNYSLTTLIQNLFNLNSDISDYEQPRNSEK 144

Query: 241 EDNGAPAKVTSEAKKLPAVKNVPAPAAKKKTESSDSSDEESEDSSDEDEEPTHVTKATPV 300
             N +     S  K     ++     A  +   S ++ + S  +   +          P 
Sbjct: 145 STNDSNKNSDSSIKNDTDTQSSKQDKADNQKAPSSNNTKPSTSNKQPNSPKP----TQPN 200

Query: 301 KKLSAVVTKNKVESSSSSDESESEEEKPPAKMDVDSSSEEESSDEEPQKKKDVKPNTKAL 360
           +  S   + +     SSS +++S  +       +DS  ++ S D +  +K     + K  
Sbjct: 201 QSNSQPASDDTANQKSSSKDNQSMSDSA-----LDSILDQYSEDAKKTQKDYASQSKKDK 255

Query: 361 KKESSSDEEDSDDEDEGE 378
            + S++       +DE +
Sbjct: 256 TETSNTKNPQLPTQDELK 273

Length = 619

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

 Score = 42.9 bits (102), Expect = 2e-05
 Identities = 25/82 (30%), Positives = 47/82 (57%), Gaps = 6/82 (7%)

Query: 521 IFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKA 580
           +++K     + +++    L+E FG  G+IT   V KD D G  KG  +++F + ++  KA
Sbjct: 4   VYVKNLGEDMDDEK----LKELFGKYGKITSAKVMKD-DEGKSKGFGFVNFENHEAAQKA 58

Query: 581 LE-MSGTEIGGYSLVVDEAKQR 601
           +E ++G E+ G  L V  A+++
Sbjct: 59  VEELNGKEVNGKKLYVGRAQKK 80

This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 80

>gnl|CDD|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant pre-mRNA-splicing factor SF2 and similar proteins

 Score = 42.8 bits (101), Expect = 2e-05
 Identities = 20/58 (34%), Positives = 31/58 (53%), Gaps = 2/58 (3%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE 475
           T++VGNLP  + + +V++ F +   +VD+ L      R  GY  +EF    DA  AI 
Sbjct: 1   TVYVGNLPGDIREREVEDLFYKYGPIVDIDLK--LPPRPPGYAFIEFEDARDAEDAIR 56

This subgroup corresponds to the RRM1 of SF2, also termed SR1 protein, a plant serine/arginine (SR)-rich phosphoprotein similar to the mammalian splicing factor SF2/ASF. It promotes splice site switching in mammalian nuclear extracts. SF2 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal domain rich in proline, serine and lysine residues (PSK domain), a composition reminiscent of histones. This PSK domain harbors a putative phosphorylation site for the mitotic kinase cyclin/p34cdc2. . Length = 72

>gnl|CDD|240947 cd12503, RRM1_hnRNPH_GRSF1_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, G-rich sequence factor 1 (GRSF-1) and similar proteins

 Score = 43.1 bits (102), Expect = 2e-05
 Identities = 22/66 (33%), Positives = 33/66 (50%), Gaps = 3/66 (4%)

Query: 424 LPFSVEQADVQNFFSE---VAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQM 480
           LP+S    DV NFFS+         +  +   +GR  G   +E  S ED  KA+E + + 
Sbjct: 7   LPWSATAEDVLNFFSDCRIKGGENGIHFTYSREGRPSGEAFIELESEEDVEKALEKHNEH 66

Query: 481 LGNRAI 486
           +G+R I
Sbjct: 67  MGHRYI 72

This subfamily corresponds to the RRM1 of hnRNP H proteins and GRSF-1. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. These proteins have similar RNA binding affinities and specifically recognize the sequence GGGA. They can either stimulate or repress splicing upon binding to a GGG motif. hnRNP H binds to the RNA substrate in the presence or absence of these proteins, whereas hnRNP F binds to the nuclear mRNA only in the presence of cap-binding proteins. hnRNP H and hnRNP H2 are almost identical; both have been found to bind nuclear-matrix proteins. hnRNP H activates exon inclusion by binding G-rich intronic elements downstream of the 5' splice site in the transcripts of c-src, human immunodeficiency virus type 1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons when bound to exonic elements in the transcripts of beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2 has been implicated in pre-mRNA 3' end formation. hnRNP H3 may be involved in splicing arrest induced by heat shock. Most family members contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), except for hnRNP H3, in which the RRM1 is absent. RRM1 and RRM2 are responsible for the binding to the RNA at DGGGD motifs, and play an important role in efficiently silencing the exon. Members in this family can regulate the alternative splicing of fibroblast growth factor receptor 2 (FGFR2) transcripts, and function as silencers of FGFR2 exon IIIc through an interaction with the exonic GGG motifs. The lack of RRM1 could account for the reduced silencing activity within hnRNP H3. Members in this family have an extensive glycine-rich region near the C-terminus, which may allow them to homo- or heterodimerize. They also include a cytoplasmic poly(A)+ mRNA binding protein, GRSF-1, which interacts with RNA in a G-rich element-dependent manner. They may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. GRSF-1 contains three potential RRMs responsible for the RNA binding, and two auxiliary domains (an acidic alpha-helical domain and an N-terminal alanine-rich region) that may play a role in protein-protein interactions and provide binding specificity. . Length = 77

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

 Score = 42.8 bits (101), Expect = 2e-05
 Identities = 22/67 (32%), Positives = 36/67 (53%), Gaps = 2/67 (2%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAIELN 477
           L V  LP+   + D++++FS   E++ V++  D   G+ KG+G V FA  ED  K +   
Sbjct: 2   LIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLS-Q 60

Query: 478 GQMLGNR 484
             M+  R
Sbjct: 61  RHMIDGR 67

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

>gnl|CDD|241040 cd12596, RRM1_SRSF6, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 6 (SRSF6)

 Score = 42.6 bits (100), Expect = 2e-05
 Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 8/75 (10%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI-ELN 477
           +++G L + V + D+Q FF    +++++ L +       GYG VEF    DA  A+ ELN
Sbjct: 2   VYIGRLSYHVREKDIQRFFGGYGKLLEIDLKN-------GYGFVEFEDSRDADDAVYELN 54

Query: 478 GQMLGNRAIRLDFAR 492
           G+ L    + ++ AR
Sbjct: 55  GKDLCGERVIVEHAR 69

This subfamily corresponds to the RRM1 of SRSF6, also termed pre-mRNA-splicing factor SRp55, which is an essential splicing regulatory serine/arginine (SR) protein that preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. For instance, it does not bind to the purine-rich sequence in the calcitonin-specific ESE, but binds to a region adjacent to the purine tract. Moreover, cellular levels of SRSF6 may control tissue-specific alternative splicing of the calcitonin/ calcitonin gene-related peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal SR domains rich in serine-arginine dipeptides. . Length = 70

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

 Score = 42.5 bits (101), Expect = 2e-05
 Identities = 23/83 (27%), Positives = 38/83 (45%), Gaps = 7/83 (8%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVV--DVRLSSDADGRF-KGYGHVEFASVEDAHK 472
           + TL +  L     + D+    S +A V   DVRL  D      +G+  VEF S+EDA +
Sbjct: 2   TNTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQ 61

Query: 473 AIELNGQMLG----NRAIRLDFA 491
            ++    +       R +R+ +A
Sbjct: 62  WMDALNNLDPFVIDGRVVRVSYA 84

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

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

 Score = 42.3 bits (100), Expect = 3e-05
 Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 11/72 (15%)

Query: 520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNK 579
           T+F+ G D +V ED++R+     FG  GEI  + +P        KG  ++ F    +   
Sbjct: 3   TVFVGGLDPAVTEDELRS----LFGPFGEIVYVKIPPG------KGCGFVQFVHRAAAEA 52

Query: 580 AL-EMSGTEIGG 590
           A+ ++ GT IGG
Sbjct: 53  AIQQLQGTIIGG 64

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

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

 Score = 42.4 bits (100), Expect = 3e-05
 Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 6/76 (7%)

Query: 521 IFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKA 580
           +F+        ED++R     HFG  G I R+ +    D+G  KG A++DF + +    A
Sbjct: 1   LFVGNLSFETTEDELR----AHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNA 56

Query: 581 LEMSGTEIGGYSLVVD 596
             + G  + G +L V+
Sbjct: 57  --LKGKHLNGRALRVE 70

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

>gnl|CDD|235334 PRK05035, PRK05035, electron transport complex protein RnfC; Provisional

 Score = 46.9 bits (112), Expect = 3e-05
 Identities = 51/230 (22%), Positives = 90/230 (39%), Gaps = 40/230 (17%)

Query: 12  KSAKKGGKREAEDAIEKLVSAKKQKGNDGVAQAVKKAKV-----EAKTQKKNKNDETSSS 66
           K A +    + +DA+   ++  K K        V KA            ++ +  +  + 
Sbjct: 474 KKAAEARAAKDKDAVAAALARVKAKKAAATQPIVIKAGARPDNSAVIAAREARKAQARAR 533

Query: 67  SSEEDSSDSEEEQKVK---AVVTNKGGKAAKPPVKESSSEEEDSSSDEEPPKKQPVAAKN 123
            +E+ ++ + + +K     A+   K  KAA+      + EE D       PKK  VAA  
Sbjct: 534 QAEKQAAAAADPKKAAVAAAIARAKAKKAAQQAANAEAEEEVD-------PKKAAVAA-- 584

Query: 124 GAVA-ATAKKSKPDSSSSDSSDDDSDEDEVPTSIKKLPVAAAKNGPSAPQKKKDDSSDSS 182
            A+A A AKK+   ++S++  +  ++ D      KK  VAAA     A  KK +  +++ 
Sbjct: 585 -AIARAKAKKAAQQAASAEPEEQVAEVDP-----KKAAVAAA--IARAKAKKAEQQANAE 636

Query: 183 DEESDESSDEDDKSTK---AIPQPKKLPASTAKKGTVAATKKSTGSSDDD 229
            EE       D +      AI + K      A+K            ++D 
Sbjct: 637 PEE-----PVDPRKAAVAAAIARAK------ARKAAQQQANAEPEEAEDP 675

Length = 695

>gnl|CDD|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit 4 (THOC4) and similar proteins

 Score = 42.2 bits (100), Expect = 3e-05
 Identities = 23/74 (31%), Positives = 33/74 (44%), Gaps = 1/74 (1%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI-EL 476
            L V NL F V   D++  F+E   +    +  D  GR  G   V F    DA KA+ + 
Sbjct: 2   KLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRSGRSLGTADVVFERRADALKAMKQY 61

Query: 477 NGQMLGNRAIRLDF 490
           NG  L  R +++  
Sbjct: 62  NGVPLDGRPMKIQL 75

This subgroup corresponds to the RRM of THOC4, also termed transcriptional coactivator Aly/REF, or ally of AML-1 and LEF-1, or bZIP-enhancing factor BEF, an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus. THOC4 was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid. It might be a novel transcription cofactor for erythroid-specific genes. . Length = 75

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

 Score = 42.6 bits (101), Expect = 3e-05
 Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 1/74 (1%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI-ELN 477
           + V NLP  V +  ++  F    EV DV++    DG+ + +G V F S EDA +A+   N
Sbjct: 3   IIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKYFN 62

Query: 478 GQMLGNRAIRLDFA 491
              +    I ++ A
Sbjct: 63  KTFIDTSKISVELA 76

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

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

 Score = 42.4 bits (100), Expect = 3e-05
 Identities = 22/72 (30%), Positives = 40/72 (55%), Gaps = 2/72 (2%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAIE-L 476
           ++VG++ F + +  ++  FS    +  + +S D    + KG+  VE+   E A  A+E +
Sbjct: 3   VYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQM 62

Query: 477 NGQMLGNRAIRL 488
           NG MLG R I++
Sbjct: 63  NGVMLGGRNIKV 74

This subfamily corresponds to the RRM1 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition. . Length = 76

>gnl|CDD|240948 cd12504, RRM2_hnRNPH_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family

 Score = 42.4 bits (100), Expect = 3e-05
 Identities = 22/64 (34%), Positives = 36/64 (56%), Gaps = 1/64 (1%)

Query: 424 LPFSVEQADVQNFFSEVAEVVD-VRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLG 482
           LPF   + ++  FFS +  V + + L  D  GR  G  +V+FAS E A +A+  + + +G
Sbjct: 8   LPFGCSKEEIAQFFSGLEIVPNGITLPMDYRGRSTGEAYVQFASQESAERALGKHKEKIG 67

Query: 483 NRAI 486
           +R I
Sbjct: 68  HRYI 71

This subfamily corresponds to the RRM2 of hnRNP H protein family which includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9). They represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing, having similar RNA binding affinities and specifically recognizing the sequence GGGA. They can either stimulate or repress splicing upon binding to a GGG motif. hnRNP H binds to the RNA substrate in the presence or absence of these proteins, whereas hnRNP F binds to the nuclear mRNA only in the presence of cap-binding proteins. Furthermore, hnRNP H and hnRNP H2 are almost identical; both have been found to bind nuclear-matrix proteins. hnRNP H activates exon inclusion by binding G-rich intronic elements downstream of the 5' splice site in the transcripts of c-src, human immunodeficiency virus type 1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons when bound to exonic elements in the transcripts of beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2 has been implicated in pre-mRNA 3' end formation. hnRNP H3 may be involved in the splicing arrest induced by heat shock. Most family members contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), except for hnRNP H3, in which the RRM1 is absent. RRM1 and RRM2 are responsible for the binding to the RNA at DGGGD motifs, and they play an important role in efficiently silencing the exon. Members in this family can regulate the alternative splicing of the fibroblast growth factor receptor 2 (FGFR2) transcripts, and function as silencers of FGFR2 exon IIIc through an interaction with the exonic GGG motifs. The lack of RRM1 could account for the reduced silencing activity within hnRNP H3. In addition, the family members have an extensive glycine-rich region near the C-terminus, which may allow them to homo- or heterodimerize. . Length = 77

>gnl|CDD|219320 pfam07172, GRP, Glycine rich protein family

 Score = 42.8 bits (101), Expect = 3e-05
 Identities = 25/59 (42%), Positives = 27/59 (45%), Gaps = 6/59 (10%)

Query: 596 DEAKQRGDFGSGGGRSGGRGGRSGGRDFGRSGGRDGGRFGGRGRGGRDGGRGGRGRGRG 654
           +E +     G GGG  GG GG  GG      GG  GG  G  G GG   G GG G G G
Sbjct: 38  NEVQDDKYGGGGGGYGGGGGGGYGG------GGYYGGGGGYGGGGGGYPGGGGGGYGGG 90

This family of proteins includes several glycine rich proteins as well as two nodulins 16 and 24. The family also contains proteins that are induced in response to various stresses. Length = 91

>gnl|CDD|241116 cd12672, RRM_DAZL, RNA recognition motif in vertebrate deleted in azoospermia-like (DAZL) proteins

 Score = 42.5 bits (100), Expect = 3e-05
 Identities = 19/58 (32%), Positives = 35/58 (60%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE 475
           T+FVG +   +++ ++++FF++   V +V++ +D  G  KGYG V F    D  K +E
Sbjct: 7   TVFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDRTGVSKGYGFVSFYDDVDVQKIVE 64

This subgroup corresponds to the RRM of DAZL, also termed SPGY-like-autosomal, encoded by the autosomal homolog of DAZ gene, DAZL. It is ancestral to the deleted in azoospermia (DAZ) protein. DAZL is germ-cell-specific RNA-binding protein that contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a DAZ motif, a protein-protein interaction domain. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 82

>gnl|CDD|237863 PRK14949, PRK14949, DNA polymerase III subunits gamma and tau; Provisional

 Score = 47.0 bits (112), Expect = 3e-05
 Identities = 53/388 (13%), Positives = 107/388 (27%), Gaps = 58/388 (14%)

Query: 66  SSSEEDSSDSEEEQKVKAVVTNKGGKAAKPPVKESSSEEEDSSSDEEPPKKQPVAAKNGA 125
            +    ++  +     +    N      K  + E ++            ++Q  AA   A
Sbjct: 380 QTPSALAAAVQAPHANEPQFVNAAPAEKKTALTEQTT-----------AQQQVQAANAEA 428

Query: 126 VAATAKKSKPDSSSSDSSDDDSDED-------------------EVPTSIKKLPVAAAKN 166
           VA     ++P  +   + DD+S+                     E  +S+     A  + 
Sbjct: 429 VAEADASAEPADTVEQALDDESELLAALNAEQAVILSQAQSQGFEASSSLDADNSAVPEQ 488

Query: 167 GPSAPQKKKDDSSDSSDEESDESSDEDDKSTKAIP-----QPKKLPASTAKKGTVAATKK 221
             S  ++   + S +  +  D S+  +  +   +      +         +      +  
Sbjct: 489 IDSTAEQSVVNPSVTDTQVDDTSASNNSAADNTVDDNYSAEDTLESNGLDEGDYAQDSAP 548

Query: 222 STGSSDDDS---SSSEDSSESEEDNGAPAKVTSEAKKLPAVKNVPAPAAKKKTESSDSSD 278
                DD     S S ++   +E + A  +    A +        +P +   T ++  +D
Sbjct: 549 LDAYQDDYVAFSSESYNALSDDEQHSANVQSAQSAAEAQPSSQSLSPISAVTTAAASLAD 608

Query: 279 EE-------SEDS--SDEDEEPTHVTKATPVKKLSAVVTKNKVESSSSSDESESEEEKPP 329
           ++       + DS  SD D       K    KK SA        S +           P 
Sbjct: 609 DDILDAVLAARDSLLSDLDALSP---KEGDGKKSSADRKPKTPPSRAPPASLSKPASSPD 665

Query: 330 AKMDVDSSSEEESSDEEPQKKKDVKPNTKALKKESSSDEEDSDDED----EGEEEEASKT 385
           A     S   +   +    +     P        + +     D  D    E   E AS  
Sbjct: 666 ASQTSASFDLDPDFELATHQS---VPEAALASGSAPAPPPVPDPYDRPPWEEAPEVASAN 722

Query: 386 PKKNVTDVKMVDAESGKKAAQTPFTPQS 413
              N      +       A+ +      
Sbjct: 723 DGPNNAAEGNLSESVE-DASNSELQAVE 749

Length = 944

>gnl|CDD|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)

 Score = 41.8 bits (98), Expect = 4e-05
 Identities = 25/73 (34%), Positives = 39/73 (53%), Gaps = 6/73 (8%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKA-IELN 477
           LFVGNLP  + + D +  F +  E  +V ++ D     +G+G +   S   A  A  EL+
Sbjct: 4   LFVGNLPTDITEEDFKKLFEKYGEPSEVFINRD-----RGFGFIRLESRTLAEIAKAELD 58

Query: 478 GQMLGNRAIRLDF 490
           G +L NR +R+ F
Sbjct: 59  GTILKNRPLRIRF 71

This subgroup corresponds to the RRM1 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Its cellular function remains unknown currently, however, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

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

 Score = 41.9 bits (99), Expect = 4e-05
 Identities = 18/70 (25%), Positives = 37/70 (52%), Gaps = 7/70 (10%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAI--- 474
           ++V ++   + + D+++ F    ++    L+ D + G+ KGYG +E+ + + A  AI   
Sbjct: 3   IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASM 62

Query: 475 ---ELNGQML 481
              +L GQ L
Sbjct: 63  NLFDLGGQQL 72

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

>gnl|CDD|240909 cd12463, RRM_G3BP1, RNA recognition motif found in ras GTPase-activating protein-binding protein 1 (G3BP1) and similar proteins

 Score = 42.2 bits (99), Expect = 4e-05
 Identities = 25/73 (34%), Positives = 39/73 (53%), Gaps = 9/73 (12%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE 475
           S  LFVGNLP  V++++++ FF +   VV++R++S   G+   +G V F   E   K   
Sbjct: 3   SHQLFVGNLPHDVDKSELKEFFQQYGNVVELRINS--GGKLPNFGFVVFDDSEPVQK--- 57

Query: 476 LNGQMLGNRAIRL 488
               +L NR I  
Sbjct: 58  ----ILSNRPIMF 66

This subgroup corresponds to the RRM of G3BP1, also termed ATP-dependent DNA helicase VIII (DH VIII), or GAP SH3 domain-binding protein 1, which has been identified as a phosphorylation-dependent endoribonuclease that interacts with the SH3 domain of RasGAP, a multi-functional protein controlling Ras activity. The acidic RasGAP binding domain of G3BP1 harbors an arsenite-regulated phosphorylation site and dominantly inhibits stress granule (SG) formation. G3BP1 also contains an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an RNA recognition motif (RRM domain), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). The RRM domain and RGG-rich region are canonically associated with RNA binding. G3BP1 co-immunoprecipitates with mRNAs. It binds to and cleaves the 3'-untranslated region (3'-UTR) of the c-myc mRNA in a phosphorylation-dependent manner. Thus, G3BP1 may play a role in coupling extra-cellular stimuli to mRNA stability. It has been shown that G3BP1 is a novel Dishevelled-associated protein that is methylated upon Wnt3a stimulation and that arginine methylation of G3BP1 regulates both Ctnnb1 mRNA and canonical Wnt/beta-catenin signaling. Furthermore, G3BP1 can be associated with the 3'-UTR of beta-F1 mRNA in cytoplasmic RNA-granules, demonstrating that G3BP1 may specifically repress the translation of the transcript. Length = 80

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

 Score = 41.8 bits (99), Expect = 4e-05
 Identities = 18/67 (26%), Positives = 34/67 (50%), Gaps = 3/67 (4%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LN 477
           L+V NLPF +   ++ + F +   +  +R+ +  + R  G   V +  + DA  A + L+
Sbjct: 5   LYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKETR--GTAFVVYEDIYDAKNACDHLS 62

Query: 478 GQMLGNR 484
           G  + NR
Sbjct: 63  GFNVANR 69

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

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

 Score = 41.4 bits (98), Expect = 4e-05
 Identities = 24/73 (32%), Positives = 39/73 (53%), Gaps = 11/73 (15%)

Query: 419 LFVGNLP-FSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI-EL 476
           +FVGNL    V + D++  FS+  +++ + L        KGYG V+F + EDA  A+   
Sbjct: 3   VFVGNLNTDKVSKEDLEEIFSKYGKILGISL-------HKGYGFVQFDNEEDARAAVAGE 55

Query: 477 NGQMLGNRAIRLD 489
           NG+ +     +LD
Sbjct: 56  NGREIAG--QKLD 66

This subfamily corresponds to the RRM in the hnRNP C-related protein family, including hnRNP C proteins, Raly, and Raly-like protein (RALYL). hnRNP C proteins, C1 and C2, are produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex; they are involved in the packaging of the hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. Raly, also termed autoantigen p542, is an RNA-binding protein that may play a critical role in embryonic development. The biological role of RALYL remains unclear. It shows high sequence homology with hnRNP C proteins and Raly. Members of this family are characterized by an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain. The Raly proteins contain a glycine/serine-rich stretch within the C-terminal regions, which is absent in the hnRNP C proteins. Thus, the Raly proteins represent a newly identified class of evolutionarily conserved autoepitopes. . Length = 68

>gnl|CDD|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate RNA-binding protein 47 (RBM47)

 Score = 41.9 bits (98), Expect = 4e-05
 Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 7/71 (9%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI-ELN 477
           +FVG +P  V + ++   F  V  + ++RL  D DG+ +GY  V +    +A +A+ ELN
Sbjct: 4   VFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFDGKNRGYAFVMYTQKHEAKRAVRELN 63

Query: 478 ------GQMLG 482
                 G++LG
Sbjct: 64  NYEIRPGRLLG 74

This subgroup corresponds to the RRM1 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

>gnl|CDD|241103 cd12659, RRM2_hnRNPM, RNA recognition motif 2 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 41.9 bits (98), Expect = 5e-05
 Identities = 25/72 (34%), Positives = 39/72 (54%), Gaps = 1/72 (1%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIEL- 476
           T+FV NL + V    ++  FS    VV   +  D DG+ +G G V F    +A +AI + 
Sbjct: 2   TVFVANLDYKVGWKKLKEVFSMAGMVVRADILEDKDGKSRGIGTVTFEQPIEAVQAISMF 61

Query: 477 NGQMLGNRAIRL 488
           NGQ+L +R + +
Sbjct: 62  NGQLLFDRPMHV 73

This subgroup corresponds to the RRM2 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 76

>gnl|CDD|241055 cd12611, RRM1_NGR1_NAM8_like, RNA recognition motif 1 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score = 41.6 bits (98), Expect = 5e-05
 Identities = 23/78 (29%), Positives = 42/78 (53%), Gaps = 4/78 (5%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEV-AEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAIE 475
           TL++G+L   +++  ++  ++ +  E V+V++      G   GY  VEF S   A  A+ 
Sbjct: 1   TLWMGDLEPWMDENFIKQVWASLGLEPVNVKVIRSRNSGLNAGYCFVEFPSPHAAQNALS 60

Query: 476 LNGQMLGN--RAIRLDFA 491
           LNG  + N  R  +L++A
Sbjct: 61  LNGTPIPNSNRTFKLNWA 78

This subgroup corresponds to the RRM1 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), 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 carboxyl terminus which also harbors a methionine-rich region. The subgroup also includes NAM8, 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 = 81

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

 Score = 42.0 bits (98), Expect = 5e-05
 Identities = 29/80 (36%), Positives = 45/80 (56%), Gaps = 3/80 (3%)

Query: 416 SKT-LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKA 473
           SKT L V  LP ++ Q ++++ F  + E+   +L  D   G+  GYG V +   +DA KA
Sbjct: 3   SKTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 62

Query: 474 IE-LNGQMLGNRAIRLDFAR 492
           I  LNG  L  + I++ +AR
Sbjct: 63  INTLNGLRLQTKTIKVSYAR 82

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

>gnl|CDD|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP DL) and similar proteins

 Score = 41.5 bits (97), Expect = 5e-05
 Identities = 22/69 (31%), Positives = 36/69 (52%), Gaps = 4/69 (5%)

Query: 521 IFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKA 580
           +F+ G      E+Q++    E+FG+ GEI  I +P D  T   +G  ++ +TD +   K 
Sbjct: 2   VFVGGLSPDTTEEQIK----EYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKL 57

Query: 581 LEMSGTEIG 589
           LE    +IG
Sbjct: 58  LESRYHQIG 66

This subgroup corresponds to the RRM2 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 75

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

 Score = 41.6 bits (98), Expect = 6e-05
 Identities = 24/80 (30%), Positives = 38/80 (47%), Gaps = 5/80 (6%)

Query: 520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNK 579
           T+F+     SV ++     L+  F   G +    V  D +TG  +G  Y+DF   +   K
Sbjct: 1   TLFVGNLSWSVDDE----WLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKK 56

Query: 580 ALE-MSGTEIGGYSLVVDEA 598
           A+E M G E+ G  + VD +
Sbjct: 57  AIEAMDGKELDGRPINVDFS 76

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

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

 Score = 41.8 bits (99), Expect = 6e-05
 Identities = 28/88 (31%), Positives = 40/88 (45%), Gaps = 14/88 (15%)

Query: 519 HTIFIKG--FDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADS 576
            T+FI+   FD++         L+E F   GE+    + KD  TG  KG A++ F   +S
Sbjct: 1   RTVFIRNLPFDATE------EELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKES 54

Query: 577 FNKALE------MSGTEIGGYSLVVDEA 598
             K LE       SG  + G  L+V  A
Sbjct: 55  AQKCLEAADNAEDSGLSLDGRRLIVTLA 82

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

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

 Score = 41.4 bits (97), Expect = 6e-05
 Identities = 28/82 (34%), Positives = 42/82 (51%), Gaps = 9/82 (10%)

Query: 516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDAD 575
           + A T+F+K    ++  D+++    E F    +I R+        GS KGIAY++F    
Sbjct: 1   RDARTLFVKNLPYNITVDELK----EVFEDAVDI-RLPS---GKDGSSKGIAYIEFKTEA 52

Query: 576 SFNKALE-MSGTEIGGYSLVVD 596
              KALE   G E+ G S+VVD
Sbjct: 53  EAEKALEEKQGAEVDGRSIVVD 74

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

>gnl|CDD|240980 cd12536, RRM1_RBM39, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39)

 Score = 41.6 bits (97), Expect = 6e-05
 Identities = 26/67 (38%), Positives = 37/67 (55%), Gaps = 1/67 (1%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADG-RFKGYGHVEFASVEDAHKAI 474
           ++T+F   L   +   D++ FFS V +V DVR+ SD +  R KG  +VEF  V     AI
Sbjct: 1   ARTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSVPLAI 60

Query: 475 ELNGQML 481
            L GQ +
Sbjct: 61  GLTGQRV 67

This subgroup corresponds to the RRM1 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor HCC1, a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Based on the specific domain composition, RBM39 has been classified into a family of non-snRNP (small nuclear ribonucleoprotein) splicing factors that are usually not complexed to snRNAs. . Length = 85

>gnl|CDD|241179 cd12735, RRM3_hnRNPH3, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein H3 (hnRNP H3) and similar proteins

 Score = 41.5 bits (97), Expect = 6e-05
 Identities = 24/65 (36%), Positives = 35/65 (53%), Gaps = 1/65 (1%)

Query: 424 LPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGN 483
           LPF   ++D+ NFFS +  +  V +   ADGR  G   VEF + EDA  A+  +   + +
Sbjct: 8   LPFRATESDIANFFSPLTPI-RVHIDIGADGRATGEADVEFVTHEDAVAAMSKDKNHMQH 66

Query: 484 RAIRL 488
           R I L
Sbjct: 67  RYIEL 71

This subgroup corresponds to the RRM3 of hnRNP H3 (also termed hnRNP 2H9), a nuclear RNA binding protein that belongs to the hnRNP H protein family that also includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), and hnRNP F. This family is involved in mRNA processing and exhibit extensive sequence homology. Currently, little is known about the functions of hnRNP H3 except for its role in the splicing arrest induced by heat shock. In addition, the typical hnRNP H proteins contain contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), except for hnRNP H3, in which the RRM1 is absent. RRM1 and RRM2 are responsible for the binding to the RNA at DGGGD motifs, and they play an important role in efficiently silencing the exon. Members in this family can regulate the alternative splicing of the fibroblast growth factor receptor 2 (FGFR2) transcripts, and function as silencers of FGFR2 exon IIIc through an interaction with the exonic GGG motifs. The lack of RRM1 could account for the reduced silencing activity within hnRNP H3. In addition, like other hnRNP H protein family members, hnRNP H3 has an extensive glycine-rich region near the C-terminus, which may allow it to homo- or heterodimerize. . Length = 75

>gnl|CDD|180777 PRK06958, PRK06958, single-stranded DNA-binding protein; Provisional

 Score = 44.0 bits (104), Expect = 6e-05
 Identities = 29/73 (39%), Positives = 33/73 (45%), Gaps = 1/73 (1%)

Query: 593 LVVDEAKQRGDFGSGGGRSGGRGGRSGGRDFGRSGGRDGGRFGGRGRGGRDGGRGGRGRG 652
           +V D+ +  G  G  GG  GG      G   G  GG  GG     G GGR  G GG G G
Sbjct: 100 IVADQMQMLGGRGGSGGGGGGGDEGGYGGGGGGGGGGYGGESRSGGGGGRASGGGGGGAG 159

Query: 653 RGTPNRPSLAAAG 665
            G  +RPS  A G
Sbjct: 160 -GGASRPSAPAGG 171

Length = 182

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

 Score = 41.1 bits (97), Expect = 7e-05
 Identities = 28/82 (34%), Positives = 42/82 (51%), Gaps = 7/82 (8%)

Query: 521 IFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKA 580
           +++K  D S+ +++    L E F   G IT   V  D + G  KG  ++ F+  +   KA
Sbjct: 4   LYVKNLDDSIDDER----LREEFSPFGTITSAKVMTD-EKGRSKGFGFVCFSSPEEATKA 58

Query: 581 L-EMSGTEIGGYSLVVDEAKQR 601
           + EM+G  IGG  L V  A QR
Sbjct: 59  VTEMNGRIIGGKPLYVALA-QR 79

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|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional

 Score = 45.9 bits (109), Expect = 7e-05
 Identities = 35/199 (17%), Positives = 58/199 (29%), Gaps = 1/199 (0%)

Query: 79  QKVKAVVTNKGGKAAKPPVKESSSEEEDSSSDEEPPKKQPVAAKNGAVAATAKKSKPDSS 138
              +          A+PP     +           P     ++   A   +A      SS
Sbjct: 177 SSPEETARAPSSPPAEPPPSTPPAAASPRPPRRSSPISASASSPAPAPGRSAADDAGASS 236

Query: 139 SSDSSDDDSDEDEVPTSIKKLPVAAAKNGPSAPQKKKDDSSDSSDEESDESSDEDDKSTK 198
           S  SS + S     P +   LP  A    P+   +    +  SS      SS    +   
Sbjct: 237 SDSSSSESSGCGWGPENECPLPRPAPITLPTRIWEASGWNGPSSRP-GPASSSSSPRERS 295

Query: 199 AIPQPKKLPASTAKKGTVAATKKSTGSSDDDSSSSEDSSESEEDNGAPAKVTSEAKKLPA 258
             P P    +  A     A++  S+      SS+S  S  S     +P    S +     
Sbjct: 296 PSPSPSSPGSGPAPSSPRASSSSSSSRESSSSSTSSSSESSRGAAVSPGPSPSRSPSPSR 355

Query: 259 VKNVPAPAAKKKTESSDSS 277
                 P++ +K      +
Sbjct: 356 PPPPADPSSPRKRPRPSRA 374

Length = 1352

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

 Score = 41.4 bits (97), Expect = 7e-05
 Identities = 20/60 (33%), Positives = 31/60 (51%)

Query: 526 FDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSG 585
           F  ++G + V   L   FG CG I  + + +D  T   KG AY+ F D ++  KAL ++ 
Sbjct: 3   FVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKALLLNE 62

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

>gnl|CDD|241000 cd12556, RRM2_RBM15B, RNA recognition motif 2 in putative RNA binding motif protein 15B (RBM15B) from vertebrate

 Score = 41.5 bits (97), Expect = 7e-05
 Identities = 18/79 (22%), Positives = 47/79 (59%), Gaps = 1/79 (1%)

Query: 415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKA- 473
            ++ LF+GNL  +V + +++  F +   + +V +   A G+   Y  ++F +++ AH+A 
Sbjct: 7   ATRNLFIGNLDHNVSEVELRRAFDKYGIIEEVVIKRPARGQGGAYAFLKFQNLDMAHRAK 66

Query: 474 IELNGQMLGNRAIRLDFAR 492
           + ++G+++G   I++ + +
Sbjct: 67  VAMSGRVIGRNPIKIGYGK 85

This subgroup corresponds to the RRM2 of RBM15B, also termed one twenty-two 3 (OTT3), a paralog of RNA binding motif protein 15 (RBM15), also known as One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. RBM15B belongs to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 85

>gnl|CDD|240420 PTZ00441, PTZ00441, sporozoite surface protein 2 (SSP2); Provisional

 Score = 45.3 bits (107), Expect = 8e-05
 Identities = 44/284 (15%), Positives = 91/284 (32%), Gaps = 32/284 (11%)

Query: 83  AVVTNKGGKAAKPPV---KESSSEEEDSSSDEEPPKKQPVAAKNGAVAATAKKSKPDSSS 139
           +V   KG  +   P+     ++   E+   +E P + +P+               P +  
Sbjct: 250 SVTCGKGTHSRSRPILHEGCTTHMVEECEEEECPVEPEPLPVPA---------PVPPTPE 300

Query: 140 SDSSDDDSDEDEVPTSIKKLPVAAAKNGPSAPQKKKDDSSDSSDEESDESSDEDDKSTKA 199
            D+     DE  VP   + L V      P  P  +  D + + +       DE    +  
Sbjct: 301 DDNPRPTDDEFAVPNFNEGLDVPDNPQDPVPPPNEGKDGNPNEENLFPPGDDEVPDESNV 360

Query: 200 IPQPKKLPASTAKKGTVAATKKSTGSSDDDSSSSEDSSESEEDNGAPAKVTSEAKKLPAV 259
            P P  +P  +  + +          + D      +  E                     
Sbjct: 361 PPNPPNVPGGSNSEFSSDVENPPNPPNPDIPEQEPNIPEDSN------------------ 402

Query: 260 KNVPAPAAKKKTESSDSSDEESEDSSDEDEEPTHVTKATPVKKLSAVVTKNKVESSSSSD 319
           K VP     +  +  D++  E +   ++ +         P+        KNK  +  +  
Sbjct: 403 KEVPEDVPMEPEDDRDNNFNEPKKPENKGDGQNEPVIPKPLDNERDQSNKNKQVNPGNRH 462

Query: 320 ESESEEEKPPAKMDVDSSSEEESSD--EEPQKKKDVKPNTKALK 361
            SE    +P  + + + +   ++SD  + P++ +  +P  K  K
Sbjct: 463 NSEDRYTRPHGRNNENRNYNNKNSDIPKHPERSEHEQPEDKKKK 506

Length = 576

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

 Score = 41.0 bits (96), Expect = 8e-05
 Identities = 24/74 (32%), Positives = 41/74 (55%), Gaps = 1/74 (1%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LN 477
           L+VGNL   V +  ++  F     V +V++  D + +   YG VE+    DA  A++ LN
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQTLN 60

Query: 478 GQMLGNRAIRLDFA 491
           G+ + N  IR+++A
Sbjct: 61  GRQIENNEIRVNWA 74

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

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

 Score = 40.8 bits (96), Expect = 9e-05
 Identities = 25/77 (32%), Positives = 42/77 (54%), Gaps = 5/77 (6%)

Query: 418 TLFVGNLPFSVEQADVQN----FFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHK 472
           T+FV     S+ + D++      FS   E+  V + +D + G  KG+ ++EF SV+   K
Sbjct: 1   TIFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEK 60

Query: 473 AIELNGQMLGNRAIRLD 489
           A+EL+G  LG   + +D
Sbjct: 61  ALELDGSDLGGGNLVVD 77

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

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 45.5 bits (107), Expect = 9e-05
 Identities = 85/392 (21%), Positives = 148/392 (37%), Gaps = 22/392 (5%)

Query: 15   KKGGKREAEDAIEKLVSAKKQKGNDGVAQAVKKAKVEAKTQKKNKNDETSSSSSEE---- 70
                K++A++A +K    KK       A+  KKA    K  ++ K  E +   +EE    
Sbjct: 1413 AAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKA 1472

Query: 71   DSSDSEEEQKVKAVVTNKGGKAAKPPVKESSSEEEDSSSDEEPPKKQPVAAKNGAVAATA 130
            D +  + E+  KA    K  + AK    E+    E     +E  KK   A K        
Sbjct: 1473 DEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEA-KKAEEAKKADEAKKAE 1531

Query: 131  KKSKPDSSSSDSSDDDSDEDEVPTSIKKLPVAAAKNGPSAPQKKKDDSSDSSDEESDESS 190
            +  K D +        +DE +    +KK             ++ K+ +   ++E      
Sbjct: 1532 EAKKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEE 1591

Query: 191  DEDDKSTKAIPQPKKLPASTAKKGTVAATKKSTGSSDDDSSSSEDSSESEEDNGAPAKVT 250
               ++  K   + KK+ A  AKK   A  K       ++     +  + +E      K  
Sbjct: 1592 ARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAE--EKKKA 1649

Query: 251  SEAKKLPAVKNVPAPAAKKKTESSDSSDEESEDSSDED--------EEPTHVTKATPVKK 302
             E KK      + A    KK E      EE++ + +++        +E     KA  +KK
Sbjct: 1650 EELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKK 1709

Query: 303  LSAVVTKNKVESSSSSDESESEEEKPPAKMDVDSSSEEESSDEEPQKKK-------DVKP 355
              A   K   E   + +E++ + E+   + + D    EE+  +E +KKK       + K 
Sbjct: 1710 KEAEEKKKAEELKKAEEENKIKAEEAKKEAEEDKKKAEEAKKDEEEKKKIAHLKKEEEKK 1769

Query: 356  NTKALKKESSSDEEDSDDEDEGEEEEASKTPK 387
              +  K++ +  EE+ D+EDE    E  K  K
Sbjct: 1770 AEEIRKEKEAVIEEELDEEDEKRRMEVDKKIK 1801

Length = 2084

>gnl|CDD|240713 cd12267, RRM_YRA1_MLO3, RNA recognition motif in yeast RNA annealing protein YRA1 (Yra1p), yeast mRNA export protein mlo3 and similar proteins

 Score = 40.9 bits (96), Expect = 9e-05
 Identities = 23/72 (31%), Positives = 41/72 (56%), Gaps = 3/72 (4%)

Query: 421 VGNLPFSVEQADVQNFF-SEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNG 478
           V NLP  V +A ++ +F S++  +  V LS +  G+  G  ++ F    DA KA +  NG
Sbjct: 4   VSNLPKDVTEAQIREYFVSQIGPIKRVLLSYNEGGKSTGIANITFKRAGDATKAYDKFNG 63

Query: 479 QML-GNRAIRLD 489
           ++  GNR ++++
Sbjct: 64  RIDDGNRKMKVE 75

This subfamily corresponds to the RRM of Yra1p and mlo3. Yra1p is an essential nuclear RNA-binding protein encoded by Saccharomyces cerevisiae YRA1 gene. It belongs to the evolutionarily conserved REF (RNA and export factor binding proteins) family of hnRNP-like proteins. Yra1p possesses potent RNA annealing activity and interacts with a number of proteins involved in nuclear transport and RNA processing. It binds to the mRNA export factor Mex67p/TAP and couples transcription to export in yeast. Yra1p is associated with Pse1p and Kap123p, two members of the beta-importin family, further mediating transport of Yra1p into the nucleus. In addition, the co-transcriptional loading of Yra1p is required for autoregulation. Yra1p consists of two highly conserved N- and C-terminal boxes and a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This subfamily includes RNA-annealing protein mlo3, also termed mRNA export protein mlo3, which has been identified in fission yeast as a protein that causes defects in chromosome segregation when overexpressed. It shows high sequence similarity with Yra1p. . Length = 77

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

 Score = 40.9 bits (96), Expect = 9e-05
 Identities = 25/63 (39%), Positives = 33/63 (52%), Gaps = 3/63 (4%)

Query: 419 LFVGNLPFSVEQADVQNFFS--EVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIEL 476
           ++  N PF V + +VQ FF+   + E  D+ L  D  G   G   V+F S E A KA  L
Sbjct: 3   IYARNFPFDVTKVEVQKFFAPFNIDED-DIYLLYDDKGVGLGEALVKFKSEEQAMKAERL 61

Query: 477 NGQ 479
           NGQ
Sbjct: 62  NGQ 64

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

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

 Score = 41.2 bits (97), Expect = 9e-05
 Identities = 22/74 (29%), Positives = 41/74 (55%), Gaps = 8/74 (10%)

Query: 415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADG-RFKGYGHVEFASVEDA--- 470
            +K +FVG LP +V + D++ +FS+   V +V +  D +  R +G+G + F S ED+   
Sbjct: 1   RTKKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFES-EDSVDQ 59

Query: 471 ---HKAIELNGQML 481
                  ++NG+ +
Sbjct: 60  VVNEHFHDINGKKV 73

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|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

 Score = 45.4 bits (107), Expect = 1e-04
 Identities = 71/370 (19%), Positives = 141/370 (38%), Gaps = 58/370 (15%)

Query: 51   EAKTQKKNKNDETSSSSSEEDSS--DSEEEQKVKAVVTNKGGKAAKPPVKE---SSSEEE 105
            E  T   N++D+    ++EED++     +E + + + ++  G      V E   S SEEE
Sbjct: 3825 EDITNTLNEDDDLEELANEEDTANQSDLDESEARELESDMNGVTKDSVVSENENSDSEEE 3884

Query: 106  DSSSDEEP---PKKQPVAAKNGA--------VAATAKKSKPDSSSSDSSDDDSDEDEVPT 154
            +   DEE    P+    +             +  T +KS   S++++ SD  S ED+   
Sbjct: 3885 NQDLDEEVNDIPEDLSNSLNEKLWDEPNEEDLLETEQKSNEQSAANNESDLVSKEDD--- 3941

Query: 155  SIKKLPVAAAKNGPSAPQKKKDDSSDSSDEESDESSDEDD-----KSTKAIPQPK----K 205
                           A + K     +  +E SD+   +D+     +   + P P+     
Sbjct: 3942 -------------NKALEDKDRQEKEDEEEMSDDVGIDDEIQPDIQENNSQPPPENEDLD 3988

Query: 206  LPASTAKKGTVAATKKSTGSSDDD-SSSSEDSSESEEDNGAPAKVTSEAKKLPAV-KNVP 263
            LP             K +   D D  ++ E+  E++ +   P +     ++   + +++ 
Sbjct: 3989 LPEDLKLDEKEGDVSKDSDLEDMDMEAADENKEEADAEKDEPMQDEDPLEENNTLDEDIQ 4048

Query: 264  APAAKKKTESSDSSDEES-EDSSDEDEEPTHVTKATPVKKLSAVVTKNKVESSSSSDESE 322
                    E  +  +E+  E++  E+EE T         +      +   +     D++ 
Sbjct: 4049 QDDFSDLAEDDEKMNEDGFEENVQENEEST---------EDGVKSDEELEQGEVPEDQAI 4099

Query: 323  SEEEKPPAKMDVDSSSEEESSDEEPQKKKDVKPNTKALKKESSSDEEDSDDEDEGEEEEA 382
                K    MD  S+     +DEE   K  V  N +  +++       +D E E  +E+ 
Sbjct: 4100 DNHPK----MDAKSTFASAEADEENTDKGIVGENEELGEEDGVRGNGTADGEFEQVQEDT 4155

Query: 383  SKTPKKNVTD 392
            S TPK+ +++
Sbjct: 4156 S-TPKEAMSE 4164

Length = 4600

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 45.0 bits (107), Expect = 1e-04
 Identities = 30/218 (13%), Positives = 63/218 (28%), Gaps = 13/218 (5%)

Query: 137 SSSSDSSDDDSDEDEVPTSIKKLPVAAAKNGPSAPQKKKDDSSDSSDEESDESSDEDDKS 196
            +++ +  + + E+E    +KKL   +   G    ++ K+                   S
Sbjct: 1   MTTASTKAELAAEEEAKKKLKKLAAKSKSKGFITKEEIKEALESKKKTPEQIDQVLIFLS 60

Query: 197 TKAIPQPKKLPASTAKKGTVAATKKSTGSSDDDSSSSEDSSESEEDNGAPAKVTSEAKKL 256
                      +   KK T  A K +  +        +D  +S +       +  +    
Sbjct: 61  GMVKDTDDATESDIPKKKTKTAAKAAA-AKAPAKKKLKDELDSSKKAEKKNALDKDDDLN 119

Query: 257 PAVKNVPAPAAKKKTESSDSSDEESEDSSDEDEEPTHVTKATPVKKLSAVVTKNKVESSS 316
                     A    +  D  D + +D  D+D++                   + V+   
Sbjct: 120 YVKDIDVLNQADDDDDDDDDDDLDDDDIDDDDDDEDDDEDD----------DDDDVDDED 169

Query: 317 SSDESESEEEKPPAKMDVDSSSEEESSDEEPQKKKDVK 354
              +   E EK     D     ++  +    Q +KD K
Sbjct: 170 EEKKEAKELEKLSDDDDFVWDEDDSEALR--QARKDAK 205

Length = 509

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 44.6 bits (106), Expect = 1e-04
 Identities = 26/210 (12%), Positives = 65/210 (30%), Gaps = 3/210 (1%)

Query: 195 KSTKAIPQPKKLPASTAKKGTVAATKKSTGSSDDDSSSSEDSSESEEDNGAPAKVTSEAK 254
            STKA    ++      KK    +  K   + ++   + E   ++ E         S   
Sbjct: 4   ASTKAELAAEEEAKKKLKKLAAKSKSKGFITKEEIKEALESKKKTPEQIDQVLIFLSGMV 63

Query: 255 KLPAVKNVPAPAAKKKTESSDSSDEESEDSSDEDEEPTHVTKATPVKKLSAVVTKNKVES 314
           K            KK   ++ ++  ++       +E     KA     L      N V+ 
Sbjct: 64  KDTDDATESDIPKKKTKTAAKAAAAKAPAKKKLKDELDSSKKAEKKNALDKDDDLNYVKD 123

Query: 315 SSSSDESESEEEKPPAKMDVDSSSEEESSDEEPQKKKDVKPNTKALKKESSSDEEDSDDE 374
               ++++ +++      D D   ++   D++ +   +   +     ++    E    ++
Sbjct: 124 IDVLNQADDDDDD---DDDDDLDDDDIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKELEK 180

Query: 375 DEGEEEEASKTPKKNVTDVKMVDAESGKKA 404
              +++                DA+    A
Sbjct: 181 LSDDDDFVWDEDDSEALRQARKDAKLTATA 210

Length = 509

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

 Score = 40.2 bits (95), Expect = 1e-04
 Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 1/53 (1%)

Query: 539 LEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGG 590
           L+E F + G +  + +P D +    +G AY++F   +   KA++ M G +I G
Sbjct: 15  LKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHMDGGQIDG 67

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

>gnl|CDD|240906 cd12460, RRM2_CID8_like, RNA recognition motif 2 in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 40.9 bits (96), Expect = 1e-04
 Identities = 27/84 (32%), Positives = 43/84 (51%), Gaps = 14/84 (16%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEV-AEVVDVRLSSDADGRFKGYGH------VEFASVE 468
           ++T++  N+   V Q+DV+ FF  +  EV  +RL  D       Y H      VEFA  E
Sbjct: 4   ARTIYCTNIDKKVTQSDVKLFFESLCGEVSRLRLLGD-------YHHSTRIAFVEFAMAE 56

Query: 469 DAHKAIELNGQMLGNRAIRLDFAR 492
            A  A+  +G +LG+  IR+  ++
Sbjct: 57  SAIAALNCSGAVLGSLPIRVSPSK 80

This subgroup corresponds to the RRM2 domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 82

>gnl|CDD|233044 TIGR00600, rad2, DNA excision repair protein (rad2)

 Score = 45.3 bits (107), Expect = 1e-04
 Identities = 65/397 (16%), Positives = 138/397 (34%), Gaps = 42/397 (10%)

Query: 70  EDSSDSEEEQKVKAVVTNKGGKAAKPPVKESSSEEEDSSSDEEPPKKQPVAAKNGAVAAT 129
            D     +E +++ VV+            +  +  +   SD+E              +  
Sbjct: 269 RDEGGFLKEVELRRVVSEDTSHYILIKGIQGKTAVKAVDSDDE--------------SLP 314

Query: 130 AKKSKPDSSSSDSSDDDSDEDEVPTSIKKLPVAAAKNGPSAPQKKKDDSSDSSDEESDES 189
           +  S+ DS+S D     S  +++    + +  A   +  +   K+    S+SS E+SDES
Sbjct: 315 SLSSQLDSNSED--LKSSPWEKLKPESESIVEAEPPSPRTLLAKQ-AAMSESSSEDSDES 371

Query: 190 SDEDDKSTKAIPQPKKLPASTAKKGTVAATKKSTGSS-DDDSSSSEDSSESEEDNGAPAK 248
             E           +   A          T ++ G + DDD      +S  ++ + +   
Sbjct: 372 EWER------QELKRNNVAFVDDGSLSPRTLQAIGQALDDDEDKKVSASSDDQASPSKKT 425

Query: 249 VTSEAKKLPA----------VKNVPAPAAKKKTESSDSSDEESEDSSDEDEEPTHV-TKA 297
                 ++             + +P  AA +   SS +S  E+  S+    E T    +A
Sbjct: 426 KMLLISRIEVEDDDLDYLDQGEGIPLMAALQL--SSVNSKPEAVASTKIAREVTSSGHEA 483

Query: 298 TPVKKLSAVVTKNKVESSSSSDESESEEEKPPAKMDVDSSSEEESSDEEPQKKKDVKPNT 357
            P     AV +     ++ S   SE       +++ ++ + +  SS+     +++ K   
Sbjct: 484 VP----KAVQSLLLGATNDSPIPSEFTILDRKSELSIERTVKPVSSEFGLPSQREDKLAI 539

Query: 358 KALKKESSSDEEDSDDEDEGEEEEASKTPKKNVTDVKMVDAESGKK-AAQTPFTPQSGGS 416
                ++     D  ++ E + E +    K N +++       G        ++  +  S
Sbjct: 540 PTEGTQNLQGISDHPEQFEFQNELSPLETKNNESNLSSDAETEGSPNPEMPSWSSVTVPS 599

Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD 453
           + L            +V+NF     +  +V  S+D  
Sbjct: 600 EALDNYETTNPSNAKEVRNFAETGIQTTNVGESADLL 636

All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 1034

>gnl|CDD|240721 cd12275, RRM1_MEI2_EAR1_like, RNA recognition motif 1 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 40.6 bits (95), Expect = 1e-04
 Identities = 20/72 (27%), Positives = 38/72 (52%), Gaps = 5/72 (6%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI- 474
           S++LFV N+P  V ++ ++  F    +V  V+    ++    G   V F  + DA +A+ 
Sbjct: 1   SRSLFVINVPRDVTESTLRRLFEVYGDVRGVQTERISE----GIVTVHFYDIRDAKRAVR 56

Query: 475 ELNGQMLGNRAI 486
           EL G+ +  +A+
Sbjct: 57  ELCGRHMQQQAL 68

This subfamily corresponds to the RRM1 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding protein family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins. . Length = 71

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

 Score = 40.6 bits (95), Expect = 1e-04
 Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 3/77 (3%)

Query: 418 TLFVGNLPFSVEQADVQNFF-SEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKA-I 474
           ++FVG+L   V ++D+ + F S        ++ +D   G  +GYG V F+   D  +A I
Sbjct: 3   SIFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALI 62

Query: 475 ELNGQMLGNRAIRLDFA 491
           E+ G   G R +R+  A
Sbjct: 63  EMQGVYCGGRPMRISTA 79

This subgroup corresponds to the RRM2 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both, RNA and single-stranded DNA (ssDNA), in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. . Length = 80

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

 Score = 40.5 bits (95), Expect = 1e-04
 Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 2/77 (2%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAIE- 475
            + + N+PFS+ +  + +   ++   +    +   D G F+G     F S E+A   +E 
Sbjct: 3   AIVIKNIPFSLRKEQLLDIIEDLGIPLPYAFNYHFDNGVFRGLAFANFRSPEEAQTVVEA 62

Query: 476 LNGQMLGNRAIRLDFAR 492
           LNG  +  R +R+++ R
Sbjct: 63  LNGYEISGRRLRVEYKR 79

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

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

 Score = 40.2 bits (94), Expect = 1e-04
 Identities = 22/69 (31%), Positives = 34/69 (49%), Gaps = 1/69 (1%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAIELN 477
           +FVG L +   + D++ +FS+  EVVD  +  D   GR +G+G V F       K ++  
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60

Query: 478 GQMLGNRAI 486
              L  R I
Sbjct: 61  EHKLDGRVI 69

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

>gnl|CDD|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen D (HuD)

 Score = 40.5 bits (94), Expect = 1e-04
 Identities = 29/80 (36%), Positives = 44/80 (55%), Gaps = 3/80 (3%)

Query: 416 SKT-LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKA 473
           SKT L V  LP ++ Q + ++ F  + E+   +L  D   G+  GYG V +   +DA KA
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 474 IE-LNGQMLGNRAIRLDFAR 492
           I  LNG  L  + I++ +AR
Sbjct: 61  INTLNGLRLQTKTIKVSYAR 80

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

>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

 Score = 44.6 bits (105), Expect = 2e-04
 Identities = 75/437 (17%), Positives = 158/437 (36%), Gaps = 38/437 (8%)

Query: 21   EAEDAIEKLVSAKKQKGNDGVAQAVKKAKVEAKTQKKNKNDETSSSSSEEDSS----DSE 76
            E  D  E L ++  +K  D   +       +   ++   N+E+   S E+D+        
Sbjct: 3891 EVNDIPEDLSNSLNEKLWDEPNEEDLLETEQKSNEQSAANNESDLVSKEDDNKALEDKDR 3950

Query: 77   EEQKVKAVVTNKGGK--AAKPPVKESSSEEEDSSSDEEPPKKQPVAAKNGAVAATAKKSK 134
            +E++ +  +++  G     +P ++E++S+    + D + P+   +  K G V+  +    
Sbjct: 3951 QEKEDEEEMSDDVGIDDEIQPDIQENNSQPPPENEDLDLPEDLKLDEKEGDVSKDSDLED 4010

Query: 135  PDSSSSDSSDDDSD-EDEVPTSIKKLPVAAAKNGPSAPQKKKDDSSDSSDEESDESSDED 193
             D  ++D + +++D E + P   +       +N       ++DD SD +  E DE  +ED
Sbjct: 4011 MDMEAADENKEEADAEKDEPMQDED---PLEENNTLDEDIQQDDFSDLA--EDDEKMNED 4065

Query: 194  DKSTKAIPQPKKLPASTA-----KKGTVAATKKSTGSSDDDSSSSEDSSESEEDNGAPAK 248
                      +            ++G V   +        D+ S+  S+E++E+N     
Sbjct: 4066 GFEENVQENEESTEDGVKSDEELEQGEVPEDQAIDNHPKMDAKSTFASAEADEENTDKGI 4125

Query: 249  VTSEAKKLPAVKNVPAPAAKKKTESSDSSDEESEDSSDEDEEPTHVTKATPVKKLSAVVT 308
            V  E ++L     V               D  +   +  + +  + +    +++      
Sbjct: 4126 V-GENEELGEEDGVRGNGTADGEFEQVQEDTSTPKEAMSEADRQYQSLGDHLREWQ---Q 4181

Query: 309  KNKVESSSSSDESESEEEKPPAKMDVDSSSEEESSDEEPQKKKDVKPNTKALKKESSSDE 368
             N++       ES+S+       M V    EE+         + +    K   K    DE
Sbjct: 4182 ANRIHEWEDLTESQSQAFDDSEFMHVKEDEEEDL--------QALGNAEKDQIKSIDRDE 4233

Query: 369  EDSDDEDEGEEEEASKTPKKNVTDVKMVDAESGKKAAQTPFTPQSGGSKTLFVGNLPFSV 428
              + + D       ++     V D ++ D +      QT       G  TL       S+
Sbjct: 4234 SANQNPDSMNSTNIAEDEADEVGDKQLQDGQDISDIKQT-------GEDTL--PTEFGSI 4284

Query: 429  EQADVQNFFSEVAEVVD 445
             Q++     SE  ++ D
Sbjct: 4285 NQSEKVFELSEDEDIED 4301

Length = 4600

>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 = 40.0 bits (94), Expect = 2e-04
 Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 5/71 (7%)

Query: 521 IFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKA 580
           +F++    +  E+     L E F + GEI+ + +P D +T   KG A++ F   +   KA
Sbjct: 2   LFVRNLPFTTTEE----ELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKA 57

Query: 581 L-EMSGTEIGG 590
             E+ G+   G
Sbjct: 58  YSELDGSIFQG 68

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|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 43.8 bits (104), Expect = 2e-04
 Identities = 38/213 (17%), Positives = 70/213 (32%), Gaps = 11/213 (5%)

Query: 42  AQAVKKAKVEAKTQKKNKNDETSSSSSEEDSSDSEEEQKVKAVVTNKGGKAAKPPVKESS 101
           A    +   E + +KK K     S S    + +  +E       T +        +    
Sbjct: 4   ASTKAELAAEEEAKKKLKKLAAKSKSKGFITKEEIKEALESKKKTPEQIDQVLIFLSGMV 63

Query: 102 SEEEDSSSDEEPPKKQPVAAKNGAVAATAKKSKPDS-SSSDSSDDDSDEDEVPTSIKKLP 160
            + +D++  + P KK   AAK  A  A AKK   D   SS  ++  +  D+         
Sbjct: 64  KDTDDATESDIPKKKTKTAAKAAAAKAPAKKKLKDELDSSKKAEKKNALDKDDDLNYVKD 123

Query: 161 VAAAKNGPSAPQKKKDDSSDSSDEESDESSDEDDKSTKAIPQPKKLPASTAKKGTVAATK 220
           +              DD  D  D++ D+  D++D                 +       K
Sbjct: 124 IDVLNQADDDDDDDDDDDLD--DDDIDDDDDDEDDDEDD-----DDDDVDDEDEEKKEAK 176

Query: 221 KSTGSSDDDSSSSEDSSESEEDNGAPAKVTSEA 253
           +    SDDD    ++    + +    A+  ++ 
Sbjct: 177 ELEKLSDDDDFVWDE---DDSEALRQARKDAKL 206

Length = 509

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 43.8 bits (104), Expect = 2e-04
 Identities = 23/211 (10%), Positives = 63/211 (29%), Gaps = 3/211 (1%)

Query: 175 KDDSSDSSDEESDESSDEDDKSTKAIPQPKKLPASTAKKGTVAATKKSTGSSDDDSSSSE 234
              S+ +     +E+  +  K          +     K+   A   K       D     
Sbjct: 2   TTASTKAELAAEEEAKKKLKKLAAKSKSKGFITKEEIKE---ALESKKKTPEQIDQVLIF 58

Query: 235 DSSESEEDNGAPAKVTSEAKKLPAVKNVPAPAAKKKTESSDSSDEESEDSSDEDEEPTHV 294
            S   ++ + A      + K   A K   A A  KK    +    +  +  +  ++   +
Sbjct: 59  LSGMVKDTDDATESDIPKKKTKTAAKAAAAKAPAKKKLKDELDSSKKAEKKNALDKDDDL 118

Query: 295 TKATPVKKLSAVVTKNKVESSSSSDESESEEEKPPAKMDVDSSSEEESSDEEPQKKKDVK 354
                +  L+     +  +     D+ + +++      D D   ++   ++E +K+    
Sbjct: 119 NYVKDIDVLNQADDDDDDDDDDDLDDDDIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKEL 178

Query: 355 PNTKALKKESSSDEEDSDDEDEGEEEEASKT 385
                       +++        ++ + + T
Sbjct: 179 EKLSDDDDFVWDEDDSEALRQARKDAKLTAT 209

Length = 509

>gnl|CDD|236304 PRK08581, PRK08581, N-acetylmuramoyl-L-alanine amidase; Validated

 Score = 44.0 bits (104), Expect = 2e-04
 Identities = 29/210 (13%), Positives = 74/210 (35%), Gaps = 15/210 (7%)

Query: 175 KDDSSDSSDEESDESSDEDDKSTKAIPQPKKLPASTAKKGTVAATKKSTGSSDDDSSSSE 234
           KD ++ ++  +S +S+D++               S+           S   ++D   S+ 
Sbjct: 32  KDSTAKTTSHDSKKSNDDETSKDT----------SSKDTDKADNNNTSNQDNNDKKFSTI 81

Query: 235 DSSESEEDN-GAPAKVTSEAKKLPAVKNVPAPAAKKKTESSDSSDEESEDSSDEDEEPTH 293
           DSS S+ +N             +  +             +   +         + E+P +
Sbjct: 82  DSSTSDSNNIIDFIYKNLPQTNINQLLTKNKYDDNYSLTTLIQNLFNLNSDISDYEQPRN 141

Query: 294 VTKATPVKKLSAVVTKNKVESSSSSDESESEEEKPPAKMDVDSSSEEESSDEEPQKKKDV 353
             K+T     ++  +      + SS + +++ +K P+     ++++  +S+++P   K  
Sbjct: 142 SEKSTNDSNKNSDSSIKNDTDTQSSKQDKADNQKAPS----SNNTKPSTSNKQPNSPKPT 197

Query: 354 KPNTKALKKESSSDEEDSDDEDEGEEEEAS 383
           +PN    +  S           + +    S
Sbjct: 198 QPNQSNSQPASDDTANQKSSSKDNQSMSDS 227

Length = 619

>gnl|CDD|241037 cd12593, RRM_RBM11, RNA recognition motif in vertebrate RNA-binding protein 11 (RBM11)

 Score = 40.3 bits (94), Expect = 2e-04
 Identities = 25/73 (34%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE- 475
           +TLFVGNL   V +  +   F +   +  V +  D +G+ K +G V F   E    AI  
Sbjct: 2   RTLFVGNLECRVREEILYELFLQAGPLTKVTICKDKEGKPKSFGFVCFKHSESVPYAIAL 61

Query: 476 LNGQMLGNRAIRL 488
           LNG  L  R I++
Sbjct: 62  LNGIRLYGRPIKV 74

This subfamily corresponds to the RRM or RBM11, a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. RBM11 is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. RBM11 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM of RBM11 is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

>gnl|CDD|240677 cd12231, RRM2_U2AF65, RNA recognition motif 2 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 39.9 bits (94), Expect = 2e-04
 Identities = 26/81 (32%), Positives = 44/81 (54%), Gaps = 5/81 (6%)

Query: 519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFN 578
           + IFI G  + + EDQV+  LE    S G++   ++ KD  TG  KG A+ ++ D    +
Sbjct: 1   NKIFIGGLPNYLSEDQVKELLE----SFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTD 56

Query: 579 KALE-MSGTEIGGYSLVVDEA 598
           +A+  ++G ++G   L V  A
Sbjct: 57  QAIAGLNGMQLGDKKLTVQRA 77

This subfamily corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 77

>gnl|CDD|241104 cd12660, RRM2_MYEF2, RNA recognition motif 2 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 40.0 bits (93), Expect = 2e-04
 Identities = 25/72 (34%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIEL- 476
           T+FV NL F V    ++  FS    V    +  D DG+ +G G V F    +A +AI + 
Sbjct: 2   TIFVANLDFKVGWKKLKEVFSIAGTVKRADIKEDKDGKSRGMGTVTFEQPIEAVQAISMF 61

Query: 477 NGQMLGNRAIRL 488
           NGQ L +R + +
Sbjct: 62  NGQFLFDRPMHV 73

This subgroup corresponds to the RRM2 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 76

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

 Score = 40.0 bits (93), Expect = 2e-04
 Identities = 22/69 (31%), Positives = 36/69 (52%), Gaps = 1/69 (1%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELN 477
           +F+G L +   + D++++FS+  EVVD  L  D   GR +G+G V F   E   K ++  
Sbjct: 1   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60

Query: 478 GQMLGNRAI 486
              L  + I
Sbjct: 61  EHKLNGKVI 69

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

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

 Score = 40.2 bits (94), Expect = 2e-04
 Identities = 18/81 (22%), Positives = 40/81 (49%), Gaps = 2/81 (2%)

Query: 419 LFVGNLPFSVEQAD-VQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-L 476
           L + NLP+S+++   ++  F    +V +  +     G+  G+  V     ++A  A+E  
Sbjct: 3   LIIRNLPWSIKKPVKLKKIFGRYGKVREATIPRKRGGKLCGFAFVTMKKRKNAEIALENT 62

Query: 477 NGQMLGNRAIRLDFARERGAY 497
           NG  +  R + +D+A ++  +
Sbjct: 63  NGLEIDGRPVAVDWAVQKNRW 83

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

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

 Score = 39.5 bits (93), Expect = 3e-04
 Identities = 20/63 (31%), Positives = 35/63 (55%), Gaps = 2/63 (3%)

Query: 537 ASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVV 595
           A L++ F   G +  +++P+  D G  KG A++ FT      KA++ ++G +I G  + V
Sbjct: 14  ADLKKLFSPFGFVWEVTIPRKPD-GKKKGFAFVQFTSKADAEKAIKGVNGKKIKGRPVAV 72

Query: 596 DEA 598
           D A
Sbjct: 73  DWA 75

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

>gnl|CDD|236304 PRK08581, PRK08581, N-acetylmuramoyl-L-alanine amidase; Validated

 Score = 43.6 bits (103), Expect = 3e-04
 Identities = 29/228 (12%), Positives = 72/228 (31%), Gaps = 26/228 (11%)

Query: 125 AVAATAKKSKPDSSSSDSSDDDSDEDEVPTSIKKLPVAAAKNGPSAPQKKKDDSSDSSDE 184
           +  A A   + DS++  +S D    ++  TS                   KD SS  +D+
Sbjct: 22  SPTAYADDPQKDSTAKTTSHDSKKSNDDETS-------------------KDTSSKDTDK 62

Query: 185 ESDESSDEDDKSTKAIPQPKKLPASTAKKGTVAATKKSTGSSDDDS----SSSEDSSESE 240
             + ++   D + K         +++     +    K+   ++ +     +  +D+    
Sbjct: 63  ADNNNTSNQDNNDKKFSTIDS--STSDSNNIIDFIYKNLPQTNINQLLTKNKYDDNYSLT 120

Query: 241 EDNGAPAKVTSEAKKLPAVKNVPAPAAKKKTESSDSSDEESEDSSDEDEEPTHVTKATPV 300
                   + S+       +N           S  S   +++  S + ++  +    +  
Sbjct: 121 TLIQNLFNLNSDISDYEQPRNSEKSTNDSNKNSDSSIKNDTDTQSSKQDKADNQKAPSSN 180

Query: 301 K-KLSAVVTKNKVESSSSSDESESEEEKPPAKMDVDSSSEEESSDEEP 347
             K S    +      +  ++S S+           SS + +S  +  
Sbjct: 181 NTKPSTSNKQPNSPKPTQPNQSNSQPASDDTANQKSSSKDNQSMSDSA 228

Length = 619

>gnl|CDD|233044 TIGR00600, rad2, DNA excision repair protein (rad2)

 Score = 43.7 bits (103), Expect = 3e-04
 Identities = 55/356 (15%), Positives = 107/356 (30%), Gaps = 31/356 (8%)

Query: 29  LVSAKKQKGNDGVAQAVKKAKVEAKTQKKNKNDETSSSSSEEDSSDSEEEQKVKAVVTNK 88
           L +  +   +D   +    +  +A   KK K     S    ED      +Q         
Sbjct: 396 LQAIGQALDDDEDKKVSASSDDQASPSKKTK-MLLISRIEVEDDDLDYLDQGEGI----P 450

Query: 89  GGKAAKPPVKESSSEEEDSSSDEEPPKKQPVAAKNGAVAATAKKSKPDSSSSDSSDDDSD 148
              A +     S  E   S+            A   AV +    +  DS           
Sbjct: 451 LMAALQLSSVNSKPEAVASTKIAREVTSSGHEAVPKAVQSLLLGATNDSP-------IPS 503

Query: 149 EDEVPTSIKKLPVAAAK---NGPSAPQKKKDDSSDSSDEESDESSDEDDKSTKAIPQPKK 205
           E  +     +L +       +       +++D      E +       D   +   Q + 
Sbjct: 504 EFTILDRKSELSIERTVKPVSSEFGLPSQREDKLAIPTEGTQNLQGISDHPEQFEFQNEL 563

Query: 206 LPASTAKKGTVAATKKSTGSSDDDSSSSEDSSESEEDNGAPAKVTSEAKKLPAVKNVPAP 265
            P  T          +S  SSD ++  S +           + VT  ++ L   +     
Sbjct: 564 SPLETK-------NNESNLSSDAETEGSPNPEMPSW-----SSVTVPSEALDNYETTNPS 611

Query: 266 AAKKKTESSDSSDEESEDSSDEDEEPTHVTKATPVKKLSAVVTKNKVESSSSSDESESEE 325
            AK+    +++  + +      D     ++    V+ +     K + ES  S  E +S  
Sbjct: 612 NAKEVRNFAETGIQTTNVGESADLLL--ISNPMEVEPME--SEKEESESDGSFIEVDSVS 667

Query: 326 EKPPAKMDVDSSSEEESSDEEPQKKKDVKPNTKALKKESSSDEEDSDDEDEGEEEE 381
                ++   S   +ES +    K   ++   +   ++   DE + D+     EEE
Sbjct: 668 STLELQVPSKSQPTDESEENAENKVASIEGEHRKEIEDLLFDESEEDNIVGMIEEE 723

All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 1034

>gnl|CDD|240872 cd12426, RRM4_PTBPH3, RNA recognition motif 4 in plant polypyrimidine tract-binding protein homolog 3 (PTBPH3)

 Score = 39.8 bits (93), Expect = 3e-04
 Identities = 25/76 (32%), Positives = 42/76 (55%), Gaps = 4/76 (5%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE 475
           +K + V NLP  V + DV N  +E   +V+V++  +++G+ +    VEFA+ E A +A+ 
Sbjct: 7   TKMIHVSNLPSDVTEEDVINHLAEHGVIVNVKV-FESNGKKQAL--VEFATEEQATEALA 63

Query: 476 L-NGQMLGNRAIRLDF 490
             +   L    IRL F
Sbjct: 64  CKHASSLNGSTIRLAF 79

This subfamily corresponds to the RRM4 of PTBPH3. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Like PTB, PTBPH3 contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 79

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

 Score = 39.4 bits (92), Expect = 3e-04
 Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 14/82 (17%)

Query: 520 TIFIKGFDSSVGEDQVRA-SLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFN 578
           T+F+ GFD        R   +E+ F   G + R  + K +        A+++F D++   
Sbjct: 1   TLFVVGFD----PGTTREEDIEKLFEPFGPLVRCDIRKTF--------AFVEFEDSEDAT 48

Query: 579 KALE-MSGTEIGGYSLVVDEAK 599
           KALE + G+ I G  L V+  K
Sbjct: 49  KALEALHGSRIDGSVLTVEFVK 70

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

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

 Score = 39.3 bits (92), Expect = 3e-04
 Identities = 25/67 (37%), Positives = 40/67 (59%), Gaps = 6/67 (8%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEF---ASVED--AHK 472
           +FVG LP  V + + + +FS+  +VVD +L  D D GR +G+G V F   ++VE   +  
Sbjct: 2   IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSAG 61

Query: 473 AIELNGQ 479
            +EL G+
Sbjct: 62  MLELGGK 68

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|147458 pfam05268, GP38, Phage tail fibre adhesin Gp38

 Score = 42.9 bits (101), Expect = 3e-04
 Identities = 28/73 (38%), Positives = 31/73 (42%), Gaps = 10/73 (13%)

Query: 589 GGYSLVVDEAKQRGDFGSGGGRSGGRGGRSGGRDFGRS--------GGRDGGRFGGRGRG 640
           GG SL        G  G GGGR  G GG+SG    G +        G   G  +GG G G
Sbjct: 159 GGASLKNSWRG-NGVCGGGGGRPFGAGGKSGSHMSGGNASLTAPGGGSGTGSAYGG-GNG 216

Query: 641 GRDGGRGGRGRGR 653
           G  G  GGR  G 
Sbjct: 217 GNVGAAGGRAWGG 229

This family contains several Gp38 proteins from T-even-like phages. Gp38, together with a second phage protein, gp57, catalyzes the organisation of gp37 but is absent from the phage particle. Gp37 is responsible for receptor recognition. Length = 261

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

 Score = 39.4 bits (92), Expect = 3e-04
 Identities = 21/69 (30%), Positives = 31/69 (44%), Gaps = 1/69 (1%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVD-VRLSSDADGRFKGYGHVEFASVEDAHKAIELN 477
           LFVG L +   Q  ++ +FS+  EVVD V +      R +G+G V+F         +   
Sbjct: 2   LFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAGG 61

Query: 478 GQMLGNRAI 486
              L  R I
Sbjct: 62  PHTLDGRTI 70

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

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

 Score = 38.9 bits (91), Expect = 4e-04
 Identities = 23/78 (29%), Positives = 43/78 (55%), Gaps = 6/78 (7%)

Query: 519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFN 578
           H +F+ G   SV +++    LE+ F   G +  + +     +G  KG+AY+++ +  S +
Sbjct: 3   HKLFVSGLPFSVTKEE----LEKLFKKHGVVKSVRLVT-NRSGKPKGLAYVEYENESSAS 57

Query: 579 KA-LEMSGTEIGGYSLVV 595
           +A L+M GTEI   ++ V
Sbjct: 58  QAVLKMDGTEIKEKTISV 75

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

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

 Score = 39.3 bits (92), Expect = 4e-04
 Identities = 22/67 (32%), Positives = 33/67 (49%), Gaps = 5/67 (7%)

Query: 521 IFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKA 580
           +F++    S  ED     LE+ F   GE++ + V  D  +G  KG AY+ F D +   KA
Sbjct: 5   LFVRNLPYSCKEDD----LEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKA 60

Query: 581 L-EMSGT 586
             E+ G 
Sbjct: 61  YKELDGK 67

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

 Score = 39.5 bits (93), Expect = 4e-04
 Identities = 19/82 (23%), Positives = 37/82 (45%), Gaps = 6/82 (7%)

Query: 519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDF---TDAD 575
           +T+ ++G D    E+ +  +L         I  + + +D  TG+ +G A+++F    DA 
Sbjct: 3   NTLILRGLDLLTTEEDILQALSAIASV--PIKDVRLIRDKLTGTSRGFAFVEFPSLEDAT 60

Query: 576 SFNKAL-EMSGTEIGGYSLVVD 596
            +  AL  +    I G  + V 
Sbjct: 61  QWMDALNNLDPFVIDGRVVRVS 82

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

>gnl|CDD|241178 cd12734, RRM3_hnRNPH_hnRNPH2_hnRNPF, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein hnRNP H , hnRNP H2, hnRNP F and similar proteins

 Score = 39.3 bits (91), Expect = 4e-04
 Identities = 23/65 (35%), Positives = 34/65 (52%), Gaps = 1/65 (1%)

Query: 424 LPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGN 483
           LP+   + D+ NFFS +   V V +    DGR  G   VEFA+ EDA  A+  +   + +
Sbjct: 8   LPYRATENDIYNFFSPL-NPVRVHIEIGPDGRVTGEADVEFATHEDAVAAMSKDKANMQH 66

Query: 484 RAIRL 488
           R + L
Sbjct: 67  RYVEL 71

This subgroup corresponds to the RRM3 of hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H') and hnRNP F, which represent a group of nuclear RNA binding proteins that play important roles in the regulation of alternative splicing decisions. hnRNP H and hnRNP F are two closely related proteins, both of which bind to the RNA sequence DGGGD. They are present in a complex with the tissue-specific splicing factor Fox2, and regulate the alternative splicing of the fibroblast growth factor receptor 2 (FGFR2) transcripts. The presence of Fox 2 can allows hnRNP H and hnRNP F to better compete with the SR protein ASF/SF2 for binding to FGFR2 exon IIIc. Thus, hnRNP H and hnRNP F can function as potent silencers of FGFR2 exon IIIc inclusion through an interaction with the exonic GGG motifs. Furthermore, hnRNP H and hnRNP H2 are almost identical; bothe have been found to bind nuclear-matrix proteins. hnRNP H activates exon inclusion by binding G-rich intronic elements downstream of the 5' splice site in the transcripts of c-src, human immunodeficiency virus type 1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons when bound to exonic elements in the transcripts of beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2 has been implicated in pre-mRNA 3' end formation. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 are responsible for the binding to the RNA at DGGGD motifs, and they play an important role in efficiently silencing the exon. In addition, the family members have an extensive glycine-rich region near the C-terminus, which may allow them to homo- or heterodimerize. . Length = 76

>gnl|CDD|237284 PRK13108, PRK13108, prolipoprotein diacylglyceryl transferase; Reviewed

 Score = 43.0 bits (101), Expect = 4e-04
 Identities = 24/134 (17%), Positives = 40/134 (29%), Gaps = 9/134 (6%)

Query: 37  GNDGVAQAVKKAKVEAKTQKKNKNDETSSSSSEEDSSDSEEEQKVKAVVTNKGGKAAKPP 96
             D VA+AVK    E   +   ++    +    E +   EE  +        G  A + P
Sbjct: 325 QPDDVAEAVKAEVAEVTDEVAAESVVQVADRDGESTPAVEETSEADIEREQPGDLAGQAP 384

Query: 97  VKESSSEEEDSSSDEEPPKKQPVAAKNGAVAATAKKSKPDSSSSDSSDDDSDEDEVPTSI 156
                  E  S++ EE P      A +       +K+ P          D  + +     
Sbjct: 385 AAHQVDAEAASAAPEE-PAALASEAHDETEPEVPEKAAPIP--------DPAKPDELAVA 435

Query: 157 KKLPVAAAKNGPSA 170
                 A  +G   
Sbjct: 436 GPGDDPAEPDGIRR 449

Length = 460

>gnl|CDD|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 39.6 bits (93), Expect = 4e-04
 Identities = 25/91 (27%), Positives = 39/91 (42%), Gaps = 18/91 (19%)

Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSS------------------DADGRFKG 458
           +T+FVGNLP + ++ D++  F +   +  VR  S                    D +   
Sbjct: 1   RTVFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNV 60

Query: 459 YGHVEFASVEDAHKAIELNGQMLGNRAIRLD 489
             +V F   E A KA++LNG       IR+D
Sbjct: 61  NAYVVFKEEESAEKALKLNGTEFEGHHIRVD 91

This subfamily corresponds to the RRM1 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 91

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 43.4 bits (103), Expect = 4e-04
 Identities = 18/58 (31%), Positives = 21/58 (36%)

Query: 596 DEAKQRGDFGSGGGRSGGRGGRSGGRDFGRSGGRDGGRFGGRGRGGRDGGRGGRGRGR 653
            + ++      GG R G R  R      G     D G   G    GR G RG R R R
Sbjct: 212 GDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDR 269

Length = 672

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

 Score = 39.0 bits (91), Expect = 4e-04
 Identities = 22/68 (32%), Positives = 34/68 (50%), Gaps = 6/68 (8%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAI--- 474
           +FVG L  +  + DV+ +FS+  +V D  L  D    R +G+G V F S +   K     
Sbjct: 2   IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEIH 61

Query: 475 --ELNGQM 480
             E+N +M
Sbjct: 62  FHEINNKM 69

This subfamily corresponds to the RRM2.in Musashi-1 (also termed Msi1), a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 42.7 bits (101), Expect = 5e-04
 Identities = 37/242 (15%), Positives = 73/242 (30%), Gaps = 30/242 (12%)

Query: 62  ETSSSSSEEDSSDSEEEQKVKAVVTNKGGKAAKPPVKESSSEEEDSSSDEEPPKKQPVAA 121
            T++S+  E +++ E ++K+K +      K+     KE   E  +S         Q +  
Sbjct: 1   MTTASTKAELAAEEEAKKKLKKLAAKS--KSKGFITKEEIKEALESKKKTPEQIDQVLIF 58

Query: 122 KNGAVAATAKKSKPDSSSSDSSDDDSDEDEVPTSIKKLPVAAAKNGPSAPQKKKDDSSDS 181
            +G V  T   ++ D     +            + KKL      +  +  +   D   D 
Sbjct: 59  LSGMVKDTDDATESDIPKKKTKTAAKAAAAKAPAKKKLKDELDSSKKAEKKNALDKDDDL 118

Query: 182 SDEESDESSDEDDKSTKAIPQPKKLPASTAKKGTVAATKKSTGSSDDDSSSSEDSSESEE 241
           +  +  +  ++ D                                DDD    +D  + E+
Sbjct: 119 NYVKDIDVLNQADDDDDDDDDDDLDDDDIDDDDDDE---------DDDEDDDDDDVDDED 169

Query: 242 DNGAPAKVTSEAKKLPAVKNVPAPAAKKKTESSDSSDEESEDSSDEDEEPTHVTKAT--P 299
           +    AK                   +K ++  D   +E +  +           AT  P
Sbjct: 170 EEKKEAK-----------------ELEKLSDDDDFVWDEDDSEALRQARKDAKLTATADP 212

Query: 300 VK 301
           VK
Sbjct: 213 VK 214

Length = 509

>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional

 Score = 43.2 bits (102), Expect = 5e-04
 Identities = 48/284 (16%), Positives = 84/284 (29%), Gaps = 20/284 (7%)

Query: 60  NDETSSSSSEEDSSDSEEEQKVKAVVTNKGGKAAKPPVKESSSEEEDSSSDEEPPKKQP- 118
                   +E  +++S           +    A   P +E S      SS + PP   P 
Sbjct: 69  TGPPPGPGTEAPANESRSTP-----TWSLSTLAPASPAREGSPTPPGPSSPDPPPPTPPP 123

Query: 119 ----------VAAKNGAVAATAKKSKPDSSSSDSSDDDSDEDEVPTSIKKLPVAAAKNGP 168
                     ++     V +          ++ +S      D   +    LP+++ +   
Sbjct: 124 ASPPPSPAPDLSEMLRPVGSPGPPPAASPPAAGASPAAVASDAASSRQAALPLSSPEETA 183

Query: 169 SAPQKKKDDSSDSSDEESDESSDEDDKSTKAIPQPKKLPASTAKKGTVAATKKSTGSSDD 228
            AP     +   S+   +         S  +       PA   +     A   S+ SS  
Sbjct: 184 RAPSSPPAEPPPSTPPAAASPRPPRRSSPISASASSPAPAP-GRSAADDAGASSSDSSSS 242

Query: 229 DSSSSEDSSESEEDNGAPAKVTSEAKKLPAVKNVPAPAAKKKTESSDSSDEESEDSSDED 288
           +SS      E+E     PA +T   +   A      P+++    SS SS  E   S    
Sbjct: 243 ESSGCGWGPENECPLPRPAPITLPTRIWEASGWNG-PSSRPGPASSSSSPRERSPSPSPS 301

Query: 289 EE--PTHVTKATPVKKLSAVVTKNKVESSSSSDESESEEEKPPA 330
                   +        S+    +   +SSSS+ S      P  
Sbjct: 302 SPGSGPAPSSPRASSSSSSSRESSSSSTSSSSESSRGAAVSPGP 345

Length = 1352

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

 Score = 43.1 bits (101), Expect = 5e-04
 Identities = 43/183 (23%), Positives = 85/183 (46%), Gaps = 14/183 (7%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAIE-L 476
           ++VG++ F + +  ++  F     +  + +S D A G+ KG+  VE+   E A  A+E +
Sbjct: 110 VYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQM 169

Query: 477 NGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVR 536
           NGQMLG R I++          P       +  Q+  +       F + + +SV  D   
Sbjct: 170 NGQMLGGRNIKVGRPSNMPQAQPII-----DMVQEEAKK------FNRIYVASVHPDLSE 218

Query: 537 ASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVV 595
             ++  F + GEI +  + +       KG  ++++ +  S ++A+  M+  ++GG  L V
Sbjct: 219 TDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRV 278

Query: 596 DEA 598
            + 
Sbjct: 279 GKC 281

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

>gnl|CDD|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 38.9 bits (91), Expect = 5e-04
 Identities = 19/74 (25%), Positives = 41/74 (55%), Gaps = 3/74 (4%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI- 474
           ++TLF+GNL  +   +D++  F    E++D+ +          Y  +++A +    KA+ 
Sbjct: 2   TRTLFIGNLEKTTTYSDLREAFERFGEIIDIDIKKQGGN--PAYAFIQYADIASVVKAMR 59

Query: 475 ELNGQMLGNRAIRL 488
           +++G+ LGN  ++L
Sbjct: 60  KMDGEYLGNNRVKL 73

This subfamily corresponds to the RRM3 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 74

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

 Score = 38.9 bits (91), Expect = 5e-04
 Identities = 17/65 (26%), Positives = 32/65 (49%), Gaps = 1/65 (1%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI-ELN 477
           L++ NLP  +++ D++       +V+  R+  D+ G+ +G G     S E     I + N
Sbjct: 3   LYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKGQSRGVGFARMESREKCEDIISKFN 62

Query: 478 GQMLG 482
           G+ L 
Sbjct: 63  GKYLK 67

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

 Score = 38.9 bits (91), Expect = 5e-04
 Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 2/76 (2%)

Query: 415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKA 473
            S  LF+ NL ++  + D++  FS+   + +V L  D    + KG+  V +   E A KA
Sbjct: 1   ESGRLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKA 60

Query: 474 I-ELNGQMLGNRAIRL 488
             EL+G +   R + L
Sbjct: 61  FAELDGTVFQGRLLHL 76

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

>gnl|CDD|236081 PRK07735, PRK07735, NADH dehydrogenase subunit C; Validated

 Score = 42.7 bits (100), Expect = 5e-04
 Identities = 45/174 (25%), Positives = 67/174 (38%), Gaps = 12/174 (6%)

Query: 16  KGGKREAEDAIEKLVSAKKQK-------GNDGVAQAVKKAKVEAKT---QKKNKNDETSS 65
           K   + A  A  K  +  KQK         +  A A  KA   AK        +  E + 
Sbjct: 92  KAKAKAAAAAKAKAAALAKQKREGTEEVTEEEKAAAKAKAAAAAKAKAAALAKQKREGTE 151

Query: 66  SSSEEDSSDSEEEQKVKAVVTNKGGKA--AKPPVKESSSEEEDSSSDEEPPKKQPVAAKN 123
             +EE+    +E+ K KA    K   A  AK    E+    E+ + +E+   K   AA  
Sbjct: 152 EVTEEEEETDKEKAKAKAAAAAKAKAAALAKQKAAEAGEGTEEVTEEEKAKAKAKAAAAA 211

Query: 124 GAVAATAKKSKPDSSSSDSSDDDSDEDEVPTSIKKLPVAAAKNGPSAPQKKKDD 177
            A AA   K K    + DS D+D+    +  +  K   AA      A  KK+++
Sbjct: 212 KAKAAALAKQKASQGNGDSGDEDAKAKAIAAAKAKAAAAARAKTKGAEGKKEEE 265

Length = 430

>gnl|CDD|240887 cd12441, RRM_Nup53_like, RNA recognition motif in nucleoporin Nup53 and similar proteins

 Score = 38.7 bits (91), Expect = 5e-04
 Identities = 11/50 (22%), Positives = 25/50 (50%), Gaps = 5/50 (10%)

Query: 437 FSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAI 486
           FS    +++VR    A+       H++++S  +A +A+  NG ++    +
Sbjct: 21  FSSCGTILEVRYPPGANWI-----HLKYSSRLEAERALSKNGTIINGGVM 65

This subfamily corresponds to the RRM domain of nucleoporin Nup53, also termed mitotic phosphoprotein 44 (MP-44), or nuclear pore complex protein Nup53, required for normal cell growth and nuclear morphology in vertebrate. It tightly associates with the nuclear envelope membrane and the nuclear lamina where it interacts with lamin B. It may also interact with a group of nucleoporins including Nup93, Nup155, and Nup205 and play a role in the association of the mitotic checkpoint protein Mad1 with the nuclear pore complex (NPC). The family also includes Saccharomyces cerevisiae Nup53p, an ortholog of vertebrate nucleoporin Nup53. A unique property of yeast Nup53p is that it contains an additional Kap121p-binding domain and interacts specifically with the karyopherin Kap121p, which is involved in the assembly of Nup53p into NPCs. Both, vertebrate Nup35 and yeast Nup53p, contain an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a C-terminal amphipathic alpha-helix and several FG repeats. This family corresponds to the RRM domain which lacks the conserved residues that typically bind RNA in canonical RRM domains. Length = 73

>gnl|CDD|237284 PRK13108, PRK13108, prolipoprotein diacylglyceryl transferase; Reviewed

 Score = 42.3 bits (99), Expect = 6e-04
 Identities = 25/163 (15%), Positives = 54/163 (33%), Gaps = 13/163 (7%)

Query: 92  AAKPPVKESSSEEEDSSSDEEPPKKQPVAAKNGAVAATAKKSKPDSSSSDSS------DD 145
           A +    E ++    S++    P       +   VA   K    + +   ++       D
Sbjct: 295 ALEREPAELAAAAVASAASAVGPVGPGEPNQPDDVAEAVKAEVAEVTDEVAAESVVQVAD 354

Query: 146 D-------SDEDEVPTSIKKLPVAAAKNGPSAPQKKKDDSSDSSDEESDESSDEDDKSTK 198
                    +E       ++ P   A   P+A Q   + +S + +E +  +S+  D++  
Sbjct: 355 RDGESTPAVEETSEADIEREQPGDLAGQAPAAHQVDAEAASAAPEEPAALASEAHDETEP 414

Query: 199 AIPQPKKLPASTAKKGTVAATKKSTGSSDDDSSSSEDSSESEE 241
            +P+        AK   +A        ++ D    +D   S  
Sbjct: 415 EVPEKAAPIPDPAKPDELAVAGPGDDPAEPDGIRRQDDFSSRR 457

Length = 460

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 43.0 bits (102), Expect = 6e-04
 Identities = 18/66 (27%), Positives = 19/66 (28%), Gaps = 2/66 (3%)

Query: 596 DEAKQRGDFGSGGGRSGGRGGRSGGRDFGRSGGRD--GGRFGGRGRGGRDGGRGGRGRGR 653
                    G    R          R+       D   GR G RGR  RD  R GR  G 
Sbjct: 219 GRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDRDRRGRRGGD 278

Query: 654 GTPNRP 659
           G   R 
Sbjct: 279 GGNERE 284

Length = 672

>gnl|CDD|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins

 Score = 38.7 bits (90), Expect = 6e-04
 Identities = 24/75 (32%), Positives = 43/75 (57%), Gaps = 2/75 (2%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAIE-L 476
           LF+G L F   +  ++  FS+  ++ +V +  D +  R +G+G V F + +DA  A+  +
Sbjct: 3   LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62

Query: 477 NGQMLGNRAIRLDFA 491
           NG+ +  R IR+D A
Sbjct: 63  NGKSVDGRQIRVDQA 77

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

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

 Score = 38.5 bits (90), Expect = 6e-04
 Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 3/74 (4%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-L 476
            ++VGNLP  + + D+++ F +   +  + L +   G    +  VEF    DA  A+   
Sbjct: 1   RIYVGNLPGDIRERDIEDLFYKYGPIKAIDLKNRRRG--PPFAFVEFEDPRDAEDAVRGR 58

Query: 477 NGQMLGNRAIRLDF 490
           +G       +R++F
Sbjct: 59  DGYDFDGYRLRVEF 72

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

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

 Score = 38.5 bits (90), Expect = 6e-04
 Identities = 28/63 (44%), Positives = 35/63 (55%), Gaps = 5/63 (7%)

Query: 529 SVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTE 587
           SV ED +R    E F   GEI  I V KD  T   KG+AY+ F  A S  +A+E M+G  
Sbjct: 13  SVTEDDLR----EAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKC 68

Query: 588 IGG 590
           +GG
Sbjct: 69  LGG 71

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

>gnl|CDD|218177 pfam04615, Utp14, Utp14 protein

 Score = 42.4 bits (100), Expect = 7e-04
 Identities = 54/263 (20%), Positives = 84/263 (31%), Gaps = 48/263 (18%)

Query: 218 ATKKSTGSSDDDSSSSEDSSESEEDNGAPAKVTSEAKKLPAVKNVPAPA----------- 266
               S    D+DS S E+  + +ED+          KKL  +K                 
Sbjct: 320 GKSVSEEDEDEDSDSEEEDEDDDEDDDDGENPWMLRKKLGKLKEGEDDEENSGLLSMKFM 379

Query: 267 ----AKKKTE-------------SSDSSDEESEDSSDEDEE------PTHVTKATPVKKL 303
               A+KK E               + SDEE  +   +         P +  K    KKL
Sbjct: 380 QRAEARKKEENDAEIEELRRELEGEEESDEEENEEPSKKNVGRRKFGPENGEKEAESKKL 439

Query: 304 SAVVTKNKVESSSSSDESESEEEKPPAKMDV-------------DSSSEEESSDEEPQKK 350
                KN+ +    SDE E  E++  AK++                  EEE  +E P  K
Sbjct: 440 KKEN-KNEFKEKKESDEEEELEDEEEAKVEKVANKLLKRSEKAQKEEEEEELDEENPWLK 498

Query: 351 KDVKPNTKALKKESSSDEEDSDDEDEGEEEEASKTPKKNVTDVKMVDAESGKKAAQTPFT 410
                   A K++S        D+   +  +A+   KK     K +D +      +    
Sbjct: 499 TTSSVGKSAKKQDSKKKSSSKLDKAANKISKAAVKVKKKKKKEKSIDLDDDLIDEEDSIK 558

Query: 411 PQSGGSKTLFVGNLPFSVEQADV 433
                 +      LPF  +Q D+
Sbjct: 559 LDVDDEEDEDDEELPFLFKQKDL 581

This protein is found to be part of a large ribonucleoprotein complex containing the U3 snoRNA. Depletion of the Utp proteins impedes production of the 18S rRNA, indicating that they are part of the active pre-rRNA processing complex. This large RNP complex has been termed the small subunit (SSU) processome. Length = 728

>gnl|CDD|220102 pfam09073, BUD22, BUD22

 Score = 42.1 bits (99), Expect = 7e-04
 Identities = 38/177 (21%), Positives = 70/177 (39%), Gaps = 14/177 (7%)

Query: 215 TVAATKKSTGSSDDDSSSSEDSSESEEDNGAPAKVTSEAKKLPAVKNVPAPAAKKKTESS 274
           T A   K+   +          S  ++D    ++   E+K   + ++      ++ ++S 
Sbjct: 144 TKAKKGKAKKKTKKSKKKEAKESSDKDDEEE-SESEDESKSEESAEDDSDDEEEEDSDSE 202

Query: 275 DSS--DEESEDSSDEDEEPTHVTKATPVKKLSAVVTKNKVESSSSSDESESEEEKPPAKM 332
           D S  D    DSSDE+E              +  +  N+  S S SDES+SE  +  +  
Sbjct: 203 DYSQYDGMLVDSSDEEEGE-----------EAPSINYNEDTSESESDESDSEISESRSVS 251

Query: 333 DVDSSSEEESSDEEPQKKKDVKPNTKALKKESSSDEEDSDDEDEGEEEEASKTPKKN 389
           D + SS      +E +      P+        S DE+D D++ + ++       +KN
Sbjct: 252 DSEESSPPSKKPKEKKTSSTFLPSLMGGYFSGSEDEDDDDEDIDPDQVVKKPVKRKN 308

BUD22 has been shown in yeast to be a nuclear protein involved in bud-site selection. It plays a role in positioning the proximal bud pole signal. More recently it has been shown to be involved in ribosome biogenesis. Length = 424

>gnl|CDD|241174 cd12730, RRM1_GRSF1, RNA recognition motif 1 in G-rich sequence factor 1 (GRSF-1) and similar proteins

 Score = 38.2 bits (89), Expect = 7e-04
 Identities = 21/68 (30%), Positives = 34/68 (50%), Gaps = 3/68 (4%)

Query: 424 LPFSVEQADVQNFFSE--VAEVVD-VRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQM 480
           LP+S    DV NFF +  +    + V    + DG+ +G   +E  S ED  KA+E +   
Sbjct: 9   LPWSCTAEDVMNFFDDCRIRNGENGVHFLLNRDGKPRGDALIELESEEDVQKALEQHRHY 68

Query: 481 LGNRAIRL 488
           +G R + +
Sbjct: 69  MGQRYVEV 76

This subgroup corresponds to the RRM1 of GRSF-1, a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. GRSF-1 contains three potential RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for the RNA binding. In addition, GRSF-1 has two auxiliary domains, an acidic alpha-helical domain and an N-terminal alanine-rich region, that may play a role in protein-protein interactions and provide binding specificity. . Length = 79

>gnl|CDD|240674 cd12228, RRM_ENOX, RNA recognition motif (RRM) in the cell surface Ecto-NOX disulfide-thiol exchanger (ECTO-NOX or ENOX) proteins

 Score = 38.5 bits (90), Expect = 7e-04
 Identities = 21/64 (32%), Positives = 34/64 (53%), Gaps = 6/64 (9%)

Query: 415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI 474
           G KT+FVG LP +  +  ++  F +  E++ +R+S       K + H+ FA      KAI
Sbjct: 5   GCKTVFVGGLPENATEEIIREVFEQCGEIIAIRMSK------KNFCHIRFAEEFAVDKAI 58

Query: 475 ELNG 478
            L+G
Sbjct: 59  YLSG 62

This subgroup corresponds to the conserved RNA recognition motif (RRM) in ECTO-NOX proteins (also termed ENOX), comprising a family of plant and animal NAD(P)H oxidases exhibiting both, oxidative and protein disulfide isomerase-like, activities. They are growth-related and drive cell enlargement, and may play roles in aging and neurodegenerative diseases. ENOX proteins function as terminal oxidases of plasma membrane electron transport (PMET) through catalyzing electron transport from plasma membrane quinones to extracellular oxygen, forming water as a product. They are also hydroquinone oxidases that oxidize externally supplied NADH, hence NOX. ENOX proteins harbor a di-copper center that lack flavin. ENOX proteins display protein disulfide interchange activity that is also possessed by protein disulfide isomerase. In contrast to the classic protein disulfide isomerases, ENOX proteins lack the double CXXC motif. This family includes two ENOX proteins, ENOX1 and ENOX2. ENOX1, also termed candidate growth-related and time keeping constitutive hydroquinone [NADH] oxidase (cCNOX), or cell proliferation-inducing gene 38 protein, or Constitutive Ecto-NOX (cNOX), is the constitutively expressed cell surface NADH (ubiquinone) oxidase that is ubiquitous and refractory to drugs. ENOX2, also termed APK1 antigen, or cytosolic ovarian carcinoma antigen 1, or tumor-associated hydroquinone oxidase (tNOX), is a cancer-specific variant of ENOX1 and plays a key role in cell proliferation and tumor progression. In contrast to ENOX1, ENOX2 is drug-responsive and harbors a drug binding site to which the cancer-specific S-peptide tagged pan-ENOX2 recombinant (scFv) is directed. Moreover, ENOX2 is specifically inhibited by a variety of quinone site inhibitors that have anticancer activity and is unique to the surface of cancer cells. ENOX proteins contain many functional motifs. Length = 84

>gnl|CDD|240980 cd12536, RRM1_RBM39, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39)

 Score = 38.5 bits (89), Expect = 8e-04
 Identities = 18/61 (29%), Positives = 35/61 (57%)

Query: 539 LEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDEA 598
           LEE F + G++  + +  D ++   KGIAY++F D  S   A+ ++G  + G  ++V  +
Sbjct: 18  LEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSVPLAIGLTGQRVLGVPIIVQAS 77

Query: 599 K 599
           +
Sbjct: 78  Q 78

This subgroup corresponds to the RRM1 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor HCC1, a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Based on the specific domain composition, RBM39 has been classified into a family of non-snRNP (small nuclear ribonucleoprotein) splicing factors that are usually not complexed to snRNAs. . Length = 85

>gnl|CDD|234526 TIGR04260, Cyano_gly_rpt, rSAM-associated Gly-rich repeat protein

 Score = 39.3 bits (92), Expect = 8e-04
 Identities = 20/48 (41%), Positives = 24/48 (50%), Gaps = 2/48 (4%)

Query: 604 FGSGGGRSGGRGGRSGGRDFGRSGGRDGGRFGGRGRGGRDGGRGGRGR 651
           +G+GGGR  G GG  GG   G  G  +GG     G G R+G  G   R
Sbjct: 73  WGNGGGRGWGNGGSGGGWVNGGGGWGNGGW--VNGGGWRNGYGGFANR 118

Members of this protein family average 125 in length, roughly half of which is the repetitive and extremely Gly-rich C-terminal region. Virtually all members occur in the Cyanobacteria, in a neighborhood that includes a radical SAM/SPASM domain, often a marker of peptide modification systems. Length = 119

>gnl|CDD|240691 cd12245, RRM_scw1_like, RNA recognition motif in yeast cell wall integrity protein scw1 and similar proteins

 Score = 38.3 bits (90), Expect = 8e-04
 Identities = 23/92 (25%), Positives = 35/92 (38%), Gaps = 33/92 (35%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGY--------GH-----VEF 464
           TLFV NL  +  + +++  FS                R  G+        G      VEF
Sbjct: 4   TLFVANLGPNTTEEELRQLFS----------------RQPGFRRLKMHNKGGGPVCFVEF 47

Query: 465 ASVEDAHKA-IELNGQML---GNRAIRLDFAR 492
             V  A +A   L G +L       IR+++A+
Sbjct: 48  EDVSFATQALNSLQGAVLSSSDRGGIRIEYAK 79

This subfamily corresponds to the RRM of the family including yeast cell wall integrity protein scw1, yeast Whi3 protein, yeast Whi4 protein and similar proteins. The strong cell wall protein 1, scw1, is a nonessential cytoplasmic RNA-binding protein that regulates septation and cell-wall structure in fission yeast. It may function as an inhibitor of septum formation, such that its loss of function allows weak SIN signaling to promote septum formation. It's RRM domain shows high homology to two budding yeast proteins, Whi3 and Whi4. Whi3 is a dose-dependent modulator of cell size and has been implicated in cell cycle control in the yeast Saccharomyces cerevisiae. It functions as a negative regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3), a G1 cyclin that promotes transcription of many genes to trigger the G1/S transition in budding yeast. It specifically binds the CLN3 mRNA and localizes it into discrete cytoplasmic loci that may locally restrict Cln3 synthesis to modulate cell cycle progression. Moreover, Whi3 plays a key role in cell fate determination in budding yeast. The RRM domain is essential for Whi3 function. Whi4 is a partially redundant homolog of Whi3, also containing one RRM. Some uncharacterized family members of this subfamily contain two RRMs; their RRM1 shows high sequence homology to the RRM of RNA-binding protein with multiple splicing (RBP-MS)-like proteins. Length = 79

>gnl|CDD|240928 cd12484, RRM1_RBM46, RNA recognition motif 1 found in vertebrate RNA-binding protein 46 (RBM46)

 Score = 38.3 bits (89), Expect = 8e-04
 Identities = 19/69 (27%), Positives = 35/69 (50%), Gaps = 4/69 (5%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNG 478
           +FVG +P  + + ++   F    ++ + RL  +  G  +GY  V + + E+A  AI    
Sbjct: 4   VFVGKIPRDMYEDELVPLFERAGKIYEFRLMMEFSGENRGYAFVMYTTKEEAQLAI---- 59

Query: 479 QMLGNRAIR 487
           ++L N  IR
Sbjct: 60  RILNNYEIR 68

This subgroup corresponds to the RRM1 of RBM46, also termed cancer/testis antigen 68 (CT68), a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM46 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

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

 Score = 38.0 bits (89), Expect = 9e-04
 Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 13/80 (16%)

Query: 521 IFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKA 580
           ++++    S  E+Q+R    E+    GE+ R+   KDY        A++ F + D   KA
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEY----GEVERVKKIKDY--------AFVHFEERDDAVKA 51

Query: 581 LE-MSGTEIGGYSLVVDEAK 599
           +E M+G E+ G  + V  AK
Sbjct: 52  MEEMNGKELEGSPIEVSLAK 71

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

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

 Score = 37.6 bits (88), Expect = 0.001
 Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 5/79 (6%)

Query: 521 IFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKA 580
           +F+        E+Q+     E F   G +    +  D DTG  KG  + +F D ++   A
Sbjct: 1   VFVGNIPYDATEEQLI----EIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASA 56

Query: 581 LE-MSGTEIGGYSLVVDEA 598
           +  ++G E  G +L VD A
Sbjct: 57  IRNLNGYEFNGRALRVDFA 75

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

>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 40.9 bits (96), Expect = 0.001
 Identities = 20/50 (40%), Positives = 20/50 (40%)

Query: 620 GRDFGRSGGRDGGRFGGRGRGGRDGGRGGRGRGRGTPNRPSLAAAGTGKK 669
           G   G  GGR GGR GG G G   GGRGG   G     R        G  
Sbjct: 1   GMGGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGGRGGGG 50

Length = 293

>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 = 37.6 bits (88), Expect = 0.001
 Identities = 20/81 (24%), Positives = 40/81 (49%), Gaps = 5/81 (6%)

Query: 520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDF-TDADSFN 578
            +F+ G  +   E +    LE  F   G +  + + KD +TG  +G  ++ F +  D+  
Sbjct: 3   KLFVSGLSTRTTEKE----LEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADA 58

Query: 579 KALEMSGTEIGGYSLVVDEAK 599
              +++G E+ G  + V++AK
Sbjct: 59  AIRDLNGKELEGRVIKVEKAK 79

This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has been implicated in the splicing control of several pre-mRNAs. Moreover, hnRNP G may function as a regulator of transcription for SREBP-1c and GnRH1. Research has shown that hnRNP G may also act as a tumor-suppressor since it upregulates the Txnip gene and promotes the fidelity of DNA end-joining activity. In addition, hnRNP G appears to play a critical role in proper neural development of zebrafish and frog embryos. The family also includes several paralogs of hnRNP G, such as hRBMY and hnRNP G-T (also termed RNA-binding motif protein, X-linked-like-2). Both, hRBMY and hnRNP G-T, are exclusively expressed in testis and critical for male fertility. Like hnRNP G, hRBMY and hnRNP G-T interact with factors implicated in the regulation of pre-mRNA splicing, such as hTra2-beta1 and T-STAR. Although members in this family share a high conserved N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), they appear to recognize different RNA targets. For instance, hRBMY interacts specifically with a stem-loop structure in which the loop is formed by the sequence CA/UCAA. In contrast, hnRNP G associates with single stranded RNA sequences containing a CCA/C motif. In addition to the RRM, hnRNP G contains a nascent transcripts targeting domain (NTD) in the middle region and a novel auxiliary RNA-binding domain (RBD) in its C-terminal region. The C-terminal RBD exhibits distinct RNA binding specificity, and would play a critical role in the regulation of alternative splicing by hnRNP G. . Length = 80

>gnl|CDD|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins

 Score = 38.3 bits (89), Expect = 0.001
 Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 5/79 (6%)

Query: 521 IFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKA 580
           +FI G      E     SLE+ F   G+I+ + V KD +T   +G  ++ F + D    A
Sbjct: 3   LFIGGLSFDTNEQ----SLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDA 58

Query: 581 LE-MSGTEIGGYSLVVDEA 598
           +  M+G  + G  + VD+A
Sbjct: 59  MMAMNGKSVDGRQIRVDQA 77

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

>gnl|CDD|240919 cd12475, RRM2_RBMS3, RNA recognition motif 2 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 38.5 bits (89), Expect = 0.001
 Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 1/64 (1%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LN 477
           L++ NLP S+++ +++N       V+  R+  DA+G  +G G     S E     I+  N
Sbjct: 4   LYISNLPVSMDEQELENMLKPFGHVISTRILRDANGVSRGVGFARMESTEKCEVVIQHFN 63

Query: 478 GQML 481
           G+ L
Sbjct: 64  GKYL 67

This subgroup corresponds to the RRM2 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 contain 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 = 88

>gnl|CDD|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 38.3 bits (89), Expect = 0.001
 Identities = 22/82 (26%), Positives = 38/82 (46%), Gaps = 7/82 (8%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFK------GYGHVEFASVEDAH 471
           TLFV NL FS     + + F  +   V  R+ +  D +        G+G V F + E A 
Sbjct: 2   TLFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQ 61

Query: 472 KAIE-LNGQMLGNRAIRLDFAR 492
            A++ ++G +L    + + F+ 
Sbjct: 62  AALKAMDGFVLDGHTLVVKFSH 83

This subfamily corresponds to the RRM4 of MRD1which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 84

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

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 22/69 (31%), Positives = 34/69 (49%), Gaps = 1/69 (1%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAIELN 477
           LF+G L +   +  ++ +FS+  EVVD  +  D   GR +G+G V FA      K +   
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAK 60

Query: 478 GQMLGNRAI 486
             +L  R I
Sbjct: 61  PHVLDGREI 69

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

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

 Score = 37.6 bits (88), Expect = 0.001
 Identities = 20/62 (32%), Positives = 29/62 (46%), Gaps = 4/62 (6%)

Query: 521 IFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKA 580
           +FI G      E+    SL E+F   GE+    + KD  TG  +G  ++ F D  S +K 
Sbjct: 1   LFIGGLSWDTTEE----SLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKV 56

Query: 581 LE 582
           L 
Sbjct: 57  LA 58

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

 Score = 37.8 bits (88), Expect = 0.001
 Identities = 17/69 (24%), Positives = 34/69 (49%), Gaps = 8/69 (11%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LN 477
           L+V   P    ++ ++  FS    V +V++          +  VEF S+E A +A + ++
Sbjct: 2   LYVRPFPPDTSESAIREIFSPYGAVKEVKM-------ISNFAFVEFESLESAIRAKDSVH 54

Query: 478 GQMLGNRAI 486
           G++L N  +
Sbjct: 55  GKVLNNNPL 63

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

>gnl|CDD|240696 cd12250, RRM2_hnRNPR_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 7/58 (12%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAE-VVDVRLSSDADG--RFKGYGHVEFASVEDAHKA 473
           LFVG +P +  + ++   FS+V E VVDV +    D   + +G+  VE+ S    H+A
Sbjct: 4   LFVGGIPKTKTKEEILEEFSKVTEGVVDVIVYRSPDDKNKNRGFAFVEYES----HRA 57

This subfamily corresponds to the RRM2 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains); DND1 harbors only two RRMs. . Length = 82

>gnl|CDD|224429 COG1512, COG1512, Beta-propeller domains of methanol dehydrogenase type [General function prediction only]

 Score = 41.2 bits (97), Expect = 0.001
 Identities = 14/39 (35%), Positives = 14/39 (35%)

Query: 613 GRGGRSGGRDFGRSGGRDGGRFGGRGRGGRDGGRGGRGR 651
           GR  RS G       G      G  G GG  GG G  G 
Sbjct: 232 GRRRRSSGSGGSGGSGGGSSGGGFSGGGGSSGGGGASGS 270

Length = 271

>gnl|CDD|224429 COG1512, COG1512, Beta-propeller domains of methanol dehydrogenase type [General function prediction only]

 Score = 40.8 bits (96), Expect = 0.001
 Identities = 20/37 (54%), Positives = 20/37 (54%), Gaps = 4/37 (10%)

Query: 606 SGGGRSGGRGGRSGGRDFGRSGGRDGGRFGGRGRGGR 642
           SG G SGG GG S G   G SGG  GG  GG G  G 
Sbjct: 238 SGSGGSGGSGGGSSG--GGFSGG--GGSSGGGGASGS 270

Length = 271

>gnl|CDD|240703 cd12257, RRM1_RBM26_like, RNA recognition motif 1 in vertebrate RNA-binding protein 26 (RBM26) and similar proteins

 Score = 37.5 bits (88), Expect = 0.001
 Identities = 17/79 (21%), Positives = 40/79 (50%), Gaps = 10/79 (12%)

Query: 416 SKTLFVGNLP---FSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHK 472
           + TL V N+P    ++ +  +   FS+   +V+++++ + +        V+F++ E+A K
Sbjct: 1   NTTLEVRNIPPELNNITK--LNEHFSKFGTIVNIQVNYNPESAL-----VQFSTSEEAKK 53

Query: 473 AIELNGQMLGNRAIRLDFA 491
           A      +  NR I++ + 
Sbjct: 54  AYRSPEAVFNNRFIKVFWH 72

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

>gnl|CDD|241028 cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 38.0 bits (88), Expect = 0.001
 Identities = 21/62 (33%), Positives = 32/62 (51%), Gaps = 4/62 (6%)

Query: 521 IFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKA 580
           IF+ G +    E+++R    E+FG  GEI  I +P D  T   +G  ++ F + D   K 
Sbjct: 7   IFVGGLNPEATEEKIR----EYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVKKV 62

Query: 581 LE 582
           LE
Sbjct: 63  LE 64

This subgroup corresponds to the RRM2 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 80

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

 Score = 37.7 bits (88), Expect = 0.001
 Identities = 18/74 (24%), Positives = 39/74 (52%), Gaps = 3/74 (4%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LN 477
           L+VGNL  +V +  +   FS++  +   +L  +       Y  VE+     A  A++ +N
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIRE--HGNDPYAFVEYYDHRSAAAALQTMN 58

Query: 478 GQMLGNRAIRLDFA 491
           G+++  + I++++A
Sbjct: 59  GRLILGQEIKVNWA 72

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

>gnl|CDD|240842 cd12396, RRM1_Nop13p_fungi, RNA recognition motif 1 in yeast nucleolar protein 13 (Nop13p) and similar proteins

 Score = 37.9 bits (88), Expect = 0.001
 Identities = 17/57 (29%), Positives = 29/57 (50%), Gaps = 4/57 (7%)

Query: 546 CGEITRISVP----KDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDEA 598
             +ITR+ +P    K       KG AY+DFT  ++   A+ +S   + G  L++ +A
Sbjct: 29  DEQITRVHMPDSKAKRKGVKQNKGFAYVDFTSQEATKAAIALSEKILNGRKLLIKDA 85

This subfamily corresponds to the RRM1 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both, Nop12p and Nop13p, are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 85

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

 Score = 37.2 bits (87), Expect = 0.001
 Identities = 18/74 (24%), Positives = 34/74 (45%), Gaps = 5/74 (6%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNG 478
           +FVG L   + + D++ +FS+  EV DV +       F+ +  V FA  E A      + 
Sbjct: 3   VFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKP----FRAFAFVTFADPEVAQSLCGED- 57

Query: 479 QMLGNRAIRLDFAR 492
            ++   ++ +  A 
Sbjct: 58  HIIKGVSVHVSNAE 71

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

>gnl|CDD|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering time control protein FCA and similar proteins

 Score = 37.6 bits (87), Expect = 0.001
 Identities = 19/63 (30%), Positives = 38/63 (60%), Gaps = 2/63 (3%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-L 476
           LFVG++P ++ + +V+  F E   V++V +  D   G  +G   V++++ ++A +AI  L
Sbjct: 2   LFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRAL 61

Query: 477 NGQ 479
           + Q
Sbjct: 62  HNQ 64

This subgroup corresponds to the RRM1 of FCA, a gene controlling flowering time in Arabidopsis, encoding a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. . Length = 80

>gnl|CDD|241102 cd12658, RRM1_MYEF2, RNA recognition motif 1 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 37.7 bits (87), Expect = 0.001
 Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 2/72 (2%)

Query: 419 LFVGNLPFSVEQADVQNFFSE-VAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-L 476
           +F+ N+P+ ++   +++   E V EV  V L  DA+G+ +G G VEF   E   KA+E +
Sbjct: 2   VFISNIPYDMKWQAIKDLMREKVGEVTYVELFKDAEGKSRGCGVVEFKDEEFVKKALEVM 61

Query: 477 NGQMLGNRAIRL 488
           N   L  R + +
Sbjct: 62  NKYDLNGRPLNI 73

This subgroup corresponds to the RRM1 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 76

>gnl|CDD|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic translation initiation factor 4H (eIF-4H) and similar proteins

 Score = 37.3 bits (87), Expect = 0.002
 Identities = 17/43 (39%), Positives = 23/43 (53%)

Query: 556 KDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDEA 598
           +D +T   KG  Y++F D +S  +ALE  G      SL VD A
Sbjct: 34  RDKETDKFKGFCYVEFEDVESLKEALEYDGALFDDRSLRVDIA 76

This subfamily corresponds to the RRM of eIF-4H, also termed Williams-Beuren syndrome chromosomal region 1 protein, which, together with elf-4B/eIF-4G, serves as the accessory protein of RNA helicase eIF-4A. eIF-4H contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It stimulates protein synthesis by enhancing the helicase activity of eIF-4A in the initiation step of mRNA translation. . Length = 76

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

 Score = 37.6 bits (88), Expect = 0.002
 Identities = 22/80 (27%), Positives = 41/80 (51%), Gaps = 5/80 (6%)

Query: 521 IFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKA 580
           I+I G    + E  +     ++    GEI  I++ +D  TG  KG A+L + D  S   A
Sbjct: 12  IYIGGLPYELTEGDILCVFSQY----GEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILA 67

Query: 581 LE-MSGTEIGGYSLVVDEAK 599
           ++ ++G ++ G ++ VD  +
Sbjct: 68  VDNLNGIKLLGRTIRVDHVR 87

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

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

 Score = 38.0 bits (89), Expect = 0.002
 Identities = 21/84 (25%), Positives = 37/84 (44%), Gaps = 5/84 (5%)

Query: 519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFN 578
            T+F+        E+    +L E F   G+I R+ + +D  TG  KG A++++       
Sbjct: 4   LTLFVGRLSLQTTEE----TLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDAL 59

Query: 579 KALE-MSGTEIGGYSLVVDEAKQR 601
           +A        I G  + VD  ++R
Sbjct: 60  RAYRDAHKLVIDGSEIFVDFERER 83

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

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

 Score = 37.2 bits (87), Expect = 0.002
 Identities = 20/83 (24%), Positives = 41/83 (49%), Gaps = 10/83 (12%)

Query: 519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVK-----GIAYLDFTD 573
            T+F+K  +    E+    +L++HF  CG +  +++ K  D          G  +++F  
Sbjct: 1   TTLFVKNLNFKTTEE----TLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKS 56

Query: 574 ADSFNKAL-EMSGTEIGGYSLVV 595
            ++  KAL  + GT + G++L +
Sbjct: 57  KEAAQKALKRLQGTVLDGHALEL 79

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

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

 Score = 37.3 bits (87), Expect = 0.002
 Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 4/78 (5%)

Query: 521 IFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKA 580
           IF+ G    V E++     +E+F   G++    + +D+DTG  +G  ++ F    +  + 
Sbjct: 2   IFVGGLPPDVTEEE----FKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERV 57

Query: 581 LEMSGTEIGGYSLVVDEA 598
                 E+GG  + V  A
Sbjct: 58  FSAGMLELGGKQVEVKRA 75

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

>gnl|CDD|237284 PRK13108, PRK13108, prolipoprotein diacylglyceryl transferase; Reviewed

 Score = 40.7 bits (95), Expect = 0.002
 Identities = 32/176 (18%), Positives = 53/176 (30%), Gaps = 12/176 (6%)

Query: 111 EEPPKKQPVAAKNGAVAATAKKSKPDSSSSDSSDDDSDEDEVPTSIKKLPVAAAKNGPSA 170
           +E  +++P      AVA+ A    P      +  DD  E  V   + ++    A      
Sbjct: 293 DEALEREPAELAAAAVASAASAVGPVGPGEPNQPDDVAEA-VKAEVAEVTDEVAAESVVQ 351

Query: 171 PQKKKDDSSDSSDEESDESSDEDDKSTKAIPQPKKLPASTAKKGTVAATKKSTGSSDDDS 230
                       D ES  + +E  ++     QP  L         V A   S    +  +
Sbjct: 352 --------VADRDGESTPAVEETSEADIEREQPGDLAGQAPAAHQVDAEAASAAPEEPAA 403

Query: 231 SSSEDSSESEE---DNGAPAKVTSEAKKLPAVKNVPAPAAKKKTESSDSSDEESED 283
            +SE   E+E    +  AP    ++  +L        PA        D        
Sbjct: 404 LASEAHDETEPEVPEKAAPIPDPAKPDELAVAGPGDDPAEPDGIRRQDDFSSRRRR 459

Length = 460

>gnl|CDD|218752 pfam05793, TFIIF_alpha, Transcription initiation factor IIF, alpha subunit (TFIIF-alpha)

 Score = 41.1 bits (96), Expect = 0.002
 Identities = 36/227 (15%), Positives = 67/227 (29%), Gaps = 12/227 (5%)

Query: 199 AIPQPKKLPASTAKKGTVAATKKSTGSSDDDSSSSEDSSESEEDNGAPAKVTSEAKKLPA 258
           A     +        G      K      DD    ++S +  ED         + K    
Sbjct: 192 AFGDEDEETEGEKGGGGRGKDLKIKDLEGDDEDDGDESDKGGEDGDEEKSKKKKKKLAKN 251

Query: 259 VKNVPAPAAKKKTESSDSSDEESEDSSDEDEEPTHVTKATPVKKLSAVVTKNKVESSSSS 318
            K +      K+    D+ + +S+D  DE  E  +++ ++     S    + + +  S  
Sbjct: 252 KKKLDDDKKGKRGGDDDADEYDSDDGDDEGREEDYISDSSA----SGNDPEEREDKLSPE 307

Query: 319 DESESEEEKPPAKMDVDSSSEEESSDEEPQKKKDVKPNTKALKKESSSDEEDSDDEDEGE 378
             ++ E E+     + +    EE      + KK  K   K    +    +   D +D   
Sbjct: 308 IPAKPEIEQDEDSEESEEEKNEEEGGLSKKGKKLKKLKGKKNGLDKDDSDSGDDSDDSDI 367

Query: 379 EEEAS--------KTPKKNVTDVKMVDAESGKKAAQTPFTPQSGGSK 417
           + E S        +   K    V    +  G      P        K
Sbjct: 368 DGEDSVSLVTAKKQKEPKKEEPVDSNPSSPGNSGPARPSPESKDKGK 414

Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) or RNA polymerase II-associating protein 74 (RAP74) is the large subunit of transcription factor IIF (TFIIF), which is essential for accurate initiation and stimulates elongation by RNA polymerase II. Length = 528

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

 Score = 37.3 bits (86), Expect = 0.002
 Identities = 20/69 (28%), Positives = 33/69 (47%), Gaps = 1/69 (1%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAIELN 477
           +F+G L +   + D+  + S   EV+D  + +D   GR +G+G V F       K +EL 
Sbjct: 2   MFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELK 61

Query: 478 GQMLGNRAI 486
              L  + I
Sbjct: 62  EHKLDGKLI 70

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

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

 Score = 36.8 bits (86), Expect = 0.002
 Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 7/74 (9%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLS-SDADGRFKGYGHVEFASVEDAHKAI-E 475
           TL V NL   +   ++++ FS+  EV D+R +      +F     VEF  +  A  A+  
Sbjct: 3   TLLVFNLDSPISDQELRSLFSQFGEVKDIRETPLRPSQKF-----VEFYDIRAAEAALDA 57

Query: 476 LNGQMLGNRAIRLD 489
           LNG+      +++ 
Sbjct: 58  LNGRPFLGGRLKVK 71

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

>gnl|CDD|217503 pfam03344, Daxx, Daxx Family

 Score = 41.1 bits (96), Expect = 0.002
 Identities = 38/203 (18%), Positives = 70/203 (34%), Gaps = 4/203 (1%)

Query: 179 SDSSDEESDESSDEDDKSTKAIPQPK-KLPASTAKKGTVAATKKSTGSSDDDSSSSEDSS 237
           S  + ++ D   +E  K  +   Q      +  +K  + +    S  S + +   S +  
Sbjct: 389 SKYAMKQDDTEEEERRKRQERERQGTSSRSSDPSKASSTSGESPSMASQESEEEESVEEE 448

Query: 238 ESEEDNGAPAKVTSEAKKLPAVKNVPAPAAKKKTESSDSSDEESEDSSDEDEEPTHVTKA 297
           E EE+     +  SE ++    +      A   +E       E +   +E EE      +
Sbjct: 449 EEEEEEEEEEEQESEEEEGEDEEEEEEVEADNGSEEEMEGSSEGDGDGEEPEEDAERRNS 508

Query: 298 TPVKKLSAVVTKNKVESSSSSDESESEEEKPPAKMDVDSSSEEESSDEEPQKKKDVKPNT 357
                +S +    +   SS   ES  EE   P  MD +S    E SDEE   ++    + 
Sbjct: 509 EM-AGISRMSEGQQPRGSSVQPESPQEEPLQPESMDAESVG--EESDEELLAEESPLSSH 565

Query: 358 KALKKESSSDEEDSDDEDEGEEE 380
             L+  ++  E       +    
Sbjct: 566 TELEGVATPVETKISSSRKLPPP 588

The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis, but precise role played by Daxx remains to be determined. Daxx forms a complex with Axin. Length = 715

>gnl|CDD|240898 cd12452, RRM_ARP_like, RNA recognition motif in yeast asparagine-rich protein (ARP) and similar proteins

 Score = 37.5 bits (87), Expect = 0.002
 Identities = 23/80 (28%), Positives = 38/80 (47%), Gaps = 13/80 (16%)

Query: 417 KTLFVGNLPFSVEQADVQNFFSE----------VAEVVDVRLSSDADGRFKGYGHVEFAS 466
           K L++ NLP    Q +++++F++          +    +    S  D      G   F S
Sbjct: 1   KVLYISNLPPDTTQLELESWFTQYGVRPVAFWTLKTPDEDAYVSSKD---SISGFAVFQS 57

Query: 467 VEDAHKAIELNGQMLGNRAI 486
            E+A +A+ LNG+ LG RAI
Sbjct: 58  HEEAMEALALNGRCLGERAI 77

This subfamily corresponds to the RRM of ARP, also termed NRP1, encoded by Saccharomyces cerevisiae YDL167C. Although its exact biological function remains unclear, ARP contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), two Ran-binding protein zinc fingers (zf-RanBP), and an asparagine-rich region. It may possess RNA-binding and zinc ion binding activities. Additional research had indicated that ARP may function as a factor involved in the stress response. . Length = 88

>gnl|CDD|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)

 Score = 37.2 bits (86), Expect = 0.002
 Identities = 23/73 (31%), Positives = 35/73 (47%), Gaps = 1/73 (1%)

Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE- 475
           +TLFVGNL   V +  +   F +   V+ V++  D DG+ K +  V F        A+  
Sbjct: 2   RTLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDGKPKQFAFVNFKHEVSVPYAMNL 61

Query: 476 LNGQMLGNRAIRL 488
           LNG  L  R + +
Sbjct: 62  LNGIKLYGRPLNI 74

This subfamily corresponds to the RRM of RBM7, a ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM7 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. . Length = 75

>gnl|CDD|147601 pfam05505, Ebola_NP, Ebola nucleoprotein

 Score = 41.1 bits (96), Expect = 0.002
 Identities = 45/253 (17%), Positives = 84/253 (33%), Gaps = 10/253 (3%)

Query: 136 DSSSSDSSDDDSDEDEVPTSIKKLPVAAAKNGPSAPQKKKDDSSDSSDEESDESSDEDDK 195
           D       DDD D D   T+I    V       +      D    ++D+    + DEDD 
Sbjct: 417 DDVQPRPMDDDPD-DSRDTTIPPGVVDPIDGESTEYSSYSDSFVGTNDDLVLFNLDEDDD 475

Query: 196 STKAIPQPKKLPASTAKKGTVAATKKSTGSSDDDSSSSEDSSES----EEDNGAPAKVTS 251
            +K IP+          +      +   GS    + +S+D + +    E+++  P   TS
Sbjct: 476 DSKPIPEQAASTYGQTSRERQGIPEPPPGSHQPGNRASQDLNNNNQKQEDESTNPIGKTS 535

Query: 252 -EAKKLPAVKNVPAPAAKKKTESSDSSDEESED----SSDEDEEPTHVTKATPVKKLSAV 306
              ++L  V+    P  +   + S     ES+D     +++  + T V    PV +    
Sbjct: 536 LRYQELTPVQEEDEPEDQTDDDDSSLPPLESDDDPGSDNEQGVDLTEVAPPAPVYRDEKE 595

Query: 307 VTKNKVESSSSSDESESEEEKPPAKMDVDSSSEEESSDEEPQKKKDVKPNTKALKKESSS 366
             +    + +  D + S        +  +S       +      +   P           
Sbjct: 596 QDEIPHPAQNPQDPTGSIGNVDSDILRSNSKPSAPLEETYMHLLRTQGPFDAINYYHMMK 655

Query: 367 DEEDSDDEDEGEE 379
           DE       +G+E
Sbjct: 656 DEPVRFSTKDGKE 668

This family consists of Ebola and Marburg virus nucleoproteins. These proteins are responsible for encapsidation of genomic RNA. It has been found that nucleoprotein DNA vaccines can offer protection from the virus. Length = 717

>gnl|CDD|240910 cd12464, RRM_G3BP2, RNA recognition motif in ras GTPase-activating protein-binding protein 2 (G3BP2) and similar proteins

 Score = 37.3 bits (86), Expect = 0.002
 Identities = 18/60 (30%), Positives = 34/60 (56%), Gaps = 1/60 (1%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAI 474
           S  LFVGNLP  +++++++ FF     VV++R+++    G+   +G V F   E   + +
Sbjct: 5   SHQLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDDSEPVQRIL 64

This subgroup corresponds to the RRM of G3BP2, also termed GAP SH3 domain-binding protein 2, a cytoplasmic protein that interacts with both IkappaBalpha and IkappaBalpha/NF-kappaB complexes, indicating that G3BP2 may play a role in the control of nucleocytoplasmic distribution of IkappaBalpha and cytoplasmic anchoring of the IkappaBalpha/NF-kappaB complex. G3BP2 contains an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing five PXXP motifs, an RNA recognition motif (RRM domain), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). It binds to the SH3 domain of RasGAP, a multi-functional protein controlling Ras activity, through its N-terminal NTF2-like domain. The acidic domain is sufficient for the interaction of G3BP2 with the IkappaBalpha cytoplasmic retention sequence. Furthermore, G3BP2 might influence stability or translational efficiency of particular mRNAs by binding to RNA-containing structures within the cytoplasm through its RNA-binding domain. Length = 83

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

 Score = 37.2 bits (86), Expect = 0.002
 Identities = 19/62 (30%), Positives = 30/62 (48%), Gaps = 2/62 (3%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAIE-L 476
           L+V NLP  + + +++  F     +V   L  D + G  +G   V +   E+A  AI  L
Sbjct: 3   LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62

Query: 477 NG 478
           NG
Sbjct: 63  NG 64

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

>gnl|CDD|241039 cd12595, RRM1_SRSF5, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 5 (SRSF5)

 Score = 36.9 bits (85), Expect = 0.002
 Identities = 24/75 (32%), Positives = 39/75 (52%), Gaps = 8/75 (10%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI-ELN 477
           +F+G L  +  + DV+ FF     + D+ L        +G+G VEF    DA  A+ EL+
Sbjct: 2   VFIGRLNPAAREKDVERFFKGYGRIRDIDLK-------RGFGFVEFDDPRDADDAVYELD 54

Query: 478 GQMLGNRAIRLDFAR 492
           G+ L N  + ++ AR
Sbjct: 55  GKELCNERVTIEHAR 69

This subgroup corresponds to the RRM1 of SRSF5, also termed delayed-early protein HRS, or pre-mRNA-splicing factor SRp40, or splicing factor, arginine/serine-rich 5 (SFRS5). SFSF5 is an essential splicing regulatory serine/arginine (SR) protein that regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and it is necessary for enhancer activation. SRSF5 also functions as a factor required for insulin-regulated splice site selection for protein kinase C (PKC) betaII mRNA. It is involved in the regulation of PKCbetaII exon inclusion by insulin via its increased phosphorylation by a phosphatidylinositol 3-kinase (PI 3-kinase) signaling pathway. Moreover, SRSF5 can regulate alternative splicing in exon 9 of glucocorticoid receptor pre-mRNA in a dose-dependent manner. SRSF5 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. The specific RNA binding by SRSF5 requires the phosphorylation of its SR domain. . Length = 70

>gnl|CDD|241101 cd12657, RRM1_hnRNPM, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 36.9 bits (85), Expect = 0.002
 Identities = 26/71 (36%), Positives = 40/71 (56%), Gaps = 2/71 (2%)

Query: 420 FVGNLPFSVEQADVQNFFSE-VAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LN 477
           F+ N+PF V+   +++   E V EV  V L  DA+G+ +G   VEF   E   KA+E LN
Sbjct: 3   FISNIPFDVKWQSLKDLVKEKVGEVTYVELLMDAEGKSRGCAVVEFKMEESMKKAVEVLN 62

Query: 478 GQMLGNRAIRL 488
             +L  R +++
Sbjct: 63  KHVLNGRPLKV 73

This subgroup corresponds to the RRM1 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 76

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 40.7 bits (95), Expect = 0.003
 Identities = 44/263 (16%), Positives = 98/263 (37%), Gaps = 16/263 (6%)

Query: 90  GKAAKPPVKESSSEEEDSSSDEEPPKKQPVAAKNGAVAATAKKSKPDSSSSDSSDDDSDE 149
           G+  + P +      E+S  + E   +     +N +      + K +       + + + 
Sbjct: 646 GEEGERPTEAEGENGEESGGEAEQEGETETKGENESEGEIPAERKGE----QEGEGEIEA 701

Query: 150 DEVPTSIKKLPVAAAKNGPSAPQKKKDDSSDSSDEESDESSDEDDKSTKAIPQPKKLPAS 209
            E     +         G +  +  +D+    + EE +E  DE +   +   + +     
Sbjct: 702 KEADHKGETEAEEVEHEGETEAEGTEDEGEIETGEEGEEVEDEGEGEAEGKHEVE----- 756

Query: 210 TAKKGTVAATKKSTGSSDDDSSSSEDSSESEEDNGAPAKVTSEAKKLPAVKNVPAPAAKK 269
                T    K++    + ++   ED  E E   G   ++  +      V++     A +
Sbjct: 757 -----TEGDRKETEHEGETEAEGKEDEDEGEIQAGEDGEMKGDEGAEGKVEHEGETEAGE 811

Query: 270 KTESSDSSDEESEDSSDEDEEPTHVTKATPVKKLSAVVTKNKVESSSSSDESESEEEKPP 329
           K E    S+ +++D+  +DE       A    +  A   +  V+    SD  +SEEE+  
Sbjct: 812 KDEHEGQSETQADDTEVKDETGEQELNAE--NQGEAKQDEKGVDGGGGSDGGDSEEEEEE 869

Query: 330 AKMDVDSSSEEESSDEEPQKKKD 352
            + + +   EEE  +EE ++ ++
Sbjct: 870 EEEEEEEEEEEEEEEEEEEENEE 892

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

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

 Score = 36.5 bits (85), Expect = 0.003
 Identities = 17/62 (27%), Positives = 31/62 (50%), Gaps = 4/62 (6%)

Query: 520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNK 579
            +F+     +VG  +++    E+F   G++   +VP D +TG  KG  ++ F+  D    
Sbjct: 1   KLFVGNLPWTVGSKELK----EYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLEN 56

Query: 580 AL 581
           AL
Sbjct: 57  AL 58

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|218752 pfam05793, TFIIF_alpha, Transcription initiation factor IIF, alpha subunit (TFIIF-alpha)

 Score = 40.3 bits (94), Expect = 0.003
 Identities = 49/256 (19%), Positives = 85/256 (33%), Gaps = 2/256 (0%)

Query: 164 AKNGPSAPQKKKDDSSDSSDEESDESSDEDDKSTKAIPQPKKLPASTAKKGTVAATKKST 223
              G     K KD   D  D+  +     +D   +   + KK  A   KK       K  
Sbjct: 205 GGGGRGKDLKIKDLEGDDEDDGDESDKGGEDGDEEKSKKKKKKLAKNKKKLDDDKKGKRG 264

Query: 224 GSSDDDSSSSEDSSESEEDNGAPAKVTSEAKKLPAVKNVPAPA-AKKKTESSDSSDEESE 282
           G  D D   S+D  +   +    +  ++        ++  +P    K     D   EESE
Sbjct: 265 GDDDADEYDSDDGDDEGREEDYISDSSASGNDPEEREDKLSPEIPAKPEIEQDEDSEESE 324

Query: 283 DSSDEDEEPTHVTKATPVKKLSAVVTKNKVESSSSSDESESEEEKPPAKMDVDSSSEEES 342
           +  +E+E           K        +K +S S  D  +S+ +   +   V +  ++E 
Sbjct: 325 EEKNEEEGGLSKKGKKLKKLKGKKNGLDKDDSDSGDDSDDSDIDGEDSVSLVTAKKQKEP 384

Query: 343 SDEEPQKKKDVKPNTKALKKESSSDEEDSDDEDEGEEEEAS-KTPKKNVTDVKMVDAESG 401
             EEP       P      + S   ++    +   E  ++    P K +       + SG
Sbjct: 385 KKEEPVDSNPSSPGNSGPARPSPESKDKGKRKAANEVSKSPASVPAKKLKTENAPKSSSG 444

Query: 402 KKAAQTPFTPQSGGSK 417
           K   QT    +S  + 
Sbjct: 445 KSTPQTFSGSKSSSNA 460

Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) or RNA polymerase II-associating protein 74 (RAP74) is the large subunit of transcription factor IIF (TFIIF), which is essential for accurate initiation and stimulates elongation by RNA polymerase II. Length = 528

>gnl|CDD|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 36.9 bits (85), Expect = 0.003
 Identities = 18/71 (25%), Positives = 40/71 (56%), Gaps = 7/71 (9%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIEL-- 476
           +F+G LP  + + ++     ++ ++ ++R+  D +G  +GY  V F++ ++A  AI+   
Sbjct: 4   IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIKQLN 63

Query: 477 -----NGQMLG 482
                NG++LG
Sbjct: 64  NYEIRNGRLLG 74

This subgroup corresponds to the RRM1 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. It contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1. . Length = 78

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

 Score = 37.0 bits (85), Expect = 0.003
 Identities = 29/80 (36%), Positives = 43/80 (53%), Gaps = 3/80 (3%)

Query: 416 SKT-LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKA 473
           SKT L V  LP ++ Q + ++ F  + E+   +L  D   G+  GYG V +    DA KA
Sbjct: 2   SKTNLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKA 61

Query: 474 IE-LNGQMLGNRAIRLDFAR 492
           I  LNG  L  + I++ +AR
Sbjct: 62  INTLNGLKLQTKTIKVSYAR 81

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

>gnl|CDD|240806 cd12360, RRM_cwf2, RNA recognition motif in yeast pre-mRNA-splicing factor Cwc2 and similar proteins

 Score = 36.9 bits (86), Expect = 0.003
 Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 8/54 (14%)

Query: 520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISV-PKDYDTGSVKGIAYLDFT 572
           T+++ G  +     Q+   L  HFG  G+I  I V P        KGIA++ + 
Sbjct: 3   TLYVGGIKAGSALKQIEEILRRHFGEWGDIEDIRVLPS-------KGIAFVRYK 49

This subfamily corresponds to the RRM of yeast protein Cwc2, also termed Complexed with CEF1 protein 2, or PRP19-associated complex protein 40 (Ntc40), or synthetic lethal with CLF1 protein 3, one of the components of the Prp19-associated complex [nineteen complex (NTC)] that can bind to RNA. NTC is composed of the scaffold protein Prp19 and a number of associated splicing factors, and plays a crucial role in intron removal during premature mRNA splicing in eukaryotes. Cwc2 functions as an RNA-binding protein that can bind both small nuclear RNAs (snRNAs) and pre-mRNA in vitro. It interacts directly with the U6 snRNA to link the NTC to the spliceosome during pre-mRNA splicing. In the N-terminal half, Cwc2 contains a CCCH-type zinc finger (ZnF domain), a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and an intervening loop, also termed RNA-binding loop or RB loop, between ZnF and RRM, all of which are necessary and sufficient for RNA binding. The ZnF is also responsible for mediating protein-protein interaction. The C-terminal flexible region of Cwc2 interacts with the WD40 domain of Prp19. Length = 78

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

 Score = 36.5 bits (85), Expect = 0.003
 Identities = 19/71 (26%), Positives = 32/71 (45%), Gaps = 12/71 (16%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-- 475
           TL+VG L   V + D+++ F +  E+  + +        +    V F + E A KA E  
Sbjct: 3   TLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPR-----QQCAFVTFTTREAAEKAAERL 57

Query: 476 -----LNGQML 481
                +NG+ L
Sbjct: 58  FNKLIINGRRL 68

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

>gnl|CDD|112562 pfam03753, HHV6-IE, Human herpesvirus 6 immediate early protein

 Score = 40.4 bits (94), Expect = 0.003
 Identities = 59/279 (21%), Positives = 106/279 (37%), Gaps = 24/279 (8%)

Query: 19  KREAEDAIEKLVSAKKQKGNDGVAQAVKKAKVEAKT-QKKNKNDETSSSSSEEDSSDSEE 77
           K   +   + +V+    K N+    ++   K   +T Q KN  D+ + + +    S +++
Sbjct: 476 KSLLDTQADSVVTQTVSKNNEAFNMSLYNLKRNEETYQDKNSRDKKTDNQAGPTFSRTDK 535

Query: 78  EQKVKAVVTNKGGKAAKPPVKESSSEEEDSSSDEEPPKKQPVAAKNGAVAATAKKSKPDS 137
           +    A +  +     K    +    E  + +D       P+ ++  +       S P  
Sbjct: 536 KTNSPAGILMERSIFNKDTQDKEQYFELFTMTDGT--LDNPLISEMLSFGYETDHSAPYE 593

Query: 138 SSSDSSDDDSDEDEVPTSIKKLPVAAAKNGPSAPQKKKDDSSDSSDEESDESSDEDDKST 197
           S SD++D+      V +  +   +       + P  K   S  S  E +   +       
Sbjct: 594 SESDNNDEIDYIASVDSGNRTNNIHMNNTNENTPFSK---SGKSPPEVTPSKTFYKRDKK 650

Query: 198 KAIPQPKKLPASTAKKGTVA-----ATKKSTGSSDDDSSSSEDSSESE-EDNGAPAKVTS 251
           K I   +K+   TAK+ TV      + K  + S   D++    SSESE E++G      S
Sbjct: 651 KDISTNRKVKKRTAKRKTVGYKTDKSKKIKSDSLPTDTNVIVISSESEDEEDGFNIIKKS 710

Query: 252 EAKKLPAVKNVPAPAAKKKTESSDSSDEESEDSSDEDEE 290
           + KK            K K+E    S  ES+D + ED E
Sbjct: 711 QLKK------------KIKSELKSESSSESDDCTSEDNE 737

The proteins in this family are poorly characterized, but an investigation has indicated that the immediate early protein is required the down-regulation of MHC class I expression in dendritic cells. Human herpesvirus 6 immediate early protein is also referred to as U90. Length = 993

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

 Score = 36.5 bits (85), Expect = 0.003
 Identities = 17/70 (24%), Positives = 33/70 (47%), Gaps = 3/70 (4%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELN 477
           T+ V NLP    +  ++ FF +  E+ +V++     G       +EF + ++A  A+  +
Sbjct: 2   TVKVKNLPKDTTENKIRQFFKDCGEIREVKIVESEGGLV---AVIEFETEDEALAALTKD 58

Query: 478 GQMLGNRAIR 487
            + LG   I 
Sbjct: 59  HKRLGGNEIS 68

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

>gnl|CDD|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 = 0.004
 Identities = 22/79 (27%), Positives = 33/79 (41%), Gaps = 4/79 (5%)

Query: 520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNK 579
            IF+ G    +       SL ++F   GEI    V  D  TG  +G  ++ F D +S  +
Sbjct: 2   KIFVGG----LPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAER 57

Query: 580 ALEMSGTEIGGYSLVVDEA 598
           A +     I G    V+ A
Sbjct: 58  ACKDPNPIIDGRKANVNLA 76

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

>gnl|CDD|240981 cd12537, RRM1_RBM23, RNA recognition motif 1 in vertebrate probable RNA-binding protein 23 (RBM23)

 Score = 36.6 bits (84), Expect = 0.004
 Identities = 16/61 (26%), Positives = 35/61 (57%)

Query: 539 LEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDEA 598
           LE+ F + G++  + +  D ++   KGIAY++F +  S   A+ ++G  + G  ++V  +
Sbjct: 18  LEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQAS 77

Query: 599 K 599
           +
Sbjct: 78  Q 78

This subgroup corresponds to the RRM1 of RBM23, also termed RNA-binding region-containing protein 4, or splicing factor SF2, which may function as a pre-mRNA splicing factor. It shows high sequence homology to RNA-binding protein 39 (RBM39 or 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). In contrast to RBM39, RBM23 contains only two RRMs. . Length = 85

>gnl|CDD|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding protein 25 and similar proteins

 Score = 36.4 bits (85), Expect = 0.004
 Identities = 24/78 (30%), Positives = 39/78 (50%), Gaps = 5/78 (6%)

Query: 519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFN 578
            T+F+      V +D +R  LE     CG++      KD  TG +K   + +F D +   
Sbjct: 1   TTVFVGNIPEGVSDDFIRKLLE----KCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGAL 56

Query: 579 KALE-MSGTEIGGYSLVV 595
           +AL  ++G E+GG  L+V
Sbjct: 57  RALRLLNGLELGGKKLLV 74

This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor. . Length = 84

>gnl|CDD|233044 TIGR00600, rad2, DNA excision repair protein (rad2)

 Score = 40.3 bits (94), Expect = 0.004
 Identities = 78/422 (18%), Positives = 134/422 (31%), Gaps = 77/422 (18%)

Query: 36  KGNDGVAQAVKKAKVEAKTQKKNKNDETSSSSSEEDSSDSEEEQKVKAVVTNKGGKAAKP 95
           KG  G   AVK    + ++     +   S+S   + S   + + + +++V  +       
Sbjct: 295 KGIQG-KTAVKAVDSDDESLPSLSSQLDSNSEDLKSSPWEKLKPESESIVEAEPPSPRTL 353

Query: 96  PVKESS-SEEEDSSSDEEPPKKQPVAAKNGAVAA-------------TAKKSKPDSSSSD 141
             K+++ SE     SDE   ++Q +   N A                 A     D   S 
Sbjct: 354 LAKQAAMSESSSEDSDESEWERQELKRNNVAFVDDGSLSPRTLQAIGQALDDDEDKKVSA 413

Query: 142 SSDD------------------DSDEDEVPTSIKKLPVAAAKNGPSAPQKKKDDSSDSSD 183
           SSDD                  + D+ +     + +P+ AA    S   K +  +S    
Sbjct: 414 SSDDQASPSKKTKMLLISRIEVEDDDLDYLDQGEGIPLMAALQLSSVNSKPEAVASTKIA 473

Query: 184 EESDESSDEDDKS---------TKAIPQPKKL-PASTAKKGTVAATKKSTGSSDDDSSSS 233
            E   S  E             T   P P +        + ++  T K   S     S  
Sbjct: 474 REVTSSGHEAVPKAVQSLLLGATNDSPIPSEFTILDRKSELSIERTVKPVSSEFGLPSQR 533

Query: 234 EDSSESEEDNGAPAKVTSEAKKLPAVKNVPAPAAKKKTESSDSSDEESEDS--------- 284
           ED      +     +  S+  +    +N  +P   K  ES+ SSD E+E S         
Sbjct: 534 EDKLAIPTEGTQNLQGISDHPEQFEFQNELSPLETKNNESNLSSDAETEGSPNPEMPSWS 593

Query: 285 ----SDEDEEPTHVTKATPVKKL-----SAVVTKNKVESS---------------SSSDE 320
                 E  +    T  +  K++     + + T N  ES+               S  +E
Sbjct: 594 SVTVPSEALDNYETTNPSNAKEVRNFAETGIQTTNVGESADLLLISNPMEVEPMESEKEE 653

Query: 321 SESEEEKPPAKMDVDSSSEEESSDEEPQK-KKDVKPNTKALKKESSSDEEDSDDEDEGEE 379
           SES+           +   +  S  +P    ++   N  A  +     E +    DE EE
Sbjct: 654 SESDGSFIEVDSVSSTLELQVPSKSQPTDESEENAENKVASIEGEHRKEIEDLLFDESEE 713

Query: 380 EE 381
           + 
Sbjct: 714 DN 715

All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 1034

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

 Score = 35.9 bits (83), Expect = 0.004
 Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 9/77 (11%)

Query: 418 TLFVGNL-PFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE- 475
           TLFV    P +  + D++  F     +V   +        K +  VEF   EDA KA+E 
Sbjct: 1   TLFVVGFDPGTTREEDIEKLFEPFGPLVRCDIR-------KTFAFVEFEDSEDATKALEA 53

Query: 476 LNGQMLGNRAIRLDFAR 492
           L+G  +    + ++F +
Sbjct: 54  LHGSRIDGSVLTVEFVK 70

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

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

 Score = 36.5 bits (85), Expect = 0.004
 Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 2/61 (3%)

Query: 427 SVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAIE-LNGQMLGNR 484
           SV + D++  F+   E+ D+ +  D      KG  +V+FA    A +A+E +NG+ LG  
Sbjct: 13  SVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLGGD 72

Query: 485 A 485
            
Sbjct: 73  T 73

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

>gnl|CDD|241111 cd12667, RRM3_RAVER1, RNA recognition motif 3 in vertebrate ribonucleoprotein PTB-binding 1 (raver-1)

 Score = 36.8 bits (85), Expect = 0.004
 Identities = 24/77 (31%), Positives = 38/77 (49%), Gaps = 2/77 (2%)

Query: 416 SKTLFVGNLPFSVEQA-DVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI 474
           SK L V  LP S+    D++  FS++      +L+   DG+ KG+  +E+ S E A    
Sbjct: 2   SKCLCVDQLPPSLCDVGDLREAFSKIHAPTFCQLACGQDGQLKGFAVLEYESAEMAEMVQ 61

Query: 475 EL-NGQMLGNRAIRLDF 490
           +  +G  L    IR+ F
Sbjct: 62  QQADGLSLAGSHIRVSF 78

This subgroup corresponds to the RRM3 of raver-1, 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-1 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB through the PTB-binding motifs at its C-terminal half, and binds to other partners, such as RNA having the sequence UCAUGCAGUCUG, through its N-terminal RRMs. Interestingly, the 12-nucleotide RNA having the sequence UCAUGCAGUCUG with micromolar affinity is found in vinculin mRNA. Additional research indicates that the RRM1 of raver-1 directs its interaction with the tail domain of activated vinculin. Then the raver1/vinculin tail (Vt) complex binds to vinculin mRNA, which is permissive for vinculin binding to F-actin. . Length = 92

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

 Score = 36.5 bits (85), Expect = 0.004
 Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 4/77 (5%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAIE-L 476
           L+V  LP ++ Q +++  FS    ++  R+  D   G  +G G + F    +A +AI+ L
Sbjct: 3   LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62

Query: 477 NGQML--GNRAIRLDFA 491
           NG +       I + FA
Sbjct: 63  NGTIPPGATEPITVKFA 79

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|241044 cd12600, RRM2_SRSF4_like, RNA recognition motif 2 in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins

 Score = 36.2 bits (84), Expect = 0.004
 Identities = 26/72 (36%), Positives = 36/72 (50%), Gaps = 5/72 (6%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-L 476
            L V NL   V   D+++F  +  EV      +DA  +    G VEFA+  D  +AIE L
Sbjct: 2   RLIVENLSSRVSWQDLKDFMRKAGEVT----YADAHKQRPNEGVVEFATYSDMKRAIEKL 57

Query: 477 NGQMLGNRAIRL 488
           +G  L  R I+L
Sbjct: 58  DGTELNGRKIKL 69

This subfamily corresponds to the RRM2 of three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an important role in both, constitutive and alternative, splicing of many pre-mRNAs. It can shuttle between the nucleus and cytoplasm. SRSF5 regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and is essential for enhancer activation. SRSF6 preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. Members in this family contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 72

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

 Score = 36.3 bits (84), Expect = 0.004
 Identities = 20/71 (28%), Positives = 32/71 (45%), Gaps = 4/71 (5%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-L 476
           T++ G  P S   +DV+  F     V  V + S      + +  + F ++E A  AIE L
Sbjct: 1   TVYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSR---TVQPHAFITFENLEAAQLAIETL 57

Query: 477 NGQMLGNRAIR 487
           NG  +    I+
Sbjct: 58  NGASVDGNCIK 68

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

>gnl|CDD|240956 cd12512, RRM3_RBM12, RNA recognition motif 3 in RNA-binding protein 12 (RBM12) and similar proteins

 Score = 37.2 bits (86), Expect = 0.004
 Identities = 21/71 (29%), Positives = 39/71 (54%), Gaps = 1/71 (1%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVD-VRLSSDADGRFKGYGHVEFASVEDAHKAIELN 477
           +++  LP+  E   V +FF ++  V D + ++   +G+  G G VEF +  D   A+  +
Sbjct: 12  VYLKGLPYEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRH 71

Query: 478 GQMLGNRAIRL 488
            Q +GNR I++
Sbjct: 72  KQYMGNRFIQV 82

This subfamily corresponds to the RRM3 of RBM12. RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two proline-rich regions, and several putative transmembrane domains. The biological role of RBM12 remains unclear. . Length = 101

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

 Score = 36.5 bits (84), Expect = 0.004
 Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 1/69 (1%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAIELN 477
           +FVG L +   + D++++F++  EV D  +  D + GR +G+G + F       K +E  
Sbjct: 2   MFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQK 61

Query: 478 GQMLGNRAI 486
              L  R I
Sbjct: 62  EHRLDGRLI 70

This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 75

>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional

 Score = 39.8 bits (93), Expect = 0.004
 Identities = 20/67 (29%), Positives = 27/67 (40%), Gaps = 4/67 (5%)

Query: 599 KQRGDFGSGGGRSGGRGGRSGGRDFGRSGGRDGGRFGGRGRGGRDGGR--GGRGRGRGTP 656
           +QRG  G G G+ GGRG + G    G  G +            R G     G  + R  P
Sbjct: 392 QQRG--GGGRGQGGGRGQQQGQPRRGEGGAKSASAKPAEKPSRRLGDAKPAGEQQRRRRP 449

Query: 657 NRPSLAA 663
            +P+ A 
Sbjct: 450 RKPAAAQ 456

Length = 456

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

 Score = 36.3 bits (84), Expect = 0.004
 Identities = 17/53 (32%), Positives = 25/53 (47%)

Query: 538 SLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGG 590
            L E+F   GEI    V +D  T   +G  ++ F+D  S +K L     E+ G
Sbjct: 14  GLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQGPHELDG 66

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

>gnl|CDD|241056 cd12612, RRM2_SECp43, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 36.1 bits (84), Expect = 0.004
 Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 3/77 (3%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEV-AEVVDVRLSSDADGRFKGYGHVEFASVEDAHKA-IE 475
           +LFVG+L   V+   +  FFS+        ++  D +G  +GYG V F+   +  +A  E
Sbjct: 3   SLFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLDQNGNSRGYGFVRFSDESEQKRALTE 62

Query: 476 LNGQM-LGNRAIRLDFA 491
           + G   LG + IR+  A
Sbjct: 63  MQGASGLGGKPIRVSLA 79

This subgroup corresponds to the RRM2 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. . Length = 82

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	675
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	100.0
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.97
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.96
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.96
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.95
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.95
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.95
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.94
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.94
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.93
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.93
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.92
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.92
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.92
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.92
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.9
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.9
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.9
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.9
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.9
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.89
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.89
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.88
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.88
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.86
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.85
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.82
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.82
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.81
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.77
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.77
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.76
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.76
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.76
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.76
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.75
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.74
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.72
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.7
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.69
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.68
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.66
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.63
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.6
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.59
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.56
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.55
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.55
KOG4210	285	consensus Nuclear localization sequence binding pr	99.53
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.52
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.52
PLN03120	260	nucleic acid binding protein; Provisional	99.52
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.51
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.5
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.49
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.49
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.49
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.49
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.48
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.47
KOG0122	270	consensus Translation initiation factor 3, subunit	99.46
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.46
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.46
PLN03121	243	nucleic acid binding protein; Provisional	99.45
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.43
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.42
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.42
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.39
PLN03213	759	repressor of silencing 3; Provisional	99.39
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.38
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.38
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.38
smart00362	72	RRM_2 RNA recognition motif.	99.36
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	99.36
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	99.34
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	99.33
KOG0122	270	consensus Translation initiation factor 3, subunit	99.33
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.32
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	99.3
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.3
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.29
PF03546	519	Treacle: Treacher Collins syndrome protein Treacle	99.29
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.28
smart00360	71	RRM RNA recognition motif.	99.26
PLN03120	260	nucleic acid binding protein; Provisional	99.26
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.26
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.24
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.22
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.21
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.21
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.17
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	99.17
PF03546	519	Treacle: Treacher Collins syndrome protein Treacle	99.17
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.17
PLN03213	759	repressor of silencing 3; Provisional	99.16
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.16
PLN03121	243	nucleic acid binding protein; Provisional	99.14
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.14
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.14
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.14
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	99.08
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.06
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.05
smart00362	72	RRM_2 RNA recognition motif.	99.05
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.03
smart00361	70	RRM_1 RNA recognition motif.	99.03
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.02
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	99.0
smart00361	70	RRM_1 RNA recognition motif.	98.99
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	98.99
smart00360	71	RRM RNA recognition motif.	98.98
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	98.97
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	98.97
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	98.94
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	98.94
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	98.92
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.91
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	98.89
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.89
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.87
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.86
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.85
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.8
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.73
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.7
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.68
KOG0226	290	consensus RNA-binding proteins [General function p	98.67
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.67
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	98.67
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	98.65
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.6
KOG1995	351	consensus Conserved Zn-finger protein [General fun	98.58
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.55
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.55
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.55
KOG1995	351	consensus Conserved Zn-finger protein [General fun	98.48
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	98.42
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.39
KOG0151	877	consensus Predicted splicing regulator, contains R	98.38
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	98.38
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	98.34
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.3
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.28
KOG0226	290	consensus RNA-binding proteins [General function p	98.2
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.19
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.16
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.13
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	98.12
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.02
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	97.98
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	97.97
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.94
KOG4210	285	consensus Nuclear localization sequence binding pr	97.92
KOG4660	549	consensus Protein Mei2, essential for commitment t	97.9
KOG3973	465	consensus Uncharacterized conserved glycine-rich p	97.87
KOG0151	877	consensus Predicted splicing regulator, contains R	97.77
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	97.76
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.71
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.7
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.63
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	97.62
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	97.58
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.57
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	97.48
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.31
KOG3152	278	consensus TBP-binding protein, activator of basal	97.3
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.28
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.27
KOG2314	698	consensus Translation initiation factor 3, subunit	97.22
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.19
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.18
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.13
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	97.05
KOG2314	698	consensus Translation initiation factor 3, subunit	96.97
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	96.94
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.89
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	96.86
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	96.78
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	96.63
KOG1996	378	consensus mRNA splicing factor [RNA processing and	96.57
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	96.42
PF05918	556	API5: Apoptosis inhibitory protein 5 (API5); Inter	96.28
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	96.19
KOG1996	378	consensus mRNA splicing factor [RNA processing and	96.19
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	96.14
KOG3152	278	consensus TBP-binding protein, activator of basal	96.13
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	95.24
KOG3262	215	consensus H/ACA small nucleolar RNP component GAR1	95.09
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	94.94
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	94.92
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	94.9
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	94.65
KOG2068	327	consensus MOT2 transcription factor [Transcription	94.53
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	94.35
KOG2135	526	consensus Proteins containing the RNA recognition	94.32
KOG2318	650	consensus Uncharacterized conserved protein [Funct	94.28
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	94.03
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	93.48
PRK06958	182	single-stranded DNA-binding protein; Provisional	93.45
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	93.02
KOG2295	648	consensus C2H2 Zn-finger protein [General function	92.91
PF05918	556	API5: Apoptosis inhibitory protein 5 (API5); Inter	92.83
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	92.82
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	92.82
KOG2135	526	consensus Proteins containing the RNA recognition	92.57
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	92.42
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	92.22
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	92.08
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	91.93
KOG2591	684	consensus c-Mpl binding protein, contains La domai	90.95
KOG3262	215	consensus H/ACA small nucleolar RNP component GAR1	90.59
KOG2068	327	consensus MOT2 transcription factor [Transcription	90.28
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	90.18
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	89.82
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	89.56
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	87.89
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	85.68
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	84.41
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	84.34
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	84.18
KOG2591	684	consensus c-Mpl binding protein, contains La domai	82.94
PHA00370	297	III attachment protein	82.89
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	82.14
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	81.58
PF14111	153	DUF4283: Domain of unknown function (DUF4283)	80.99

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=100.00  E-value=5.9e-34  Score=302.68  Aligned_cols=170  Identities=25%  Similarity=0.494  Sum_probs=153.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ...++|||+|||+++|+++|++||..||.|+.|+|+++. +++++|||||+|.+.++|.+||. ||++.|.+++|+|.++
T Consensus       105 ~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~a  184 (346)
T TIGR01659       105 NSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYA  184 (346)
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeecc
Confidence            457899999999999999999999999999999999997 89999999999999999999997 9999999999999987


Q ss_pred             cccCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEe
Q 045516          492 RERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDF  571 (675)
Q Consensus       492 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F  571 (675)
                      .....                  ....++|||.|||..+++++    |+++|..||.|..|.|+++..+|.++|||||+|
T Consensus       185 ~p~~~------------------~~~~~~lfV~nLp~~vtee~----L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F  242 (346)
T TIGR01659       185 RPGGE------------------SIKDTNLYVTNLPRTITDDQ----LDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRF  242 (346)
T ss_pred             ccccc------------------ccccceeEEeCCCCcccHHH----HHHHHHhcCCEEEEEEeecCCCCccceEEEEEE
Confidence            64321                  11256899999999999998    778999999999999999999999999999999


Q ss_pred             CCHHHHHHHHH-hCCceeCC--eeeEEeccccCCCCC
Q 045516          572 TDADSFNKALE-MSGTEIGG--YSLVVDEAKQRGDFG  605 (675)
Q Consensus       572 ~~~e~A~~Al~-lng~~~~G--r~l~V~~a~~r~~~~  605 (675)
                      .+.++|.+||. ||+..|.+  +.|+|.++..+....
T Consensus       243 ~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a~~~~~~~  279 (346)
T TIGR01659       243 NKREEAQEAISALNNVIPEGGSQPLTVRLAEEHGKAK  279 (346)
T ss_pred             CCHHHHHHHHHHhCCCccCCCceeEEEEECCcccccc
Confidence            99999999998 99999866  789999998765443

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).

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

Probab=99.97  E-value=9e-29  Score=275.62  Aligned_cols=179  Identities=21%  Similarity=0.413  Sum_probs=141.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccC-CeeEEEEec
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLG-NRAIRLDFA  491 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~-gr~i~V~~a  491 (675)
                      ...++|||+|||+++++++|+++|.+||.|..|+|+++.+|+++|||||+|.+.++|.+||+ ||+..|. |+.|.|.++
T Consensus        56 ~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S  135 (578)
T TIGR01648        56 GRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCIS  135 (578)
T ss_pred             CCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECCCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccccc
Confidence            34689999999999999999999999999999999999999999999999999999999998 9998885 676655543


Q ss_pred             cccCC---------------------C-----------CC----CCCCC------------------CCCC---------
Q 045516          492 RERGA---------------------Y-----------TP----YSGGN------------------ESNS---------  508 (675)
Q Consensus       492 ~~~~~---------------------~-----------~~----~~~~~------------------~~~~---------  508 (675)
                      .....                     .           .+    ...+.                  ....         
T Consensus       136 ~~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~  215 (578)
T TIGR01648       136 VDNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIA  215 (578)
T ss_pred             ccCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceEE
Confidence            21100                     0           00    00000                  0000         


Q ss_pred             --ccC------CCCCCCceEEEEecCCCCcCHHHHHHHHHhhhccc--CcEEEEEecccCCCCCeeeEEEEEeCCHHHHH
Q 045516          509 --FQK------GGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSC--GEITRISVPKDYDTGSVKGIAYLDFTDADSFN  578 (675)
Q Consensus       509 --~~~------~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~--G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~  578 (675)
                        +..      .......++|||+||+..+++++    |+++|..|  |.|.+|.+++        +||||+|.+.++|.
T Consensus       216 VdwA~p~~~~d~~~~~~~k~LfVgNL~~~~tee~----L~~~F~~f~~G~I~rV~~~r--------gfAFVeF~s~e~A~  283 (578)
T TIGR01648       216 VDWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEI----IEKSFSEFKPGKVERVKKIR--------DYAFVHFEDREDAV  283 (578)
T ss_pred             EEeecccccccccccccccEEEEeCCCCCCCHHH----HHHHHHhcCCCceEEEEeec--------CeEEEEeCCHHHHH
Confidence              000      00112357899999999999998    78889999  9999998754        59999999999999


Q ss_pred             HHHH-hCCceeCCeeeEEeccccCCCC
Q 045516          579 KALE-MSGTEIGGYSLVVDEAKQRGDF  604 (675)
Q Consensus       579 ~Al~-lng~~~~Gr~l~V~~a~~r~~~  604 (675)
                      +||. ||+..|+|+.|+|.|++++...
T Consensus       284 kAi~~lnG~~i~Gr~I~V~~Akp~~~~  310 (578)
T TIGR01648       284 KAMDELNGKELEGSEIEVTLAKPVDKK  310 (578)
T ss_pred             HHHHHhCCCEECCEEEEEEEccCCCcc
Confidence            9998 9999999999999999886543

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

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

Probab=99.96  E-value=5.1e-29  Score=277.78  Aligned_cols=180  Identities=23%  Similarity=0.434  Sum_probs=154.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ...++|||+|||+.+++++|+++|..||.|.+|+|++++ +|+++|||||+|.+.++|.+||. |||+.|.||.|+|.+.
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp  184 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  184 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeeccc
Confidence            456899999999999999999999999999999999997 89999999999999999999997 9999999999999864


Q ss_pred             cccCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEe
Q 045516          492 RERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDF  571 (675)
Q Consensus       492 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F  571 (675)
                      .......+..     ..+.  ......++|||+||+..+++++    |+++|..||.|..|+|+++..+|.++|||||+|
T Consensus       185 ~~~p~a~~~~-----~~~~--~~~~~~~rLfVgnLp~~vteed----Lk~lFs~FG~I~svrl~~D~~tgksKGfGFVeF  253 (612)
T TIGR01645       185 SNMPQAQPII-----DMVQ--EEAKKFNRIYVASVHPDLSETD----IKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEY  253 (612)
T ss_pred             cccccccccc-----cccc--ccccccceEEeecCCCCCCHHH----HHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEE
Confidence            4321111100     0000  1112357999999999999998    778999999999999999999999999999999


Q ss_pred             CCHHHHHHHHH-hCCceeCCeeeEEeccccCCCC
Q 045516          572 TDADSFNKALE-MSGTEIGGYSLVVDEAKQRGDF  604 (675)
Q Consensus       572 ~~~e~A~~Al~-lng~~~~Gr~l~V~~a~~r~~~  604 (675)
                      .+.++|..||. ||+..|+|+.|+|.++......
T Consensus       254 e~~e~A~kAI~amNg~elgGr~LrV~kAi~pP~~  287 (612)
T TIGR01645       254 NNLQSQSEAIASMNLFDLGGQYLRVGKCVTPPDA  287 (612)
T ss_pred             CCHHHHHHHHHHhCCCeeCCeEEEEEecCCCccc
Confidence            99999999998 9999999999999999865443

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.

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

Probab=99.96  E-value=4e-28  Score=236.13  Aligned_cols=181  Identities=30%  Similarity=0.507  Sum_probs=156.2

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEE
Q 045516          410 TPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIR  487 (675)
Q Consensus       410 ~~~~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~  487 (675)
                      ++..+.+..|||+.|...++.+.|++.|.+||+|.+++|++|. +++++||+||.|.+.++|++||. |||..|++|.|+
T Consensus        56 k~t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IR  135 (321)
T KOG0148|consen   56 KPTSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIR  135 (321)
T ss_pred             CCccccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceee
Confidence            3345568899999999999999999999999999999999998 99999999999999999999997 999999999999


Q ss_pred             EEeccccCCCCCCCCCCCCCCcc--CCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeee
Q 045516          488 LDFARERGAYTPYSGGNESNSFQ--KGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKG  565 (675)
Q Consensus       488 V~~a~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG  565 (675)
                      -.|+.++.......    ...|.  -....+..++|||+||+..++++.    |+++|..||.|..|||+++      +|
T Consensus       136 TNWATRKp~e~n~~----~ltfdeV~NQssp~NtsVY~G~I~~~lte~~----mr~~Fs~fG~I~EVRvFk~------qG  201 (321)
T KOG0148|consen  136 TNWATRKPSEMNGK----PLTFDEVYNQSSPDNTSVYVGNIASGLTEDL----MRQTFSPFGPIQEVRVFKD------QG  201 (321)
T ss_pred             ccccccCccccCCC----CccHHHHhccCCCCCceEEeCCcCccccHHH----HHHhcccCCcceEEEEecc------cc
Confidence            99998776211110    11111  111344589999999999999987    8899999999999999998      79


Q ss_pred             EEEEEeCCHHHHHHHHH-hCCceeCCeeeEEeccccCCCC
Q 045516          566 IAYLDFTDADSFNKALE-MSGTEIGGYSLVVDEAKQRGDF  604 (675)
Q Consensus       566 ~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~~a~~r~~~  604 (675)
                      |+||.|.+.+.|.+||. ||+..|.|+.++|.|.+.....
T Consensus       202 YaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe~~~~  241 (321)
T KOG0148|consen  202 YAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKEGDDG  241 (321)
T ss_pred             eEEEEecchhhHHHHHHHhcCceeCceEEEEeccccCCCC
Confidence            99999999999999997 9999999999999999865443

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

Probab=99.95  E-value=4.7e-27  Score=262.77  Aligned_cols=180  Identities=29%  Similarity=0.467  Sum_probs=155.4

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEE
Q 045516          411 PQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLD  489 (675)
Q Consensus       411 ~~~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~  489 (675)
                      ......++|||+|||+.+++++|++||..||.|..|+|+.+. +++++|||||+|.+.++|.+||.|||..|.|++|.|.
T Consensus        84 ~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~l~g~~~~g~~i~v~  163 (457)
T TIGR01622        84 EAERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQ  163 (457)
T ss_pred             ccccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHHhCCCEECCeeeEEe
Confidence            334567899999999999999999999999999999999997 8999999999999999999999999999999999998


Q ss_pred             eccccCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEE
Q 045516          490 FARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYL  569 (675)
Q Consensus       490 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV  569 (675)
                      +............      .......+..++|||+||++.+++++    |+++|..||.|..|.|+++..+|.++|||||
T Consensus       164 ~~~~~~~~~~~~~------~~~~~~~p~~~~l~v~nl~~~~te~~----l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV  233 (457)
T TIGR01622       164 SSQAEKNRAAKAA------THQPGDIPNFLKLYVGNLHFNITEQE----LRQIFEPFGDIEDVQLHRDPETGRSKGFGFI  233 (457)
T ss_pred             ecchhhhhhhhcc------cccCCCCCCCCEEEEcCCCCCCCHHH----HHHHHHhcCCeEEEEEEEcCCCCccceEEEE
Confidence            8654322111100      00011122368999999999999998    7788999999999999999999999999999


Q ss_pred             EeCCHHHHHHHHH-hCCceeCCeeeEEecccc
Q 045516          570 DFTDADSFNKALE-MSGTEIGGYSLVVDEAKQ  600 (675)
Q Consensus       570 ~F~~~e~A~~Al~-lng~~~~Gr~l~V~~a~~  600 (675)
                      +|.+.+.|..||. |||..|.|+.|.|.|+..
T Consensus       234 ~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~  265 (457)
T TIGR01622       234 QFHDAEEAKEALEVMNGFELAGRPIKVGYAQD  265 (457)
T ss_pred             EECCHHHHHHHHHhcCCcEECCEEEEEEEccC
Confidence            9999999999998 999999999999999863

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.

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.95  E-value=1.2e-26  Score=250.75  Aligned_cols=185  Identities=24%  Similarity=0.416  Sum_probs=151.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCC--eeEEEEe
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGN--RAIRLDF  490 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~g--r~i~V~~  490 (675)
                      ..++|||+|||+.+++++|+.+|..||.|..++|+.+. ++.++|||||+|.+.++|..||. |||..+.|  ++|.|.+
T Consensus        88 ~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~~  167 (352)
T TIGR01661        88 KGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKF  167 (352)
T ss_pred             ccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEE
Confidence            45789999999999999999999999999999999887 78999999999999999999997 99999987  6688888


Q ss_pred             ccccCCCCCC--------------CCCCCC--------------------------------------------C-----
Q 045516          491 ARERGAYTPY--------------SGGNES--------------------------------------------N-----  507 (675)
Q Consensus       491 a~~~~~~~~~--------------~~~~~~--------------------------------------------~-----  507 (675)
                      +.........              ......                                            .     
T Consensus       168 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  247 (352)
T TIGR01661       168 ANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRASPP  247 (352)
T ss_pred             CCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhhhcccccccccccCCCc
Confidence            7543211000              000000                                            0     


Q ss_pred             -------Cc----cCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHH
Q 045516          508 -------SF----QKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADS  576 (675)
Q Consensus       508 -------~~----~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~  576 (675)
                             .+    ..........+|||+|||+.+++++    |+++|++||.|.+|+|+++..||.++|||||+|.+.++
T Consensus       248 ~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~~e~~----L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~  323 (352)
T TIGR01661       248 ATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETV----LWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDE  323 (352)
T ss_pred             cccccccccccCCCCCCCCCCCcEEEEeCCCCCCCHHH----HHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHH
Confidence                   00    0000011234799999999999998    77899999999999999999999999999999999999


Q ss_pred             HHHHHH-hCCceeCCeeeEEeccccCCC
Q 045516          577 FNKALE-MSGTEIGGYSLVVDEAKQRGD  603 (675)
Q Consensus       577 A~~Al~-lng~~~~Gr~l~V~~a~~r~~  603 (675)
                      |..||. |||..|+||.|+|.|...+..
T Consensus       324 A~~Ai~~lnG~~~~gr~i~V~~~~~~~~  351 (352)
T TIGR01661       324 AAMAILSLNGYTLGNRVLQVSFKTNKAY  351 (352)
T ss_pred             HHHHHHHhCCCEECCeEEEEEEccCCCC
Confidence            999998 999999999999999987653

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.95  E-value=8.4e-27  Score=251.83  Aligned_cols=165  Identities=28%  Similarity=0.541  Sum_probs=149.7

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEeccc
Q 045516          416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       416 ~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~  493 (675)
                      .++|||+|||+.+++++|++||..||+|..|+|+++. +|+++|||||+|.+.++|.+||. |||..|.|+.|+|.++.+
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~~   82 (352)
T TIGR01661         3 KTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARP   82 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeecc
Confidence            5799999999999999999999999999999999997 89999999999999999999997 999999999999999865


Q ss_pred             cCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCC
Q 045516          494 RGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTD  573 (675)
Q Consensus       494 ~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~  573 (675)
                      ....                  ....+|||+|||..+++++    |+.+|..||.|..+.|+.+..++.++|||||+|.+
T Consensus        83 ~~~~------------------~~~~~l~v~~l~~~~~~~~----l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~  140 (352)
T TIGR01661        83 SSDS------------------IKGANLYVSGLPKTMTQHE----LESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDK  140 (352)
T ss_pred             cccc------------------cccceEEECCccccCCHHH----HHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECC
Confidence            3211                  1256899999999999988    78899999999999999998889999999999999


Q ss_pred             HHHHHHHHH-hCCceeCC--eeeEEeccccCC
Q 045516          574 ADSFNKALE-MSGTEIGG--YSLVVDEAKQRG  602 (675)
Q Consensus       574 ~e~A~~Al~-lng~~~~G--r~l~V~~a~~r~  602 (675)
                      .++|..||. |||..+.|  +.|.|.|+....
T Consensus       141 ~~~A~~ai~~l~g~~~~g~~~~i~v~~a~~~~  172 (352)
T TIGR01661       141 RDEADRAIKTLNGTTPSGCTEPITVKFANNPS  172 (352)
T ss_pred             HHHHHHHHHHhCCCccCCCceeEEEEECCCCC
Confidence            999999998 99999987  578888886544

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

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

Probab=99.94  E-value=8.5e-26  Score=233.43  Aligned_cols=178  Identities=22%  Similarity=0.431  Sum_probs=145.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCccc-CCeeEEEE
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQML-GNRAIRLD  489 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~-~gr~i~V~  489 (675)
                      ..-.+-|||+.||.++.+++|.-||+..|+|-.+||++++ +|.++|||||.|.+.+.|+.||. ||++.| .|+.|.|.
T Consensus        80 p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc  159 (506)
T KOG0117|consen   80 PPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVC  159 (506)
T ss_pred             CCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEE
Confidence            4567999999999999999999999999999999999997 99999999999999999999998 999988 68888887


Q ss_pred             eccccCCC-------------------------------------CCCCC----------------C-CCCCCcc-----
Q 045516          490 FARERGAY-------------------------------------TPYSG----------------G-NESNSFQ-----  510 (675)
Q Consensus       490 ~a~~~~~~-------------------------------------~~~~~----------------~-~~~~~~~-----  510 (675)
                      ++......                                     ..+++                + .....++     
T Consensus       160 ~Svan~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~  239 (506)
T KOG0117|consen  160 VSVANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNA  239 (506)
T ss_pred             EeeecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCceeecCCc
Confidence            76533110                                     00000                0 0000000     


Q ss_pred             ------C------CCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHH
Q 045516          511 ------K------GGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFN  578 (675)
Q Consensus       511 ------~------~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~  578 (675)
                            .      ...+...+.|||+||+.++|++.    |+.+|+.||.|.+|..++|        ||||+|.+.++|.
T Consensus       240 ~tVdWAep~~e~ded~ms~VKvLYVRNL~~~tTeE~----lk~~F~~~G~veRVkk~rD--------YaFVHf~eR~dav  307 (506)
T KOG0117|consen  240 ITVDWAEPEEEPDEDTMSKVKVLYVRNLMESTTEET----LKKLFNEFGKVERVKKPRD--------YAFVHFAEREDAV  307 (506)
T ss_pred             ceeeccCcccCCChhhhhheeeeeeeccchhhhHHH----HHHHHHhccceEEeecccc--------eeEEeecchHHHH
Confidence                  0      00122468999999999999998    7788888899999998876        8999999999999


Q ss_pred             HHHH-hCCceeCCeeeEEeccccCC
Q 045516          579 KALE-MSGTEIGGYSLVVDEAKQRG  602 (675)
Q Consensus       579 ~Al~-lng~~~~Gr~l~V~~a~~r~  602 (675)
                      +||. +||..|+|..|.|.+|+|..
T Consensus       308 kAm~~~ngkeldG~~iEvtLAKP~~  332 (506)
T KOG0117|consen  308 KAMKETNGKELDGSPIEVTLAKPVD  332 (506)
T ss_pred             HHHHHhcCceecCceEEEEecCChh
Confidence            9998 99999999999999998753

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

Probab=99.94  E-value=2.5e-25  Score=254.96  Aligned_cols=183  Identities=28%  Similarity=0.503  Sum_probs=153.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccC----CeeEEE
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLG----NRAIRL  488 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~----gr~i~V  488 (675)
                      ...++|||+|||+.+++++|+++|..||.|..|.|+++.+|+++|||||.|.+.++|.+||+ |||..|.    |+.|.|
T Consensus       176 ~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~~g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~~~g~~l~v  255 (562)
T TIGR01628       176 KKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYV  255 (562)
T ss_pred             cCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCcEecccccceeeEe
Confidence            34578999999999999999999999999999999999999999999999999999999997 9999999    999999


Q ss_pred             EeccccCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEE
Q 045516          489 DFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAY  568 (675)
Q Consensus       489 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~af  568 (675)
                      .++..+.........................+|||+||+..+++++    |+++|..||.|..|.|+.+ .+|.++||||
T Consensus       256 ~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~----L~~~F~~~G~i~~~~i~~d-~~g~~~g~gf  330 (562)
T TIGR01628       256 GRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEK----LRELFSECGEITSAKVMLD-EKGVSRGFGF  330 (562)
T ss_pred             ecccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeCCCCccCHHH----HHHHHHhcCCeEEEEEEEC-CCCCcCCeEE
Confidence            8876543221000000000000001122367899999999999988    7789999999999999999 7799999999


Q ss_pred             EEeCCHHHHHHHHH-hCCceeCCeeeEEeccccC
Q 045516          569 LDFTDADSFNKALE-MSGTEIGGYSLVVDEAKQR  601 (675)
Q Consensus       569 V~F~~~e~A~~Al~-lng~~~~Gr~l~V~~a~~r  601 (675)
                      |+|.+.++|.+||. |||..|+|+.|.|.++..+
T Consensus       331 V~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~~k  364 (562)
T TIGR01628       331 VCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRK  364 (562)
T ss_pred             EEeCCHHHHHHHHHHhcCCeeCCceeEEEeccCc
Confidence            99999999999998 9999999999999998754

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

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

Probab=99.93  E-value=4.6e-26  Score=210.27  Aligned_cols=171  Identities=27%  Similarity=0.447  Sum_probs=152.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ....||||+||+..++++.|++||-++|+|++|+|++++ +...+|||||+|.++++|.-||. ||...|.||+|+|..+
T Consensus         7 nqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~ka   86 (203)
T KOG0131|consen    7 NQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKA   86 (203)
T ss_pred             CCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEec
Confidence            456899999999999999999999999999999999998 88899999999999999999999 9999999999999988


Q ss_pred             cccCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEE-EecccCCCCCeeeEEEEE
Q 045516          492 RERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRI-SVPKDYDTGSVKGIAYLD  570 (675)
Q Consensus       492 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v-~i~~d~~tG~~rG~afV~  570 (675)
                      ......                 ...+..|||+||.+.+.+..    |+++|+.||.|... .|+++..||.++||+||.
T Consensus        87 s~~~~n-----------------l~vganlfvgNLd~~vDe~~----L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~  145 (203)
T KOG0131|consen   87 SAHQKN-----------------LDVGANLFVGNLDPEVDEKL----LYDTFSAFGVLISPPKIMRDPDTGNPKGFGFIN  145 (203)
T ss_pred             cccccc-----------------ccccccccccccCcchhHHH----HHHHHHhccccccCCcccccccCCCCCCCeEEe
Confidence            622211                 12257899999999888876    88999999988764 688899999999999999


Q ss_pred             eCCHHHHHHHHH-hCCceeCCeeeEEeccccCCCCC
Q 045516          571 FTDADSFNKALE-MSGTEIGGYSLVVDEAKQRGDFG  605 (675)
Q Consensus       571 F~~~e~A~~Al~-lng~~~~Gr~l~V~~a~~r~~~~  605 (675)
                      |.+.+.+.+||. |||..++.++|+|.++..+...+
T Consensus       146 ~~sfeasd~ai~s~ngq~l~nr~itv~ya~k~~~kg  181 (203)
T KOG0131|consen  146 YASFEASDAAIGSMNGQYLCNRPITVSYAFKKDTKG  181 (203)
T ss_pred             chhHHHHHHHHHHhccchhcCCceEEEEEEecCCCc
Confidence            999999999998 99999999999999998665443

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

Probab=99.93  E-value=3.7e-25  Score=253.48  Aligned_cols=163  Identities=28%  Similarity=0.512  Sum_probs=145.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEeccccC
Q 045516          418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARERG  495 (675)
Q Consensus       418 tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~~~  495 (675)
                      +|||+|||+++|+++|++||..||.|.+|+|+++. +++++|||||+|.+.++|.+||. ||+..|.|+.|+|.|+....
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~~~   81 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRDP   81 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccccc
Confidence            79999999999999999999999999999999998 79999999999999999999997 99999999999999875432


Q ss_pred             CCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHH
Q 045516          496 AYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDAD  575 (675)
Q Consensus       496 ~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e  575 (675)
                      ...                .....+|||+||+.++++.+    |+++|+.||.|..|.|+.+ .+|.++|||||+|.+.+
T Consensus        82 ~~~----------------~~~~~~vfV~nLp~~~~~~~----L~~~F~~~G~i~~~~i~~~-~~g~skg~afV~F~~~e  140 (562)
T TIGR01628        82 SLR----------------RSGVGNIFVKNLDKSVDNKA----LFDTFSKFGNILSCKVATD-ENGKSRGYGFVHFEKEE  140 (562)
T ss_pred             ccc----------------ccCCCceEEcCCCccCCHHH----HHHHHHhcCCcceeEeeec-CCCCcccEEEEEECCHH
Confidence            111                11246899999999999998    7888999999999999988 46889999999999999


Q ss_pred             HHHHHHH-hCCceeCCeeeEEeccccC
Q 045516          576 SFNKALE-MSGTEIGGYSLVVDEAKQR  601 (675)
Q Consensus       576 ~A~~Al~-lng~~~~Gr~l~V~~a~~r  601 (675)
                      +|..||. |||..|+|+.|.|.....+
T Consensus       141 ~A~~Ai~~lng~~~~~~~i~v~~~~~~  167 (562)
T TIGR01628       141 SAKAAIQKVNGMLLNDKEVYVGRFIKK  167 (562)
T ss_pred             HHHHHHHHhcccEecCceEEEeccccc
Confidence            9999998 9999999999999765543

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

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

Probab=99.92  E-value=9.1e-25  Score=230.18  Aligned_cols=185  Identities=24%  Similarity=0.460  Sum_probs=156.7

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecccc
Q 045516          417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARER  494 (675)
Q Consensus       417 ~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~~  494 (675)
                      .||||++|||.++.++|.+||+.+|+|..|.++.+. .+.++||+||.|.-.+++++||. +++..|.||.|+|.++..+
T Consensus         6 ~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~R   85 (678)
T KOG0127|consen    6 ATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKKR   85 (678)
T ss_pred             ceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceeccccccccc
Confidence            799999999999999999999999999999999998 77899999999999999999997 9999999999999999876


Q ss_pred             CCCCCCCCCCC---CCCccC-----CCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeE
Q 045516          495 GAYTPYSGGNE---SNSFQK-----GGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGI  566 (675)
Q Consensus       495 ~~~~~~~~~~~---~~~~~~-----~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~  566 (675)
                      ........+..   ...+..     .-...+--.|.|+|||+.+...+    |+.+|+.||.|..|.|++..+++.+ ||
T Consensus        86 ~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~d----Lk~vFs~~G~V~Ei~IP~k~dgklc-GF  160 (678)
T KOG0127|consen   86 ARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPD----LKNVFSNFGKVVEIVIPRKKDGKLC-GF  160 (678)
T ss_pred             ccchhcccccchhhhcccccCCcchhhccCccceEEeecCCcccCcHH----HHHHHhhcceEEEEEcccCCCCCcc-ce
Confidence            54331111100   001111     11122357899999999999987    8999999999999999988776666 99


Q ss_pred             EEEEeCCHHHHHHHHH-hCCceeCCeeeEEeccccCCCCCC
Q 045516          567 AYLDFTDADSFNKALE-MSGTEIGGYSLVVDEAKQRGDFGS  606 (675)
Q Consensus       567 afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~~a~~r~~~~~  606 (675)
                      |||+|.+..+|..||+ ||+..|+||+|-|+||.+...+..
T Consensus       161 aFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~ye~  201 (678)
T KOG0127|consen  161 AFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKDTYED  201 (678)
T ss_pred             EEEEEeeHHHHHHHHHhccCceecCceeEEeeecccccccc
Confidence            9999999999999999 999999999999999998877654

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

Probab=99.92  E-value=2.9e-24  Score=243.45  Aligned_cols=180  Identities=23%  Similarity=0.406  Sum_probs=143.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhC------------CCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcc
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEV------------AEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQM  480 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~------------G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~  480 (675)
                      ....++|||+|||+.+|+++|++||..|            +.|..|++.     ..+|||||+|.+.++|..||.|||+.
T Consensus       172 ~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~~-----~~kg~afVeF~~~e~A~~Al~l~g~~  246 (509)
T TIGR01642       172 TRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNIN-----KEKNFAFLEFRTVEEATFAMALDSII  246 (509)
T ss_pred             CccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEEC-----CCCCEEEEEeCCHHHHhhhhcCCCeE
Confidence            5577999999999999999999999975            345555554     45899999999999999999999999


Q ss_pred             cCCeeEEEEeccccCCCCCC---CCC-CCC---CCc----cCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcE
Q 045516          481 LGNRAIRLDFARERGAYTPY---SGG-NES---NSF----QKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEI  549 (675)
Q Consensus       481 ~~gr~i~V~~a~~~~~~~~~---~~~-~~~---~~~----~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I  549 (675)
                      |.|+.|.|............   ... ...   ...    .........++|||+|||+.+++++    |.++|..||.|
T Consensus       247 ~~g~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~----l~~~f~~~G~i  322 (509)
T TIGR01642       247 YSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQ----IKELLESFGDL  322 (509)
T ss_pred             eeCceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCe
Confidence            99999999754332210000   000 000   000    0011123468999999999999998    77888889999


Q ss_pred             EEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEeccccC
Q 045516          550 TRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVDEAKQR  601 (675)
Q Consensus       550 ~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~~a~~r  601 (675)
                      ..|.|+.+..+|.++|||||+|.+.+.|..||. |||..|+|+.|.|.++...
T Consensus       323 ~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~  375 (509)
T TIGR01642       323 KAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVG  375 (509)
T ss_pred             eEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccC
Confidence            999999999999999999999999999999998 9999999999999998643

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

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

Probab=99.92  E-value=6.8e-24  Score=240.45  Aligned_cols=187  Identities=18%  Similarity=0.357  Sum_probs=150.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ...++|||+|||+.+++++|++||..||.|..|.|+.+. +|.++|||||+|.+.+.|..||. |||+.|.|+.|.|.++
T Consensus       293 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a  372 (509)
T TIGR01642       293 DSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRA  372 (509)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            356899999999999999999999999999999999987 89999999999999999999997 9999999999999998


Q ss_pred             cccCCCCCCCCCC-------CCCCcc---CCCCCCCceEEEEecCCCC------cCHHHHHHHHHhhhcccCcEEEEEec
Q 045516          492 RERGAYTPYSGGN-------ESNSFQ---KGGRGQAAHTIFIKGFDSS------VGEDQVRASLEEHFGSCGEITRISVP  555 (675)
Q Consensus       492 ~~~~~~~~~~~~~-------~~~~~~---~~~~~~~~~~lfV~nLp~~------~te~~i~~~L~~~F~~~G~I~~v~i~  555 (675)
                      .............       ....+.   ......+..+|+|.||...      ....+|.+.|+++|.+||.|..|.|+
T Consensus       373 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~  452 (509)
T TIGR01642       373 CVGANQATIDTSNGMAPVTLLAKALSQSILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIP  452 (509)
T ss_pred             ccCCCCCCccccccccccccccccchhhhccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEee
Confidence            6432211110000       000000   0011335789999999642      23456778899999999999999998


Q ss_pred             ccC---CCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEecccc
Q 045516          556 KDY---DTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVDEAKQ  600 (675)
Q Consensus       556 ~d~---~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~~a~~  600 (675)
                      ++.   .++...||+||+|.+.+.|..||. |||..|+|+.|.|.|...
T Consensus       453 ~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~~~gr~v~~~~~~~  501 (509)
T TIGR01642       453 RPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDRVVVAAFYGE  501 (509)
T ss_pred             ccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEeCH
Confidence            753   345678999999999999999998 999999999999998754

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

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

Probab=99.92  E-value=3.2e-24  Score=226.07  Aligned_cols=183  Identities=31%  Similarity=0.569  Sum_probs=154.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecccc
Q 045516          416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARER  494 (675)
Q Consensus       416 ~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~~  494 (675)
                      -.+|+|+||||.|...+|..+|+.||.|+.|.|++...|+..|||||.|.+..+|..||+ ||+..|+||+|-|+|+..+
T Consensus       117 k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~K  196 (678)
T KOG0127|consen  117 KWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDK  196 (678)
T ss_pred             cceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeeccc
Confidence            579999999999999999999999999999999988888888999999999999999998 9999999999999999887


Q ss_pred             CCCCCCCC----------------------CC--------------C--CCC---cc-------------CC---C----
Q 045516          495 GAYTPYSG----------------------GN--------------E--SNS---FQ-------------KG---G----  513 (675)
Q Consensus       495 ~~~~~~~~----------------------~~--------------~--~~~---~~-------------~~---~----  513 (675)
                      ..|.....                      +.              .  ...   +.             ..   +    
T Consensus       197 d~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~edeEe~D~~se~~ee~~~~Eee~~~vDd~e~S~~~~~  276 (678)
T KOG0127|consen  197 DTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDEEETDGNSEAFEEGEESEEEEDDVDDEESSGKKES  276 (678)
T ss_pred             ccccccchhhhhhhhhccchhhhcccccccccccchhcccccccccccccccchhhhccccccccccccccccccccCcc
Confidence            65543210                      00              0  000   00             00   0    


Q ss_pred             -----------CCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH
Q 045516          514 -----------RGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE  582 (675)
Q Consensus       514 -----------~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~  582 (675)
                                 ......+|||+||||++++++    |.++|.+||.|.++.|+.+..||++.|.|||.|.+...|..||.
T Consensus       277 ~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEe----l~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~  352 (678)
T KOG0127|consen  277 DKKAQNKTTRENITEGKTVFVRNLPFDTTEEE----LKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIE  352 (678)
T ss_pred             cchhccccccccccccceEEEecCCccccHHH----HHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHH
Confidence                       011248999999999999998    88999999999999999999999999999999999999999997


Q ss_pred             -h-----CC-ceeCCeeeEEeccccCC
Q 045516          583 -M-----SG-TEIGGYSLVVDEAKQRG  602 (675)
Q Consensus       583 -l-----ng-~~~~Gr~l~V~~a~~r~  602 (675)
                       .     .| ..|.||.|.|..+..|.
T Consensus       353 ~Aspa~e~g~~ll~GR~Lkv~~Av~Rk  379 (678)
T KOG0127|consen  353 AASPASEDGSVLLDGRLLKVTLAVTRK  379 (678)
T ss_pred             hcCccCCCceEEEeccEEeeeeccchH
Confidence             3     23 67899999999997654

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

Probab=99.90  E-value=2.1e-22  Score=225.66  Aligned_cols=167  Identities=19%  Similarity=0.234  Sum_probs=138.2

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH---hCCcccCCeeEEEEecc
Q 045516          416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE---LNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       416 ~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~---l~g~~~~gr~i~V~~a~  492 (675)
                      +++|||+|||+.+++++|+++|+.||.|..|.|+++     +|||||+|.+.++|.+||.   +|+..|.|+.|+|.|+.
T Consensus         2 s~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~-----k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s~   76 (481)
T TIGR01649         2 SPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPG-----KRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYST   76 (481)
T ss_pred             ccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECC-----CCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEecC
Confidence            689999999999999999999999999999999853     7899999999999999997   47899999999999997


Q ss_pred             ccCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeC
Q 045516          493 ERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFT  572 (675)
Q Consensus       493 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~  572 (675)
                      .+.......     ..+. ........+|||.||++.+++++    |+++|+.||.|..|.|+++..    +++|||+|.
T Consensus        77 ~~~~~~~~~-----~~~~-~~~~~~~~~v~v~nl~~~vt~~~----L~~~F~~~G~V~~v~i~~~~~----~~~afVef~  142 (481)
T TIGR01649        77 SQEIKRDGN-----SDFD-SAGPNKVLRVIVENPMYPITLDV----LYQIFNPYGKVLRIVTFTKNN----VFQALVEFE  142 (481)
T ss_pred             CcccccCCC-----Cccc-CCCCCceEEEEEcCCCCCCCHHH----HHHHHhccCCEEEEEEEecCC----ceEEEEEEC
Confidence            543221110     0000 01112245899999999999987    889999999999999987643    479999999


Q ss_pred             CHHHHHHHHH-hCCceeCC--eeeEEeccccC
Q 045516          573 DADSFNKALE-MSGTEIGG--YSLVVDEAKQR  601 (675)
Q Consensus       573 ~~e~A~~Al~-lng~~~~G--r~l~V~~a~~r  601 (675)
                      +.++|.+|+. |||..|.|  +.|+|.|+++.
T Consensus       143 ~~~~A~~A~~~Lng~~i~~~~~~l~v~~sk~~  174 (481)
T TIGR01649       143 SVNSAQHAKAALNGADIYNGCCTLKIEYAKPT  174 (481)
T ss_pred             CHHHHHHHHHHhcCCcccCCceEEEEEEecCC
Confidence            9999999998 99999964  58999998763

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

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

Probab=99.90  E-value=6.9e-24  Score=218.28  Aligned_cols=169  Identities=25%  Similarity=0.475  Sum_probs=146.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCc-ccC--CeeEEE
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQ-MLG--NRAIRL  488 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~-~~~--gr~i~V  488 (675)
                      .+.-.|||+-||..++|.+|++||++||.|..|.|++|+ ++.++|||||.|.+.++|.+|+. ||+. .|-  ..+|.|
T Consensus        32 ~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqv  111 (510)
T KOG0144|consen   32 GSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQV  111 (510)
T ss_pred             chhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceee
Confidence            456789999999999999999999999999999999998 99999999999999999999997 7655 454  467888


Q ss_pred             EeccccCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEE
Q 045516          489 DFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAY  568 (675)
Q Consensus       489 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~af  568 (675)
                      .++.......                 ...+.|||+-|+..+++.+    ++.+|.+||.|++|+|+++.+ +.+|||||
T Consensus       112 k~Ad~E~er~-----------------~~e~KLFvg~lsK~~te~e----vr~iFs~fG~Ied~~ilrd~~-~~sRGcaF  169 (510)
T KOG0144|consen  112 KYADGERERI-----------------VEERKLFVGMLSKQCTENE----VREIFSRFGHIEDCYILRDPD-GLSRGCAF  169 (510)
T ss_pred             cccchhhhcc-----------------ccchhhhhhhccccccHHH----HHHHHHhhCccchhhheeccc-ccccceeE
Confidence            8875432211                 2258899999999999998    778999999999999999954 99999999


Q ss_pred             EEeCCHHHHHHHHH-hCCce-eCC--eeeEEeccccCCCC
Q 045516          569 LDFTDADSFNKALE-MSGTE-IGG--YSLVVDEAKQRGDF  604 (675)
Q Consensus       569 V~F~~~e~A~~Al~-lng~~-~~G--r~l~V~~a~~r~~~  604 (675)
                      |.|.+.+.|..||. |||.. +.|  .+|.|.|+.+..+.
T Consensus       170 V~fstke~A~~Aika~ng~~tmeGcs~PLVVkFADtqkdk  209 (510)
T KOG0144|consen  170 VKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQKDK  209 (510)
T ss_pred             EEEehHHHHHHHHHhhccceeeccCCCceEEEecccCCCc
Confidence            99999999999998 99865 555  58999999876654

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

Probab=99.90  E-value=2e-23  Score=215.69  Aligned_cols=176  Identities=24%  Similarity=0.426  Sum_probs=160.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEeccc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a~~  493 (675)
                      +.++|||++|+|.++++.|+.+|.+||.|.+|.+++++ +++++||+||+|.+.+.+..+|....+.|.|+.|.+..+.+
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~h~~dgr~ve~k~av~   84 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNARTHKLDGRSVEPKRAVS   84 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecccccccCCccccceeccC
Confidence            67899999999999999999999999999999999998 89999999999999999999999888999999999999887


Q ss_pred             cCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCC
Q 045516          494 RGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTD  573 (675)
Q Consensus       494 ~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~  573 (675)
                      +.......            .......|||++|+.++++.+    |+++|.+||.|..+.|+.|..+.+++||+||.|.+
T Consensus        85 r~~~~~~~------------~~~~tkkiFvGG~~~~~~e~~----~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~  148 (311)
T KOG4205|consen   85 REDQTKVG------------RHLRTKKIFVGGLPPDTTEED----FKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDS  148 (311)
T ss_pred             cccccccc------------cccceeEEEecCcCCCCchHH----HhhhhhccceeEeeEEeecccccccccceeeEecc
Confidence            75433222            112478999999999999998    88999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhCCceeCCeeeEEeccccCCCCCC
Q 045516          574 ADSFNKALEMSGTEIGGYSLVVDEAKQRGDFGS  606 (675)
Q Consensus       574 ~e~A~~Al~lng~~~~Gr~l~V~~a~~r~~~~~  606 (675)
                      .+.+.+++..+-+.|+|+.+.|..|.++.....
T Consensus       149 e~sVdkv~~~~f~~~~gk~vevkrA~pk~~~~~  181 (311)
T KOG4205|consen  149 EDSVDKVTLQKFHDFNGKKVEVKRAIPKEVMQS  181 (311)
T ss_pred             ccccceecccceeeecCceeeEeeccchhhccc
Confidence            999999999999999999999999999876553

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

Probab=99.90  E-value=7.7e-23  Score=229.22  Aligned_cols=178  Identities=21%  Similarity=0.304  Sum_probs=143.8

Q ss_pred             CCCceEEEcCCCC-CCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          414 GGSKTLFVGNLPF-SVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       414 ~~~~tlfV~nLp~-~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ..+++|||+||++ .+++++|++||+.||.|..|+|+++.    +|||||+|.+.++|..||. |||..|.|+.|+|.++
T Consensus       273 ~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~----~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s  348 (481)
T TIGR01649       273 GPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK----KETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPS  348 (481)
T ss_pred             CCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEc
Confidence            3568999999998 69999999999999999999999863    7999999999999999997 9999999999999998


Q ss_pred             cccCCCCCCCC-------------CCCCCCccCC------CCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCc--EE
Q 045516          492 RERGAYTPYSG-------------GNESNSFQKG------GRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGE--IT  550 (675)
Q Consensus       492 ~~~~~~~~~~~-------------~~~~~~~~~~------~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~--I~  550 (675)
                      .......+...             ......+...      ....++.+|||.|||..+++++    |+++|..||.  |.
T Consensus       349 ~~~~~~~~~~~~~~~~~~~~~d~~~~~~~r~~~~~~~~~~~~~~ps~~L~v~NLp~~~tee~----L~~lF~~~G~~~i~  424 (481)
T TIGR01649       349 KQQNVQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLHLSNIPLSVSEED----LKELFAENGVHKVK  424 (481)
T ss_pred             ccccccCCCCCcCcCCCcccccccCCccccCCCcccccccccCCCCcEEEEecCCCCCCHHH----HHHHHHhcCCccce
Confidence            65432111100             0000011110      1234678999999999999998    7788889998  88


Q ss_pred             EEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCee------eEEeccccC
Q 045516          551 RISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYS------LVVDEAKQR  601 (675)
Q Consensus       551 ~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~------l~V~~a~~r  601 (675)
                      .|+|+...  +..++||||+|.+.++|..||. ||++.|.|+.      |+|.|+++|
T Consensus       425 ~ik~~~~~--~~~~~~gfVeF~~~e~A~~Al~~ln~~~l~~~~~~~~~~lkv~fs~~~  480 (481)
T TIGR01649       425 KFKFFPKD--NERSKMGLLEWESVEDAVEALIALNHHQLNEPNGSAPYHLKVSFSTSR  480 (481)
T ss_pred             EEEEecCC--CCcceeEEEEcCCHHHHHHHHHHhcCCccCCCCCCccceEEEEeccCC
Confidence            88887643  2358999999999999999998 9999999985      999998875

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

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

Probab=99.90  E-value=2.2e-23  Score=201.55  Aligned_cols=164  Identities=26%  Similarity=0.507  Sum_probs=150.8

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEeccc
Q 045516          416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       416 ~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~  493 (675)
                      .+.|.|.-||.++|+++|+.||...|+|..|+|++|+ +|++.||+||.|-++.+|.+||. |||..|....|+|.|+++
T Consensus        41 kTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyARP  120 (360)
T KOG0145|consen   41 KTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYARP  120 (360)
T ss_pred             cceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEeccC
Confidence            3569999999999999999999999999999999999 99999999999999999999998 999999999999999986


Q ss_pred             cCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCC
Q 045516          494 RGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTD  573 (675)
Q Consensus       494 ~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~  573 (675)
                      ....                  .....|||.+||..++..+    |+++|.+||.|..-||..|..||.+||.+||.|..
T Consensus       121 Ss~~------------------Ik~aNLYvSGlPktMtqke----lE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDK  178 (360)
T KOG0145|consen  121 SSDS------------------IKDANLYVSGLPKTMTQKE----LEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDK  178 (360)
T ss_pred             Chhh------------------hcccceEEecCCccchHHH----HHHHHHHhhhhhhhhhhhhcccceecceeEEEecc
Confidence            5432                  1156899999999999988    88999999999999999999999999999999999


Q ss_pred             HHHHHHHHH-hCCceeCCe--eeEEeccccC
Q 045516          574 ADSFNKALE-MSGTEIGGY--SLVVDEAKQR  601 (675)
Q Consensus       574 ~e~A~~Al~-lng~~~~Gr--~l~V~~a~~r  601 (675)
                      ..+|..||. |||+.--|.  +|.|.|+...
T Consensus       179 r~EAe~AIk~lNG~~P~g~tepItVKFannP  209 (360)
T KOG0145|consen  179 RIEAEEAIKGLNGQKPSGCTEPITVKFANNP  209 (360)
T ss_pred             hhHHHHHHHhccCCCCCCCCCCeEEEecCCc
Confidence            999999998 999998775  7999998643

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

Probab=99.89  E-value=8.9e-23  Score=200.79  Aligned_cols=152  Identities=23%  Similarity=0.454  Sum_probs=138.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEeccccC
Q 045516          417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARERG  495 (675)
Q Consensus       417 ~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~~~  495 (675)
                      -.|||+|||..+++.+|+.||++||.|+.|.|+       +.||||...+...+.-||. ||+..|+|..|.|.-+..+.
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIv-------KNYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksKs   75 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIV-------KNYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSKS   75 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeee-------cccceEEeecccccHHHHhhcccceecceEEEEEeccccC
Confidence            479999999999999999999999999999999       6799999999999999998 99999999999999887652


Q ss_pred             CCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHH
Q 045516          496 AYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDAD  575 (675)
Q Consensus       496 ~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e  575 (675)
                                          ....+|||+||-+.++.++    |+..|.+||.|..|.|.++        |+||.|...+
T Consensus        76 --------------------k~stkl~vgNis~tctn~E----lRa~fe~ygpviecdivkd--------y~fvh~d~~e  123 (346)
T KOG0109|consen   76 --------------------KASTKLHVGNISPTCTNQE----LRAKFEKYGPVIECDIVKD--------YAFVHFDRAE  123 (346)
T ss_pred             --------------------CCccccccCCCCccccCHH----HhhhhcccCCceeeeeecc--------eeEEEEeecc
Confidence                                1268999999999999998    7788999999999999875        7999999999


Q ss_pred             HHHHHHH-hCCceeCCeeeEEeccccCCCCCCC
Q 045516          576 SFNKALE-MSGTEIGGYSLVVDEAKQRGDFGSG  607 (675)
Q Consensus       576 ~A~~Al~-lng~~~~Gr~l~V~~a~~r~~~~~g  607 (675)
                      +|..||. |+|..|+|++|+|.....|-.-..|
T Consensus       124 da~~air~l~~~~~~gk~m~vq~stsrlrtapg  156 (346)
T KOG0109|consen  124 DAVEAIRGLDNTEFQGKRMHVQLSTSRLRTAPG  156 (346)
T ss_pred             chHHHHhcccccccccceeeeeeeccccccCCC
Confidence            9999998 9999999999999998876554433

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

Probab=99.89  E-value=6.6e-22  Score=221.24  Aligned_cols=181  Identities=24%  Similarity=0.447  Sum_probs=144.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEeccc
Q 045516          416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       416 ~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~  493 (675)
                      .++|||+|||+.+++++|++||..||.|..|.|+++. +|+++|||||+|.+.++|.+||. |||..|.|+.|.|.|+..
T Consensus       186 ~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~  265 (457)
T TIGR01622       186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQD  265 (457)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccC
Confidence            6899999999999999999999999999999999998 67999999999999999999997 999999999999999642


Q ss_pred             cCCCCC------------------------------------------CCCC------------CCC-------------
Q 045516          494 RGAYTP------------------------------------------YSGG------------NES-------------  506 (675)
Q Consensus       494 ~~~~~~------------------------------------------~~~~------------~~~-------------  506 (675)
                      ......                                          ....            ...             
T Consensus       266 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  345 (457)
T TIGR01622       266 STYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQRDGIIDPNIPSRYATGALA  345 (457)
T ss_pred             CCccccchhhhccccccccCCcCCCccchHHHHHhhccCCCCccccCCCccchhhhhccccccccccccccccccccccc
Confidence            110000                                          0000            000             


Q ss_pred             -----CCccCCCCCCCceEEEEecCCCCcCH------HHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHH
Q 045516          507 -----NSFQKGGRGQAAHTIFIKGFDSSVGE------DQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDAD  575 (675)
Q Consensus       507 -----~~~~~~~~~~~~~~lfV~nLp~~~te------~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e  575 (675)
                           ..........+..+|+|.||......      .+|.+.|.+.|.+||.|..|.|...    ...|++||.|.+.+
T Consensus       346 ~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~~~~~~~~~~~dv~~e~~k~G~v~~v~v~~~----~~~G~~fV~F~~~e  421 (457)
T TIGR01622       346 IMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFDNEILDDVKEECSKYGGVVHIYVDTK----NSAGKIYLKFSSVD  421 (457)
T ss_pred             cccCCCCCCcccCCCCCcEEEEecCCCCcccccchHHHHHHHHHHHHHHhcCCeeEEEEeCC----CCceeEEEEECCHH
Confidence                 00000002245788999999654432      4667789999999999999999743    35799999999999


Q ss_pred             HHHHHHH-hCCceeCCeeeEEecccc
Q 045516          576 SFNKALE-MSGTEIGGYSLVVDEAKQ  600 (675)
Q Consensus       576 ~A~~Al~-lng~~~~Gr~l~V~~a~~  600 (675)
                      .|..|+. |||.+|+|+.|.|.|...
T Consensus       422 ~A~~A~~~lnGr~f~gr~i~~~~~~~  447 (457)
T TIGR01622       422 AALAAFQALNGRYFGGKMITAAFVVN  447 (457)
T ss_pred             HHHHHHHHhcCcccCCeEEEEEEEcH
Confidence            9999998 999999999999998754

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.

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

Probab=99.88  E-value=3.7e-22  Score=193.13  Aligned_cols=182  Identities=27%  Similarity=0.473  Sum_probs=151.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCC--eeEEEEe
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGN--RAIRLDF  490 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~g--r~i~V~~  490 (675)
                      ..-.|||.+||..+|..+|..+|++||.|..-||+.|. +|.++|.+||.|....+|..||. |||+.-.|  .+|.|.|
T Consensus       126 k~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKF  205 (360)
T KOG0145|consen  126 KDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKF  205 (360)
T ss_pred             cccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEe
Confidence            45689999999999999999999999999999999987 99999999999999999999998 99998876  5799999


Q ss_pred             ccccCCCC-----------C--CCCCCCCC------------------CccC--------------CCCCCCceEEEEec
Q 045516          491 ARERGAYT-----------P--YSGGNESN------------------SFQK--------------GGRGQAAHTIFIKG  525 (675)
Q Consensus       491 a~~~~~~~-----------~--~~~~~~~~------------------~~~~--------------~~~~~~~~~lfV~n  525 (675)
                      +.......           +  +.+++...                  .|..              .+......+|||-|
T Consensus       206 annPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~~~~~~~~~~~rfsP~~~d~m~~l~~~~lp~~~~~g~ciFvYN  285 (360)
T KOG0145|consen  206 ANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLDNLLNPHAAQARFSPMTIDGMSGLAGVNLPGGPGGGWCIFVYN  285 (360)
T ss_pred             cCCcccccchhhhHHhhcCccccCCCcccchhhhhccccccchhhhhccCCCccccccceeeeeccCCCCCCeeEEEEEe
Confidence            87543211           0  00011000                  0000              00112367999999


Q ss_pred             CCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEecccc
Q 045516          526 FDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVDEAKQ  600 (675)
Q Consensus       526 Lp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~~a~~  600 (675)
                      |..+..+..    |+++|+.||-|..|.|++|+.|..++||+||.+.+.++|..||. |||..|++|.|.|.|-..
T Consensus       286 Lspd~de~~----LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFKtn  357 (360)
T KOG0145|consen  286 LSPDADESI----LWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTN  357 (360)
T ss_pred             cCCCchHhH----HHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEecC
Confidence            999988876    88999999999999999999999999999999999999999998 999999999999998654

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

Probab=99.88  E-value=1.1e-22  Score=204.85  Aligned_cols=176  Identities=23%  Similarity=0.445  Sum_probs=150.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~  492 (675)
                      -.|+||||.|.|.+.++.|+..|..||+|.+|.|..|+ +++++|||||+|.-++.|+.|++ |||..|+||.|+|.+..
T Consensus       112 iMcRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPs  191 (544)
T KOG0124|consen  112 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  191 (544)
T ss_pred             HhHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCC
Confidence            36899999999999999999999999999999999998 99999999999999999999998 99999999999997443


Q ss_pred             ccCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeC
Q 045516          493 ERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFT  572 (675)
Q Consensus       493 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~  572 (675)
                      .-....+..     ...+.  .....++|||..+..++++++    |+.+|..||.|.+|.+.++..++.++||+||+|.
T Consensus       192 NmpQAQpiI-----D~vqe--eAk~fnRiYVaSvHpDLSe~D----iKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~  260 (544)
T KOG0124|consen  192 NMPQAQPII-----DMVQE--EAKKFNRIYVASVHPDLSETD----IKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYN  260 (544)
T ss_pred             CCcccchHH-----HHHHH--HHHhhheEEeeecCCCccHHH----HHHHHHhhcceeeEEeeccCCCCCccceeeEEec
Confidence            221111000     00000  011258999999999999999    6678888899999999999999999999999999


Q ss_pred             CHHHHHHHHH-hCCceeCCeeeEEeccccC
Q 045516          573 DADSFNKALE-MSGTEIGGYSLVVDEAKQR  601 (675)
Q Consensus       573 ~~e~A~~Al~-lng~~~~Gr~l~V~~a~~r  601 (675)
                      +......||. ||-+.|+|+.|+|-.+...
T Consensus       261 n~qs~~eAiasMNlFDLGGQyLRVGk~vTP  290 (544)
T KOG0124|consen  261 NLQSQSEAIASMNLFDLGGQYLRVGKCVTP  290 (544)
T ss_pred             cccchHHHhhhcchhhcccceEecccccCC
Confidence            9999999998 9999999999999877543

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

Probab=99.86  E-value=1.2e-21  Score=213.33  Aligned_cols=172  Identities=26%  Similarity=0.487  Sum_probs=147.8

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCC----cccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecc
Q 045516          418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGR----FKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       418 tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~----~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~  492 (675)
                      +|||.||+|.++.+.|..+|..+|.|+.|.|...++..    +.|||||+|.+.++|+.||. |+|+.|+|+.|.|.++.
T Consensus       517 ~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~  596 (725)
T KOG0110|consen  517 KLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISE  596 (725)
T ss_pred             hhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEecc
Confidence            39999999999999999999999999999998877543    56999999999999999998 99999999999999997


Q ss_pred             ccCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeC
Q 045516          493 ERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFT  572 (675)
Q Consensus       493 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~  572 (675)
                      .....+..         .........+.|+|+|||+..+-.+    ++.+|..||.|..|+|+.-...+.+||||||.|.
T Consensus       597 ~k~~~~~g---------K~~~~kk~~tKIlVRNipFeAt~rE----Vr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~  663 (725)
T KOG0110|consen  597 NKPASTVG---------KKKSKKKKGTKILVRNIPFEATKRE----VRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFL  663 (725)
T ss_pred             Cccccccc---------cccccccccceeeeeccchHHHHHH----HHHHHhcccceeeeccchhhcchhhccceeeecc
Confidence            32211111         0111122268999999999999887    7899999999999999998777889999999999


Q ss_pred             CHHHHHHHHH-hCCceeCCeeeEEeccccCC
Q 045516          573 DADSFNKALE-MSGTEIGGYSLVVDEAKQRG  602 (675)
Q Consensus       573 ~~e~A~~Al~-lng~~~~Gr~l~V~~a~~r~  602 (675)
                      ++..|.+|+. |....|.||+|.+.|+....
T Consensus       664 t~~ea~nA~~al~STHlyGRrLVLEwA~~d~  694 (725)
T KOG0110|consen  664 TPREAKNAFDALGSTHLYGRRLVLEWAKSDN  694 (725)
T ss_pred             CcHHHHHHHHhhcccceechhhheehhccch
Confidence            9999999998 99999999999999997543

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

Probab=99.85  E-value=8.2e-22  Score=209.67  Aligned_cols=185  Identities=29%  Similarity=0.452  Sum_probs=158.1

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEE
Q 045516          411 PQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLD  489 (675)
Q Consensus       411 ~~~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~  489 (675)
                      +...+.+|||+-.|...++..+|++||+.+|.|.+|+|+.++ +++++|.|||+|.+.+.+..||.|.|+.++|.+|.|.
T Consensus       174 ~eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aiaLsGqrllg~pv~vq  253 (549)
T KOG0147|consen  174 PEERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIALSGQRLLGVPVIVQ  253 (549)
T ss_pred             chHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhhhcCCcccCceeEec
Confidence            335678999999999999999999999999999999999998 8999999999999999999999999999999999998


Q ss_pred             eccccCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEE
Q 045516          490 FARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYL  569 (675)
Q Consensus       490 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV  569 (675)
                      +...-....    ......++..+...+...|||+||.+++++.+    |..+|..||.|..|.+++|..||+++||+||
T Consensus       254 ~sEaeknr~----a~~s~a~~~k~~~~p~~rl~vgnLHfNite~~----lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi  325 (549)
T KOG0147|consen  254 LSEAEKNRA----ANASPALQGKGFTGPMRRLYVGNLHFNITEDM----LRGIFEPFGKIENVQLTKDSETGRSKGFGFI  325 (549)
T ss_pred             ccHHHHHHH----HhccccccccccccchhhhhhcccccCchHHH----HhhhccCcccceeeeeccccccccccCcceE
Confidence            765322111    11122233222233344599999999999998    7799999999999999999999999999999


Q ss_pred             EeCCHHHHHHHHH-hCCceeCCeeeEEeccccCCC
Q 045516          570 DFTDADSFNKALE-MSGTEIGGYSLVVDEAKQRGD  603 (675)
Q Consensus       570 ~F~~~e~A~~Al~-lng~~~~Gr~l~V~~a~~r~~  603 (675)
                      +|.+.+.|.+|+. |||..|.||.|+|.....+-.
T Consensus       326 ~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r~~  360 (549)
T KOG0147|consen  326 TFVNKEDARKALEQLNGFELAGRLIKVSVVTERVD  360 (549)
T ss_pred             EEecHHHHHHHHHHhccceecCceEEEEEeeeecc
Confidence            9999999999987 999999999999987765543

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

Probab=99.82  E-value=4.5e-19  Score=164.00  Aligned_cols=163  Identities=18%  Similarity=0.379  Sum_probs=129.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecc
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~  492 (675)
                      ...++|||+|||.++.+.+|.+||.+||.|..|.|...+  ....||||+|.++.+|..||. -||..++|..|+|.|+.
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~--g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfpr   81 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRP--GPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPR   81 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCC--CCCCeeEEEecCccchhhhhhcccccccCcceEEEEecc
Confidence            457999999999999999999999999999999987543  236899999999999999998 99999999999999998


Q ss_pred             ccCCCCCCCCCCCCC--------CccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCee
Q 045516          493 ERGAYTPYSGGNESN--------SFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVK  564 (675)
Q Consensus       493 ~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~r  564 (675)
                      .........+.....        ....+........|.|.+||...+|++    |++|+...|.|.+..+.+|       
T Consensus        82 ggr~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQD----LKDHmReaGdvCfadv~rD-------  150 (241)
T KOG0105|consen   82 GGRSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQD----LKDHMREAGDVCFADVQRD-------  150 (241)
T ss_pred             CCCcccccccccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHH----HHHHHHhhCCeeeeeeecc-------
Confidence            654222221111000        011111223467999999999999999    5566666699999999887       


Q ss_pred             eEEEEEeCCHHHHHHHHH-hCCceeC
Q 045516          565 GIAYLDFTDADSFNKALE-MSGTEIG  589 (675)
Q Consensus       565 G~afV~F~~~e~A~~Al~-lng~~~~  589 (675)
                      |++.|.|...+++.-|+. |....|.
T Consensus       151 g~GvV~~~r~eDMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  151 GVGVVEYLRKEDMKYAVRKLDDQKFR  176 (241)
T ss_pred             cceeeeeeehhhHHHHHHhhcccccc
Confidence            689999999999999997 8877664

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

Probab=99.82  E-value=1.6e-19  Score=193.43  Aligned_cols=154  Identities=29%  Similarity=0.497  Sum_probs=141.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEeccccC
Q 045516          417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARERG  495 (675)
Q Consensus       417 ~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~~~  495 (675)
                      ..||||   +++|+..|+++|+.+|.|+.|+|+++. + +.|||||.|.++.+|.+||. ||...|.|++|+|-|+....
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t-slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd~   76 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T-SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRDP   76 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecC-C-ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccCC
Confidence            479999   999999999999999999999999999 6 99999999999999999997 99999999999999986542


Q ss_pred             CCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHH
Q 045516          496 AYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDAD  575 (675)
Q Consensus       496 ~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e  575 (675)
                                             ..|||.||+..++...    |.++|+.||.|..|.+.++.. | ++|| ||+|.+.+
T Consensus        77 -----------------------~~~~i~nl~~~~~~~~----~~d~f~~~g~ilS~kv~~~~~-g-~kg~-FV~f~~e~  126 (369)
T KOG0123|consen   77 -----------------------SLVFIKNLDESIDNKS----LYDTFSEFGNILSCKVATDEN-G-SKGY-FVQFESEE  126 (369)
T ss_pred             -----------------------ceeeecCCCcccCcHH----HHHHHHhhcCeeEEEEEEcCC-C-ceee-EEEeCCHH
Confidence                                   2299999999999988    889999999999999999965 4 9999 99999999


Q ss_pred             HHHHHHH-hCCceeCCeeeEEeccccCCCCC
Q 045516          576 SFNKALE-MSGTEIGGYSLVVDEAKQRGDFG  605 (675)
Q Consensus       576 ~A~~Al~-lng~~~~Gr~l~V~~a~~r~~~~  605 (675)
                      .|.+||. |||..+.|..|.|.....+..+.
T Consensus       127 ~a~~ai~~~ng~ll~~kki~vg~~~~~~er~  157 (369)
T KOG0123|consen  127 SAKKAIEKLNGMLLNGKKIYVGLFERKEERE  157 (369)
T ss_pred             HHHHHHHHhcCcccCCCeeEEeeccchhhhc
Confidence            9999998 99999999999998887665544

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

Probab=99.81  E-value=1.2e-18  Score=195.04  Aligned_cols=79  Identities=22%  Similarity=0.437  Sum_probs=74.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~  492 (675)
                      ..++|||+|||+++++++|+++|+.||.|..|+|.++. +++++|||||+|.+.++|.+||. ||+..|+|+.|+|.++.
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi  282 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  282 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecC
Confidence            45799999999999999999999999999999999997 78899999999999999999997 99999999999998876


Q ss_pred             c
Q 045516          493 E  493 (675)
Q Consensus       493 ~  493 (675)
                      .
T Consensus       283 ~  283 (612)
T TIGR01645       283 T  283 (612)
T ss_pred             C
Confidence            4

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.

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

Probab=99.77  E-value=3.4e-19  Score=173.28  Aligned_cols=189  Identities=26%  Similarity=0.431  Sum_probs=153.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCccc-CC--eeEEE
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQML-GN--RAIRL  488 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~-~g--r~i~V  488 (675)
                      .++.|.||||-|...-.|++++.+|..||.|..|.+.+..+|.++||+||.|.+.-+|+.||. |||..- -|  ..|.|
T Consensus        16 g~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVV   95 (371)
T KOG0146|consen   16 GGDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVV   95 (371)
T ss_pred             CccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEE
Confidence            347899999999999999999999999999999999999999999999999999999999998 988654 33  44666


Q ss_pred             EeccccC---------------CCCC------------------------------------------------------
Q 045516          489 DFARERG---------------AYTP------------------------------------------------------  499 (675)
Q Consensus       489 ~~a~~~~---------------~~~~------------------------------------------------------  499 (675)
                      .|+....               .+.+                                                      
T Consensus        96 K~ADTdkER~lRRMQQma~qlGm~~Pl~l~~g~~~ay~qalmQqQa~~~at~~~~~L~p~~~~~~~~mQ~~aA~~angl~  175 (371)
T KOG0146|consen   96 KFADTDKERTLRRMQQMAGQLGMFNPLALPFGAYGAYAQALMQQQAALLATVAGPYLSPMAAFAAAQMQQMAALNANGLA  175 (371)
T ss_pred             EeccchHHHHHHHHHHHHHHhcccCccccccchhHHHHHHHHHHHHHHHHhhcccccChhhhhHHHHHHHHHHHhhcccc
Confidence            6663210               0000                                                      


Q ss_pred             ------CCCCCC-----------------CCCccC---------------------------------------------
Q 045516          500 ------YSGGNE-----------------SNSFQK---------------------------------------------  511 (675)
Q Consensus       500 ------~~~~~~-----------------~~~~~~---------------------------------------------  511 (675)
                            ..+...                 .+.+..                                             
T Consensus       176 A~Pv~p~s~~~~pp~~~a~~~~~~~A~~g~ng~~~l~~q~~gqpa~~~vy~ng~~pypaQsp~va~~lq~a~~g~~~Y~A  255 (371)
T KOG0146|consen  176 AAPVTPASGGSTPPGIGATAVPGIPAPIGVNGFTGLPPQPNGQPAAEAVYANGLHPYPAQSPTVADPLQQAYAGVQQYAA  255 (371)
T ss_pred             cCCcCccccCCCCCcccccccCCcccccccccccCCCCCCCCCcchhHHhhcCCccCCCCCccccchhhhhhhhHHHHhh
Confidence                  000000                 000000                                             


Q ss_pred             -----------------------CCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEE
Q 045516          512 -----------------------GGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAY  568 (675)
Q Consensus       512 -----------------------~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~af  568 (675)
                                             ...++..+.|||-+||..+++.+    |.+.|-.||.|....++.|+-|+.++.|+|
T Consensus       256 aypaays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaE----liQmF~PFGhivSaKVFvDRATNQSKCFGF  331 (371)
T KOG0146|consen  256 AYPAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAE----LIQMFLPFGHIVSAKVFVDRATNQSKCFGF  331 (371)
T ss_pred             hcchhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHH----HHHHhccccceeeeeeeehhccccccceee
Confidence                                   00134589999999999999998    778999999999999999999999999999


Q ss_pred             EEeCCHHHHHHHHH-hCCceeCCeeeEEeccccCCCCC
Q 045516          569 LDFTDADSFNKALE-MSGTEIGGYSLVVDEAKQRGDFG  605 (675)
Q Consensus       569 V~F~~~e~A~~Al~-lng~~~~Gr~l~V~~a~~r~~~~  605 (675)
                      |.|.++..+..||. |||..|+-++|+|.+-+|+..++
T Consensus       332 VSfDNp~SaQaAIqAMNGFQIGMKRLKVQLKRPkdanR  369 (371)
T KOG0146|consen  332 VSFDNPASAQAAIQAMNGFQIGMKRLKVQLKRPKDANR  369 (371)
T ss_pred             EecCCchhHHHHHHHhcchhhhhhhhhhhhcCccccCC
Confidence            99999999999999 99999999999999999887653

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

Probab=99.77  E-value=2.9e-17  Score=173.01  Aligned_cols=172  Identities=22%  Similarity=0.303  Sum_probs=134.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEeccc
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a~~  493 (675)
                      ....-|-+++|||.+|+++|++||+.|+ |.++.|.+ .+|+..|-|||+|.+.+++++||+++...+..|.|.|..+..
T Consensus         8 ~~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r-~~Gr~sGeA~Ve~~seedv~~AlkkdR~~mg~RYIEVf~~~~   85 (510)
T KOG4211|consen    8 STAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPR-RNGRPSGEAYVEFTSEEDVEKALKKDRESMGHRYIEVFTAGG   85 (510)
T ss_pred             CcceEEEecCCCccccHHHHHHHHhcCc-eeEEEEec-cCCCcCcceEEEeechHHHHHHHHhhHHHhCCceEEEEccCC
Confidence            3457899999999999999999999995 77755544 379999999999999999999999999999999999987754


Q ss_pred             cCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEE-EEecccCCCCCeeeEEEEEeC
Q 045516          494 RGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITR-ISVPKDYDTGSVKGIAYLDFT  572 (675)
Q Consensus       494 ~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~-v~i~~d~~tG~~rG~afV~F~  572 (675)
                      .........      . .........+|.|++||+.|++++|.++|..|    -.|.. |.|+.+ ..+++.|-|||+|.
T Consensus        86 ~e~d~~~~~------~-g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL----~Iv~~gi~l~~d-~rgR~tGEAfVqF~  153 (510)
T KOG4211|consen   86 AEADWVMRP------G-GPNSSANDGVVRLRGLPFSCTEEDIVEFFAGL----EIVPDGILLPMD-QRGRPTGEAFVQFE  153 (510)
T ss_pred             ccccccccC------C-CCCCCCCCceEEecCCCccCcHHHHHHHhcCC----cccccceeeecc-CCCCcccceEEEec
Confidence            432111110      0 00111246899999999999999966554443    44444 334444 45889999999999


Q ss_pred             CHHHHHHHHHhCCceeCCeeeEEeccc
Q 045516          573 DADSFNKALEMSGTEIGGYSLVVDEAK  599 (675)
Q Consensus       573 ~~e~A~~Al~lng~~~~Gr~l~V~~a~  599 (675)
                      +.+.|+.||..|...|+.|.|.|..+.
T Consensus       154 sqe~ae~Al~rhre~iGhRYIEvF~Ss  180 (510)
T KOG4211|consen  154 SQESAEIALGRHRENIGHRYIEVFRSS  180 (510)
T ss_pred             CHHHHHHHHHHHHHhhccceEEeehhH
Confidence            999999999999999999999998764

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

Probab=99.76  E-value=2e-18  Score=168.79  Aligned_cols=141  Identities=21%  Similarity=0.462  Sum_probs=118.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEeccc
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a~~  493 (675)
                      .+.|||||+||...+|++-|..||.+.|.|..++|+.+                                 .|+|.++..
T Consensus         4 ~~prtlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~---------------------------------e~~v~wa~~   50 (321)
T KOG0148|consen    4 DEPRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFD---------------------------------ELKVNWATA   50 (321)
T ss_pred             CCCceEEeeccChhhHHHHHHHHHHhccccccceeehh---------------------------------hhccccccC
Confidence            45699999999999999999999999999999999864                                 344555443


Q ss_pred             cCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCC
Q 045516          494 RGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTD  573 (675)
Q Consensus       494 ~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~  573 (675)
                      .......             .......|||+-|...+..+.    |++.|.+||+|..++|++|..|++++||+||.|-+
T Consensus        51 p~nQsk~-------------t~~~hfhvfvgdls~eI~~e~----lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~  113 (321)
T KOG0148|consen   51 PGNQSKP-------------TSNQHFHVFVGDLSPEIDNEK----LREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPN  113 (321)
T ss_pred             cccCCCC-------------ccccceeEEehhcchhcchHH----HHHHhccccccccceEeecccCCcccceeEEeccc
Confidence            3111000             011156799999999999887    77899999999999999999999999999999999


Q ss_pred             HHHHHHHHH-hCCceeCCeeeEEeccccCCCC
Q 045516          574 ADSFNKALE-MSGTEIGGYSLVVDEAKQRGDF  604 (675)
Q Consensus       574 ~e~A~~Al~-lng~~~~Gr~l~V~~a~~r~~~  604 (675)
                      .++|..||. |||.+|++|.|+-.|+..+...
T Consensus       114 k~dAEnAI~~MnGqWlG~R~IRTNWATRKp~e  145 (321)
T KOG0148|consen  114 KEDAENAIQQMNGQWLGRRTIRTNWATRKPSE  145 (321)
T ss_pred             hHHHHHHHHHhCCeeeccceeeccccccCccc
Confidence            999999998 9999999999999999876643

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

Probab=99.76  E-value=5.8e-18  Score=181.37  Aligned_cols=168  Identities=28%  Similarity=0.532  Sum_probs=146.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecccc
Q 045516          416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARER  494 (675)
Q Consensus       416 ~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~~  494 (675)
                      ...|||.||+..++...|+++|+.||.|++|++..+.+| ++|| ||+|.+.+.|.+||. |||..+.|+.|.|.+...+
T Consensus        76 ~~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~  153 (369)
T KOG0123|consen   76 PSLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENG-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERK  153 (369)
T ss_pred             CceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCC-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccch
Confidence            344999999999999999999999999999999999988 8999 999999999999998 9999999999999888765


Q ss_pred             CCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCH
Q 045516          495 GAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDA  574 (675)
Q Consensus       495 ~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~  574 (675)
                      ........         . .......++|.|++..++...    |..+|..||.|..+.++.+.. |.++||+||.|.++
T Consensus       154 ~er~~~~~---------~-~~~~~t~v~vk~~~~~~~~~~----l~~~f~~~g~i~s~~v~~~~~-g~~~~~gfv~f~~~  218 (369)
T KOG0123|consen  154 EEREAPLG---------E-YKKRFTNVYVKNLEEDSTDEE----LKDLFSAYGSITSVAVMRDSI-GKSKGFGFVNFENP  218 (369)
T ss_pred             hhhccccc---------c-hhhhhhhhheeccccccchHH----HHHhhcccCcceEEEEeecCC-CCCCCccceeecCh
Confidence            43322110         1 122357889999998888887    788999999999999999854 66999999999999


Q ss_pred             HHHHHHHH-hCCceeCCeeeEEecccc
Q 045516          575 DSFNKALE-MSGTEIGGYSLVVDEAKQ  600 (675)
Q Consensus       575 e~A~~Al~-lng~~~~Gr~l~V~~a~~  600 (675)
                      +.|..|+. ||+..+.+..+.|..+..
T Consensus       219 e~a~~av~~l~~~~~~~~~~~V~~aqk  245 (369)
T KOG0123|consen  219 EDAKKAVETLNGKIFGDKELYVGRAQK  245 (369)
T ss_pred             hHHHHHHHhccCCcCCccceeeccccc
Confidence            99999998 999999999999987765

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

Probab=99.76  E-value=3.7e-18  Score=181.95  Aligned_cols=183  Identities=26%  Similarity=0.479  Sum_probs=141.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      .+..++|||+||+++++++.|+.+|+.||.|..|.++++. +|+++||+||+|.+.++|.+|+. |||.+|-||.|+|..
T Consensus       275 ~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~  354 (549)
T KOG0147|consen  275 TGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSV  354 (549)
T ss_pred             ccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEE
Confidence            3455569999999999999999999999999999999998 99999999999999999999997 999999999999976


Q ss_pred             ccccCCCCCC------------------CCCCC------------------------------CCCcc------CCCCC-
Q 045516          491 ARERGAYTPY------------------SGGNE------------------------------SNSFQ------KGGRG-  515 (675)
Q Consensus       491 a~~~~~~~~~------------------~~~~~------------------------------~~~~~------~~~~~-  515 (675)
                      ...+......                  .++..                              ...+.      ..... 
T Consensus       355 v~~r~~~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~kla~~~~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~p~~  434 (549)
T KOG0147|consen  355 VTERVDTKEAAVTQFDFDEDDRQGLSLGSGGRNQLMAKLAEGKGRSLPSTAISALLLLAKLASAAQFNGVVRVRSVDPAD  434 (549)
T ss_pred             eeeecccccccccccccchhhccccccccccHHHHHHHHhccCCccccchhhhHHHhccccchHHhhcCCcCccccCccc
Confidence            6543211100                  00000                              00000      00011 


Q ss_pred             ------CCceEEEEecCCCCcC------HHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-
Q 045516          516 ------QAAHTIFIKGFDSSVG------EDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-  582 (675)
Q Consensus       516 ------~~~~~lfV~nLp~~~t------e~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-  582 (675)
                            .++.++.|.|+-...+      .++|++.+.+.+++||.|.+|.|..+     +-|+.||.|.+.+.|..|+. 
T Consensus       435 ~~p~~~i~t~C~lL~nMFdpstete~n~d~eI~edV~Eec~k~g~v~hi~vd~n-----s~g~VYvrc~s~~~A~~a~~a  509 (549)
T KOG0147|consen  435 ASPAFDIPTQCLLLSNMFDPSTETEPNWDQEIREDVIEECGKHGKVCHIFVDKN-----SAGCVYVRCPSAEAAGTAVKA  509 (549)
T ss_pred             cccccCCccHHHHHhhcCCcccccCcchhhHHHHHHHHHHHhcCCeeEEEEccC-----CCceEEEecCcHHHHHHHHHH
Confidence                  3355666677643222      26889999999999999999988665     23999999999999999998 


Q ss_pred             hCCceeCCeeeEEecccc
Q 045516          583 MSGTEIGGYSLVVDEAKQ  600 (675)
Q Consensus       583 lng~~~~Gr~l~V~~a~~  600 (675)
                      |||.||.|+.|.+.|-..
T Consensus       510 lhgrWF~gr~Ita~~~~~  527 (549)
T KOG0147|consen  510 LHGRWFAGRMITAKYLPL  527 (549)
T ss_pred             HhhhhhccceeEEEEeeh
Confidence            999999999999987653

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

Probab=99.76  E-value=1.8e-17  Score=155.09  Aligned_cols=84  Identities=25%  Similarity=0.514  Sum_probs=78.5

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEE
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVV  595 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V  595 (675)
                      ..++|||+||++.+++++    |+++|.+||.|..|.|+.+..+++++|||||+|.+.++|..||. ||+..|+|+.|+|
T Consensus        33 ~~~~lfVgnL~~~~te~~----L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V  108 (144)
T PLN03134         33 MSTKLFIGGLSWGTDDAS----LRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRV  108 (144)
T ss_pred             CCCEEEEeCCCCCCCHHH----HHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            378999999999999998    78899999999999999999999999999999999999999998 9999999999999


Q ss_pred             eccccCCCC
Q 045516          596 DEAKQRGDF  604 (675)
Q Consensus       596 ~~a~~r~~~  604 (675)
                      .++..+...
T Consensus       109 ~~a~~~~~~  117 (144)
T PLN03134        109 NPANDRPSA  117 (144)
T ss_pred             EeCCcCCCC
Confidence            999876553

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

Probab=99.75  E-value=3.3e-17  Score=157.99  Aligned_cols=173  Identities=19%  Similarity=0.362  Sum_probs=140.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHH----HhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEE
Q 045516          415 GSKTLFVGNLPFSVEQADVQN----FFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLD  489 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~----~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~  489 (675)
                      ...||||.||+..+..++|+.    ||++||.|++|....  +.+.+|.|||.|.+.+.|..|+. |+|..|.|.+|+|.
T Consensus         8 pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k--t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriq   85 (221)
T KOG4206|consen    8 PNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK--TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQ   85 (221)
T ss_pred             CCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC--CCCccCceEEEecChhHHHHHHHHhcCCcccCchhhee
Confidence            345999999999999999888    999999999998875  57889999999999999999997 99999999999999


Q ss_pred             eccccCCCCCCCC-------------------------CC--------CCCCccCCCCCCCceEEEEecCCCCcCHHHHH
Q 045516          490 FARERGAYTPYSG-------------------------GN--------ESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVR  536 (675)
Q Consensus       490 ~a~~~~~~~~~~~-------------------------~~--------~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~  536 (675)
                      |+...........                         +.        ....+. ....++..+||+.|||..++.+.  
T Consensus        86 yA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~-~~~~ppn~ilf~~niP~es~~e~--  162 (221)
T KOG4206|consen   86 YAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFL-AQMAPPNNILFLTNIPSESESEM--  162 (221)
T ss_pred             cccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCcc-ccCCCCceEEEEecCCcchhHHH--
Confidence            9976532211100                         00        000010 22356789999999999999887  


Q ss_pred             HHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeC-CeeeEEeccc
Q 045516          537 ASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIG-GYSLVVDEAK  599 (675)
Q Consensus       537 ~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~-Gr~l~V~~a~  599 (675)
                        |..+|.+|.....|+++...     .++|||+|.+...+..|+. +.+..|- ...|.|.++.
T Consensus       163 --l~~lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  163 --LSDLFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFAK  220 (221)
T ss_pred             --HHHHHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhhhhccceeccCceEEecccC
Confidence              88899999999999988764     6899999999999999998 9888886 8888887764

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

Probab=99.74  E-value=2.3e-17  Score=154.49  Aligned_cols=82  Identities=33%  Similarity=0.601  Sum_probs=76.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      ...+++|||+|||+++++++|+++|.+||.|.+|+|+.+. +++++|||||+|.+.++|+.||. ||++.|.|+.|+|.+
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~  110 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNP  110 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            3457899999999999999999999999999999999997 89999999999999999999997 999999999999999


Q ss_pred             cccc
Q 045516          491 ARER  494 (675)
Q Consensus       491 a~~~  494 (675)
                      +..+
T Consensus       111 a~~~  114 (144)
T PLN03134        111 ANDR  114 (144)
T ss_pred             CCcC
Confidence            8643

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

Probab=99.72  E-value=1.6e-17  Score=171.70  Aligned_cols=185  Identities=26%  Similarity=0.425  Sum_probs=151.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcc-cCC--eeEEEEe
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQM-LGN--RAIRLDF  490 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~-~~g--r~i~V~~  490 (675)
                      +.+.|||+-|+..+|+.+|+++|.+||.|.+|+|+++..+.+||||||.|.+.+.|..||+ |||.. +.|  .+|.|.|
T Consensus       123 ~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkF  202 (510)
T KOG0144|consen  123 EERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKF  202 (510)
T ss_pred             cchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEe
Confidence            4689999999999999999999999999999999999999999999999999999999998 99875 444  6789988


Q ss_pred             ccccCCCC-------------------CCC----------------------------------C---------------
Q 045516          491 ARERGAYT-------------------PYS----------------------------------G---------------  502 (675)
Q Consensus       491 a~~~~~~~-------------------~~~----------------------------------~---------------  502 (675)
                      +.......                   ++.                                  +               
T Consensus       203 ADtqkdk~~~~lqq~~~~~~qql~~~~~~~n~~~~~~l~~~~~~~~Qq~~~sqn~g~l~g~~~L~~l~a~~~qq~~~~~~  282 (510)
T KOG0144|consen  203 ADTQKDKDGKRLQQLNPALLQQLGNGQNPQNLASLGALSNGYQGPQQQTQQSQNVGTLGGLPPLGPLNATQLQQAAALAA  282 (510)
T ss_pred             cccCCCchHHHHHhhhHHHHHHhcCCCCccchhhhhccCcccCchhhhccccCCCcccccccCCCCcchhHHHHHHHhhh
Confidence            85321000                   000                                  0               


Q ss_pred             -------------C--------------C------CCCC-----------------------ccCC--------------
Q 045516          503 -------------G--------------N------ESNS-----------------------FQKG--------------  512 (675)
Q Consensus       503 -------------~--------------~------~~~~-----------------------~~~~--------------  512 (675)
                                   +              .      ....                       +...              
T Consensus       283 ~~ta~q~~~~s~q~~pl~~qts~~~~~~~~~~~~~~ss~~~~s~~~~aq~~~~q~~p~t~~~~n~~~~~a~a~~~sp~aa  362 (510)
T KOG0144|consen  283 AATAAQKTASSTQGLPLRTQTSFPGSQTSPQSASAPSSSLSTSQNPLAQLGARQTFPGTPANYNLAGGMAGAGTTSPVAA  362 (510)
T ss_pred             hcccccCCCCCcccCccccccCCccccCCCccccCccccCcccccchhhhhHhhcCCCCchhcccccccccccccCcccc
Confidence                         0              0      0000                       0000              


Q ss_pred             --------------------------------------------------------CCCCCceEEEEecCCCCcCHHHHH
Q 045516          513 --------------------------------------------------------GRGQAAHTIFIKGFDSSVGEDQVR  536 (675)
Q Consensus       513 --------------------------------------------------------~~~~~~~~lfV~nLp~~~te~~i~  536 (675)
                                                                              ..++....|||.+||..+.+.+  
T Consensus       363 ~~~~lq~~~ltp~~~~~~~~~tQa~q~~~q~a~~a~~~l~~q~~~~qq~~~~~~~q~eGpeGanlfiyhlPqefgdq~--  440 (510)
T KOG0144|consen  363 SLANLQQIGLTPFAGAAALDHTQAMQQYAQSANLAAPGLVGQQATTQQAQMVGNGQVEGPEGANLFIYHLPQEFGDQD--  440 (510)
T ss_pred             cccccccccCCChhhhhhHhHHHhhhHhhhhhhhcccchhhhhHhhhhhhcccCccccCCCccceeeeeCchhhhhHH--
Confidence                                                                    0123467899999999999988  


Q ss_pred             HHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEeccccCCC
Q 045516          537 ASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVDEAKQRGD  603 (675)
Q Consensus       537 ~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~~a~~r~~  603 (675)
                        |-..|..||.|....++.|..||.++.|+||.|++...|..||. |||..|++.+|+|...+.+.+
T Consensus       441 --l~~~f~pfG~Vlsakvfidk~tnlskcfgfvSyen~~sa~~aI~amngfQig~KrlkVQlk~~~~n  506 (510)
T KOG0144|consen  441 --LIATFQPFGGVLSAKVFIDKVTNLSKCFGFVSYENAQSAQNAISAMNGFQIGSKRLKVQLKRDRNN  506 (510)
T ss_pred             --HHHHhccccceeEEEEEEecccCHhhhcCcccccchhhhHHHHHHhcchhhccccceEEeeeccCC
Confidence              77889999999999999999999999999999999999999998 999999999999998876654

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

Probab=99.70  E-value=3e-16  Score=175.71  Aligned_cols=123  Identities=23%  Similarity=0.257  Sum_probs=95.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhC--CCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEV--AEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~--G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ..++|||+||++.+++++|+++|..|  |.|..|.++       ++||||+|.+.++|.+||. ||+..|.|+.|+|.|+
T Consensus       232 ~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~-------rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~A  304 (578)
T TIGR01648       232 KVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI-------RDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLA  304 (578)
T ss_pred             cccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee-------cCeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            45899999999999999999999999  999999887       5799999999999999997 9999999999999999


Q ss_pred             cccCCCCCC-----CCCC---CCC--CccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCc
Q 045516          492 RERGAYTPY-----SGGN---ESN--SFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGE  548 (675)
Q Consensus       492 ~~~~~~~~~-----~~~~---~~~--~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~  548 (675)
                      .+.......     .++.   ...  ........+...++++.||+++.++..    ++.+|..+|.
T Consensus       305 kp~~~~~~~~~~rg~gg~~~~~~~~~~~~g~~~sp~s~~~~~g~~~~~~~~~~----~~~~f~~~g~  367 (578)
T TIGR01648       305 KPVDKKSYVRYTRGTGGRGKERQAARQSLGQVYDPASRSLAYEDYYYHPPYAP----SLHFPRMPGP  367 (578)
T ss_pred             cCCCcccccccccccCCCcccccccccccCcccCccccccccccccccccccc----hhhccccCcc
Confidence            765322100     0000   000  011112334589999999999998886    7778877764

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.

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

Probab=99.69  E-value=1e-16  Score=156.25  Aligned_cols=160  Identities=24%  Similarity=0.525  Sum_probs=131.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEeccccC
Q 045516          417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARERG  495 (675)
Q Consensus       417 ~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~~~  495 (675)
                      ..|||++||+.+.+.+|..||..||.|.+|.|.       .||+||+|.+.-+|.-||. ||+.+|.|..|.|.++....
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk-------~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~~   74 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMK-------NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGKR   74 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceee-------cccceeccCchhhhhcccchhcCceecceeeeeecccccc
Confidence            479999999999999999999999999999998       6899999999999999997 99999999999999988643


Q ss_pred             CCCCCCCCCCCC--CccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCC
Q 045516          496 AYTPYSGGNESN--SFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTD  573 (675)
Q Consensus       496 ~~~~~~~~~~~~--~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~  573 (675)
                      .......+....  ...........+.|+|.||...+.|++    |.++|..+|.+....+        .++++||+|..
T Consensus        75 ~~~g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qd----l~d~~~~~g~~~~~~~--------~~~~~~v~Fs~  142 (216)
T KOG0106|consen   75 RGRGRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQD----LKDHFRPAGEVTYVDA--------RRNFAFVEFSE  142 (216)
T ss_pred             cccCCCCCCCccchhhccCCcccccceeeeccchhhhhHHH----HhhhhcccCCCchhhh--------hccccceeehh
Confidence            333111111000  111112234578899999999998888    8899999999955554        26799999999


Q ss_pred             HHHHHHHHH-hCCceeCCeeeEE
Q 045516          574 ADSFNKALE-MSGTEIGGYSLVV  595 (675)
Q Consensus       574 ~e~A~~Al~-lng~~~~Gr~l~V  595 (675)
                      .+++..||. |++..|.++.|.+
T Consensus       143 ~~da~ra~~~l~~~~~~~~~l~~  165 (216)
T KOG0106|consen  143 QEDAKRALEKLDGKKLNGRRISV  165 (216)
T ss_pred             hhhhhhcchhccchhhcCceeee
Confidence            999999999 9999999999999

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

Probab=99.68  E-value=1.5e-15  Score=153.55  Aligned_cols=184  Identities=17%  Similarity=0.336  Sum_probs=145.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeE--------EEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCC
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVV--------DVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGN  483 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~--------~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~g  483 (675)
                      ..-...|||.|||.++|.+++.++|+.||.|.        .|.|+++..|+.+|-|.|.|-..+++..||. |++..|.|
T Consensus       131 ~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg  210 (382)
T KOG1548|consen  131 PKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELRG  210 (382)
T ss_pred             cccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccccC
Confidence            34456799999999999999999999999874        4889999999999999999999999999998 99999999


Q ss_pred             eeEEEEecccc--CCCCCCCCCC------------------CCCCccCCCCCCCceEEEEecCCC----CcC---HHHHH
Q 045516          484 RAIRLDFARER--GAYTPYSGGN------------------ESNSFQKGGRGQAAHTIFIKGFDS----SVG---EDQVR  536 (675)
Q Consensus       484 r~i~V~~a~~~--~~~~~~~~~~------------------~~~~~~~~~~~~~~~~lfV~nLp~----~~t---e~~i~  536 (675)
                      +.|+|..+.-.  +.+.+.....                  ..............++|.|.||-.    ..+   ..+|+
T Consensus       211 ~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlk  290 (382)
T KOG1548|consen  211 KKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFEKNPDLLNDLK  290 (382)
T ss_pred             cEEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhccCHHHHHHHH
Confidence            99999988642  2221111100                  011111222344578999999753    233   34667


Q ss_pred             HHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEecccc
Q 045516          537 ASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVDEAKQ  600 (675)
Q Consensus       537 ~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~~a~~  600 (675)
                      +.|.+-+.+||.|..|.|.-.    .+.|.+.|.|.+.+.|..||+ |+|++|+||.|+...-..
T Consensus       291 edl~eec~K~G~v~~vvv~d~----hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG  351 (382)
T KOG1548|consen  291 EDLTEECEKFGQVRKVVVYDR----HPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWDG  351 (382)
T ss_pred             HHHHHHHHHhCCcceEEEecc----CCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeCC
Confidence            778888999999999988653    458999999999999999999 999999999999876543

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

Probab=99.66  E-value=3.5e-15  Score=154.18  Aligned_cols=180  Identities=23%  Similarity=0.419  Sum_probs=143.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhh-hCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFS-EVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~-~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~  492 (675)
                      -.|.+||.||||++.+++|++||. ..|.|..|.|+.|..|+.+|||.|+|.+++.+++|++ ||.+.+.||.|.|.-..
T Consensus        43 r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~  122 (608)
T KOG4212|consen   43 RDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDH  122 (608)
T ss_pred             ccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccC
Confidence            356799999999999999999998 5899999999999999999999999999999999998 99999999999996554


Q ss_pred             ccCC--CC-----------------------CCCC--------------------CC----CCCC---------------
Q 045516          493 ERGA--YT-----------------------PYSG--------------------GN----ESNS---------------  508 (675)
Q Consensus       493 ~~~~--~~-----------------------~~~~--------------------~~----~~~~---------------  508 (675)
                      ....  +.                       ....                    +.    ..+.               
T Consensus       123 d~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lfgl~~~  202 (608)
T KOG4212|consen  123 DEQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLFGLSAS  202 (608)
T ss_pred             chhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccccccccchhhhcccchhh
Confidence            3100  00                       0000                    00    0000               


Q ss_pred             ccC---CCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hC
Q 045516          509 FQK---GGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MS  584 (675)
Q Consensus       509 ~~~---~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-ln  584 (675)
                      |..   .-..+....+||.||.+.+....    |.+.|.-.|.|..|.+-.+.. |..+|||.|+|.++-.|..||. |+
T Consensus       203 Flr~~h~f~pPl~~k~fvanl~~~vg~~k----L~qvfgmAGkv~~vdf~idKe-G~s~G~~vi~y~hpveavqaIsml~  277 (608)
T KOG4212|consen  203 FLRSLHIFSPPLHNKVFVANLDYKVGNKK----LKQVFGMAGKVQSVDFSIDKE-GNSRGFAVIEYDHPVEAVQAISMLD  277 (608)
T ss_pred             hhhhccCCCCCccceeeeeccccccchHH----HHHHhccceeeeeeceeeccc-cccCCeeEEEecchHHHHHHHHhhc
Confidence            000   00223467899999999999765    888998899999999999866 6899999999999999999998 78


Q ss_pred             CceeCCeeeEEeccc
Q 045516          585 GTEIGGYSLVVDEAK  599 (675)
Q Consensus       585 g~~~~Gr~l~V~~a~  599 (675)
                      +.-+..+++.+.+.+
T Consensus       278 ~~g~~~~~~~~Rl~~  292 (608)
T KOG4212|consen  278 RQGLFDRRMTVRLDR  292 (608)
T ss_pred             cCCCccccceeeccc
Confidence            777778888777654

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.63  E-value=5.6e-15  Score=157.64  Aligned_cols=80  Identities=25%  Similarity=0.473  Sum_probs=73.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCC--eeEEEEe
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGN--RAIRLDF  490 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~g--r~i~V~~  490 (675)
                      ..++|||+|||+.+++++|++||.+||.|..|+|+++. +++++|||||+|.+.++|.+||+ ||++.|.+  ++|+|.+
T Consensus       192 ~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~  271 (346)
T TIGR01659       192 KDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRL  271 (346)
T ss_pred             ccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEE
Confidence            35689999999999999999999999999999999997 89999999999999999999998 99999876  6888888


Q ss_pred             cccc
Q 045516          491 ARER  494 (675)
Q Consensus       491 a~~~  494 (675)
                      +...
T Consensus       272 a~~~  275 (346)
T TIGR01659       272 AEEH  275 (346)
T ss_pred             CCcc
Confidence            7543

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).

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

Probab=99.60  E-value=1.2e-14  Score=149.50  Aligned_cols=162  Identities=30%  Similarity=0.462  Sum_probs=121.7

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEeccc
Q 045516          416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       416 ~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~  493 (675)
                      .++|||+|||+.+++++|+++|..||.|..|+|..+. ++.++|||||.|.+.+.|..||. |++..|.|+.|.|.+...
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~  194 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQP  194 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeecccc
Confidence            6999999999999999999999999999999999997 99999999999999999999998 999999999999999653


Q ss_pred             ----cCCCCCC--CCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEE
Q 045516          494 ----RGAYTPY--SGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIA  567 (675)
Q Consensus       494 ----~~~~~~~--~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~a  567 (675)
                          +......  ....................+++.+++..+....    +..+|..+|.+..+.+...........+.
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  270 (306)
T COG0724         195 ASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEE----LADLFKSRGDIVRASLPPSKDGKIPKSRS  270 (306)
T ss_pred             ccccccccccccchhhhccccccccccccccceeeccccccccchhH----HHHhccccccceeeeccCCCCCccccccc
Confidence                1111100  0000001111222344578999999999999887    77888999999888777765544444444


Q ss_pred             EEEeCCHHHHHHHH
Q 045516          568 YLDFTDADSFNKAL  581 (675)
Q Consensus       568 fV~F~~~e~A~~Al  581 (675)
                      ++.+.....+...+
T Consensus       271 ~~~~~~~~~~~~~~  284 (306)
T COG0724         271 FVGNEASKDALESN  284 (306)
T ss_pred             ccchhHHHhhhhhh
Confidence            44444444444433

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

Probab=99.59  E-value=9.6e-14  Score=146.70  Aligned_cols=179  Identities=22%  Similarity=0.358  Sum_probs=133.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEE-EEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEeccc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVD-VRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~-v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a~~  493 (675)
                      ....|-+++|||.||+++|.+||+-.-.|.. |.|+.+..+++.|-|||.|.+.+.|++||..|...|..|.|.|..+..
T Consensus       102 ~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~rhre~iGhRYIEvF~Ss~  181 (510)
T KOG4211|consen  102 NDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALGRHRENIGHRYIEVFRSSR  181 (510)
T ss_pred             CCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHHHHHHhhccceEEeehhHH
Confidence            5679999999999999999999998766655 667888889999999999999999999999999999999999866532


Q ss_pred             cC----------------CCCC---CCC--------CCCC-----------------------------------CCccC
Q 045516          494 RG----------------AYTP---YSG--------GNES-----------------------------------NSFQK  511 (675)
Q Consensus       494 ~~----------------~~~~---~~~--------~~~~-----------------------------------~~~~~  511 (675)
                      ..                .+..   .+.        ....                                   ..+..
T Consensus       182 ~e~~~~~~~~~~~~~rpGpy~~~~a~Rg~~d~~~~~~~~~~~~r~g~~~~g~~g~~~~~~~~d~~~~gs~~~~~~~~~~~  261 (510)
T KOG4211|consen  182 AEVKRAAGPGDGRVGRPGPYDRPGAPRGGYDYGQGRDPGRNATRYGAGGEGYYGFSRYPSLQDYGNFGSYGGGRDPNYPV  261 (510)
T ss_pred             HHHHhhccccccccCCCCccccccCCccccccccccCCCccccccccccCCccccccCccccccccccccccccccccCC
Confidence            10                0000   000        0000                                   00000


Q ss_pred             ------------CCC-CCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHH
Q 045516          512 ------------GGR-GQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFN  578 (675)
Q Consensus       512 ------------~~~-~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~  578 (675)
                                  ... ......+++++||+..+..+    +..+|+..-.+ .|+|... .+|+..|-|+|+|.+.++|.
T Consensus       262 ~~g~~~~g~~g~~~~~~~~g~fv~MRGlpy~a~~~d----i~nfFspl~p~-~v~i~ig-~dGr~TGEAdveF~t~edav  335 (510)
T KOG4211|consen  262 SSGPHRQGGAGDYGNGGPGGHFVHMRGLPYDATEND----IANFFSPLNPY-RVHIEIG-PDGRATGEADVEFATGEDAV  335 (510)
T ss_pred             CCCcccCCCcccccCCCCCCceeeecCCCccCCCcc----hhhhcCCCCce-eEEEEeC-CCCccCCcceeecccchhhH
Confidence                        000 11237889999999999998    55667644333 5555554 34999999999999999999


Q ss_pred             HHHHhCCceeCCeeeEEeccc
Q 045516          579 KALEMSGTEIGGYSLVVDEAK  599 (675)
Q Consensus       579 ~Al~lng~~~~Gr~l~V~~a~  599 (675)
                      .||.-++..++.+.|.+....
T Consensus       336 ~Amskd~anm~hrYVElFln~  356 (510)
T KOG4211|consen  336 GAMGKDGANMGHRYVELFLNG  356 (510)
T ss_pred             hhhccCCcccCcceeeecccC
Confidence            999999999999998887664

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

Probab=99.56  E-value=2.6e-14  Score=134.90  Aligned_cols=81  Identities=23%  Similarity=0.431  Sum_probs=76.4

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~  596 (675)
                      ...|.|-||-+.++.++    |..+|.+||.|.+|.|++|..|+.++|||||.|....+|..||+ |+|..|+|+.|+|+
T Consensus        13 m~SLkVdNLTyRTspd~----LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq   88 (256)
T KOG4207|consen   13 MTSLKVDNLTYRTSPDD----LRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQ   88 (256)
T ss_pred             ceeEEecceeccCCHHH----HHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeeh
Confidence            68999999999999998    78899999999999999999999999999999999999999999 99999999999999


Q ss_pred             ccccCC
Q 045516          597 EAKQRG  602 (675)
Q Consensus       597 ~a~~r~  602 (675)
                      +++-..
T Consensus        89 ~arygr   94 (256)
T KOG4207|consen   89 MARYGR   94 (256)
T ss_pred             hhhcCC
Confidence            986543

>PF00076 RRM_1: RNA recognition motif

Probab=99.55  E-value=1.4e-14  Score=117.84  Aligned_cols=69  Identities=43%  Similarity=0.814  Sum_probs=66.9

Q ss_pred             EEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEE
Q 045516          419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIR  487 (675)
Q Consensus       419 lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~  487 (675)
                      |||+|||+++++++|+++|.+||.|..|.|..+..++.+|||||+|.+.++|..||. |||..|.|+.|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            899999999999999999999999999999998889999999999999999999998 999999999986

(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 ....

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

Probab=99.55  E-value=7.6e-15  Score=128.50  Aligned_cols=79  Identities=29%  Similarity=0.526  Sum_probs=74.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ..++||||+||++.+++++|++||+.||.|..|.|-.++ +..+.|||||+|.+.++|..||. +||+.|+.++|+|+|.
T Consensus        34 r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D  113 (153)
T KOG0121|consen   34 RKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWD  113 (153)
T ss_pred             hhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeecc
Confidence            457999999999999999999999999999999999998 78899999999999999999999 9999999999999886


Q ss_pred             c
Q 045516          492 R  492 (675)
Q Consensus       492 ~  492 (675)
                      .
T Consensus       114 ~  114 (153)
T KOG0121|consen  114 A  114 (153)
T ss_pred             c
Confidence            4

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=99.53  E-value=2.7e-14  Score=147.84  Aligned_cols=180  Identities=34%  Similarity=0.469  Sum_probs=148.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHhCCc-ccCCeeEEEEec
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNGQ-MLGNRAIRLDFA  491 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~l~g~-~~~gr~i~V~~a  491 (675)
                      +...++||++|.+++.+.++..+|..+|.+..+.+.... ...++||++|.|...+.+..||.+.+. .+.++.+...+.
T Consensus        86 ~~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~  165 (285)
T KOG4210|consen   86 GSSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLN  165 (285)
T ss_pred             cccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCccc
Confidence            567899999999999999999999999998888887755 788999999999999999999997774 677777777766


Q ss_pred             cccCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEe
Q 045516          492 RERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDF  571 (675)
Q Consensus       492 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F  571 (675)
                      ..+..+...       .............++|.||++.++.++    |+.+|..||.|..|+++.+..++.+.||+||.|
T Consensus       166 ~~~~~~~~n-------~~~~~~~~~s~~~~~~~~~~f~~~~d~----~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~  234 (285)
T KOG4210|consen  166 TRRGLRPKN-------KLSRLSSGPSDTIFFVGELDFSLTRDD----LKEHFVSSGEITSVRLPTDEESGDSKGFAYVDF  234 (285)
T ss_pred             ccccccccc-------hhcccccCccccceeecccccccchHH----HhhhccCcCcceeeccCCCCCccchhhhhhhhh
Confidence            655421111       111122233344455999999999999    559999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHhCCceeCCeeeEEeccccCCCC
Q 045516          572 TDADSFNKALEMSGTEIGGYSLVVDEAKQRGDF  604 (675)
Q Consensus       572 ~~~e~A~~Al~lng~~~~Gr~l~V~~a~~r~~~  604 (675)
                      .....+..+|..+...+.+++++|.+..++...
T Consensus       235 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  267 (285)
T KOG4210|consen  235 SAGNSKKLALNDQTRSIGGRPLRLEEDEPRPKS  267 (285)
T ss_pred             hhchhHHHHhhcccCcccCcccccccCCCCccc
Confidence            999999999877788899999999998877654

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

Probab=99.52  E-value=2.2e-13  Score=135.56  Aligned_cols=84  Identities=27%  Similarity=0.487  Sum_probs=78.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      ...-+||||+-|++.+++..|+..|..||.|..|+|+++. +|+++|||||+|.++-++..|+. .+|+.|+|+.|.|++
T Consensus        98 gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDv  177 (335)
T KOG0113|consen   98 GDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDV  177 (335)
T ss_pred             CCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEe
Confidence            3567999999999999999999999999999999999997 99999999999999999999997 999999999999999


Q ss_pred             ccccCC
Q 045516          491 ARERGA  496 (675)
Q Consensus       491 a~~~~~  496 (675)
                      -..+..
T Consensus       178 ERgRTv  183 (335)
T KOG0113|consen  178 ERGRTV  183 (335)
T ss_pred             cccccc
Confidence            876643

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

Probab=99.52  E-value=5.9e-14  Score=152.27  Aligned_cols=187  Identities=17%  Similarity=0.363  Sum_probs=149.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      -..+.|||+|||..+++.+|.+++..||.+...+++.+. +|.++||||.+|.++.....|+. |||+.+++..|.|..+
T Consensus       287 ~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A  366 (500)
T KOG0120|consen  287 DSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRA  366 (500)
T ss_pred             cccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehh
Confidence            456899999999999999999999999999999999998 79999999999999999999998 9999999999999988


Q ss_pred             cccCCCCCCCCCCCCCCcc------CCCCCCCceEEEEecCC------CCcCHHHHHHHHHhhhcccCcEEEEEecccCC
Q 045516          492 RERGAYTPYSGGNESNSFQ------KGGRGQAAHTIFIKGFD------SSVGEDQVRASLEEHFGSCGEITRISVPKDYD  559 (675)
Q Consensus       492 ~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~lfV~nLp------~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~  559 (675)
                      .................+.      ....+.+..+|++.|+-      .+....+|.+.|+.-+++||.|..|.|++.+.
T Consensus       367 ~~g~~~~~~~~~~~~~~~~~i~~~~~q~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~~~  446 (500)
T KOG0120|consen  367 IVGASNANVNFNISQSQVPGIPLLMTQMAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRPYP  446 (500)
T ss_pred             hccchhccccCCccccccccchhhhcccCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCCCC
Confidence            6543322111110000111      12234456777777642      23344678888888899999999999999843


Q ss_pred             C---CCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEecccc
Q 045516          560 T---GSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVDEAKQ  600 (675)
Q Consensus       560 t---G~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~~a~~  600 (675)
                      .   ....|-.||+|.+.+++++|+. |+|..|+||.|.+.|...
T Consensus       447 ~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYyde  491 (500)
T KOG0120|consen  447 DENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDE  491 (500)
T ss_pred             CCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCH
Confidence            3   3356889999999999999998 999999999999988754

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.52  E-value=4.5e-14  Score=141.41  Aligned_cols=77  Identities=21%  Similarity=0.359  Sum_probs=71.9

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEecccc
Q 045516          416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARER  494 (675)
Q Consensus       416 ~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a~~~  494 (675)
                      .++|||+|||+.+++++|++||+.||.|.+|+|+++..  .+|||||+|.+.++|..||.|||..|.|+.|+|.++...
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~--~~GfAFVtF~d~eaAe~AllLnG~~l~gr~V~Vt~a~~~   80 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE--RSQIAYVTFKDPQGAETALLLSGATIVDQSVTITPAEDY   80 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC--CCCEEEEEeCcHHHHHHHHHhcCCeeCCceEEEEeccCC
Confidence            58999999999999999999999999999999998753  579999999999999999999999999999999998643

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

Probab=99.51  E-value=3e-13  Score=125.08  Aligned_cols=77  Identities=26%  Similarity=0.512  Sum_probs=72.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEeccc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~  493 (675)
                      ..+.|||+||+..++..+|..+|..||.|..|||..++    .|||||+|.++.+|..|+. |||..|.|..|+|+++..
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP----PGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G   84 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP----PGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTG   84 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC----CCceEEeccCcccHHHHHhhcCCccccCceEEEEeecC
Confidence            36899999999999999999999999999999999864    8999999999999999998 999999999999999875


Q ss_pred             cC
Q 045516          494 RG  495 (675)
Q Consensus       494 ~~  495 (675)
                      ..
T Consensus        85 ~~   86 (195)
T KOG0107|consen   85 RP   86 (195)
T ss_pred             Cc
Confidence            43

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

Probab=99.50  E-value=1.3e-13  Score=151.25  Aligned_cols=178  Identities=21%  Similarity=0.328  Sum_probs=136.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ....+.|+|+|||..+..++|..+|..||.|..|.|+.  .|   -.++|+|.++.+|..|+. |....|...+|++.++
T Consensus       382 ~rs~~vil~kNlpa~t~~~elt~~F~~fG~i~rvllp~--~G---~~aiv~fl~p~eAr~Afrklaysr~k~~plyle~a  456 (725)
T KOG0110|consen  382 ERSDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLLPP--GG---TGAIVEFLNPLEARKAFRKLAYSRFKSAPLYLEWA  456 (725)
T ss_pred             hhhcceeeeccCccccccHHHHHHhhcccccceeecCc--cc---ceeeeeecCccchHHHHHHhchhhhccCccccccC
Confidence            34568999999999999999999999999999996652  22   249999999999999998 9999999999999887


Q ss_pred             cccCCC-----CCCCC--CCC-------C-CCccC-----C------------CCCCCceEEEEecCCCCcCHHHHHHHH
Q 045516          492 RERGAY-----TPYSG--GNE-------S-NSFQK-----G------------GRGQAAHTIFIKGFDSSVGEDQVRASL  539 (675)
Q Consensus       492 ~~~~~~-----~~~~~--~~~-------~-~~~~~-----~------------~~~~~~~~lfV~nLp~~~te~~i~~~L  539 (675)
                      ....-.     .....  ...       . .....     .            ......++|||.||++..+.+.    |
T Consensus       457 P~dvf~~~pka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~~t~lfvkNlnf~Tt~e~----l  532 (725)
T KOG0110|consen  457 PEDVFTEDPKADDLSAESRSKMEENPSERVSAEDGQVEEDKDPTEESSLARVAEDEETETKLFVKNLNFDTTLED----L  532 (725)
T ss_pred             hhhhccCCccccccccccccccccCcceecccccccccccCCccccccchhhhhccccchhhhhhcCCcccchhH----H
Confidence            542211     00000  000       0 00000     0            0111233499999999999988    7


Q ss_pred             HhhhcccCcEEEEEecccCCCC---CeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEeccc
Q 045516          540 EEHFGSCGEITRISVPKDYDTG---SVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVDEAK  599 (675)
Q Consensus       540 ~~~F~~~G~I~~v~i~~d~~tG---~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~~a~  599 (675)
                      ..+|..+|.|..|.|....+.-   .+.|||||+|.+.++|..||. |+|+.|+|+.|.|.+..
T Consensus       533 ~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~  596 (725)
T KOG0110|consen  533 EDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISE  596 (725)
T ss_pred             HHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEecc
Confidence            7888889999999888765421   245999999999999999998 99999999999999988

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

Probab=99.49  E-value=1.3e-13  Score=143.65  Aligned_cols=76  Identities=33%  Similarity=0.468  Sum_probs=70.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEeccc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~  493 (675)
                      .-+.|||+||+.++|++.|+.+|.+||.|..|..++|       ||||.|.+.++|-+||+ +||+.|.|..|.|.++.+
T Consensus       258 ~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD-------YaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP  330 (506)
T KOG0117|consen  258 KVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD-------YAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKP  330 (506)
T ss_pred             heeeeeeeccchhhhHHHHHHHHHhccceEEeecccc-------eeEEeecchHHHHHHHHHhcCceecCceEEEEecCC
Confidence            3478999999999999999999999999999998854       99999999999999997 999999999999999987


Q ss_pred             cCCC
Q 045516          494 RGAY  497 (675)
Q Consensus       494 ~~~~  497 (675)
                      ....
T Consensus       331 ~~k~  334 (506)
T KOG0117|consen  331 VDKK  334 (506)
T ss_pred             hhhh
Confidence            6543

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

Probab=99.49  E-value=4.3e-13  Score=135.98  Aligned_cols=185  Identities=18%  Similarity=0.341  Sum_probs=138.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~  492 (675)
                      .-++|||..++.++++++|+.+|+-||+|+.|.|.+.+ .+.++||+||+|.+......||. ||-+.|+|+.|+|..+.
T Consensus       209 ~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~v  288 (544)
T KOG0124|consen  209 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  288 (544)
T ss_pred             hhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEeccccc
Confidence            34799999999999999999999999999999999998 56699999999999999999998 99999999999997664


Q ss_pred             ccCCCC--CCC----------------------------------CC---------------------------------
Q 045516          493 ERGAYT--PYS----------------------------------GG---------------------------------  503 (675)
Q Consensus       493 ~~~~~~--~~~----------------------------------~~---------------------------------  503 (675)
                      ......  +..                                  +.                                 
T Consensus       289 TPP~aLl~Pat~s~~P~aaaVAaAAaTAKi~A~eAvAg~avlg~~G~~~~vSpA~~aa~p~~~l~qa~~a~~~pgvi~~v  368 (544)
T KOG0124|consen  289 TPPDALLQPATVSAIPAAAAVAAAAATAKIMAAEAVAGSAVLGTVGAPGLVSPAPRAAQPLGTLPQAVMAAQAPGVITGV  368 (544)
T ss_pred             CCCchhcCCCCcccCchHHHHHHHHHHHHHHHHHHhccCCcccccCCccccCccccccCCCCCccccchhccCCceeccC
Confidence            321000  000                                  00                                 


Q ss_pred             -CCCC----CccC----------------------------------------------------------CCCCCCceE
Q 045516          504 -NESN----SFQK----------------------------------------------------------GGRGQAAHT  520 (675)
Q Consensus       504 -~~~~----~~~~----------------------------------------------------------~~~~~~~~~  520 (675)
                       +...    ....                                                          .-+...++.
T Consensus       369 tP~~P~iP~~i~p~g~v~P~LA~ppT~g~L~kkkeKe~eelqpkl~~~~~L~~QE~msI~G~sARhlvMqkLmR~~~S~V  448 (544)
T KOG0124|consen  369 TPARPPIPVTIPPVGVVNPILASPPTLGLLEKKKEKEEEELQPKLERPEMLSEQEHMSISGSSARHLVMQKLMRKQESTV  448 (544)
T ss_pred             CCCCCCCCccCCCcceechhhcCCCchhhcchhhhhhHhhhcccccCHHHhhhhhCccccCccHHHHHHHHHhccccCcE
Confidence             0000    0000                                                          001234678


Q ss_pred             EEEecCCCC-cCHHHHHHHHHhhhcccCcEEEEEecccCCCCC----eeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          521 IFIKGFDSS-VGEDQVRASLEEHFGSCGEITRISVPKDYDTGS----VKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       521 lfV~nLp~~-~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~----~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      |.++|+-.. --+++|...+++.+++||.|.+|.|.....++.    .---.||+|.....+.+|++ |+|++|+||.+.
T Consensus       449 ivLRNMV~P~DiDe~LegEi~EECgKfG~V~rViI~nekq~e~edaeiiVKIFVefS~~~e~~rak~ALdGRfFgGr~Vv  528 (544)
T KOG0124|consen  449 IVLRNMVDPKDIDEDLEGEITEECGKFGAVNRVIIYNEKQGEEEDAEIIVKIFVEFSIASETHRAKQALDGRFFGGRKVV  528 (544)
T ss_pred             EEEeccCChhhhhhHHHHHHHHHHhcccceeEEEEEecccccccchhhhheeeeeechhhHHHHHHHhhccceecCceee
Confidence            888987332 223456667788999999999999987765542    12347999999999999998 999999999988


Q ss_pred             Eeccc
Q 045516          595 VDEAK  599 (675)
Q Consensus       595 V~~a~  599 (675)
                      .....
T Consensus       529 AE~YD  533 (544)
T KOG0124|consen  529 AEVYD  533 (544)
T ss_pred             hhhhh
Confidence            76543

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

Probab=99.49  E-value=3.3e-13  Score=134.29  Aligned_cols=89  Identities=27%  Similarity=0.484  Sum_probs=81.9

Q ss_pred             CCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCee
Q 045516          514 RGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYS  592 (675)
Q Consensus       514 ~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~  592 (675)
                      ...+-+||||.-|++.+++..    |+..|..||.|..|+|+++..||.++|||||+|.+.-++..|.. .+|..|+|+.
T Consensus        97 ~gDPy~TLFv~RLnydT~Esk----LrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrr  172 (335)
T KOG0113|consen   97 IGDPYKTLFVARLNYDTSESK----LRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRR  172 (335)
T ss_pred             cCCccceeeeeeccccccHHH----HHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcE
Confidence            446789999999999999998    88999999999999999999999999999999999999999998 9999999999


Q ss_pred             eEEeccccCCCCCC
Q 045516          593 LVVDEAKQRGDFGS  606 (675)
Q Consensus       593 l~V~~a~~r~~~~~  606 (675)
                      |.|++.+.+...+.
T Consensus       173 i~VDvERgRTvkgW  186 (335)
T KOG0113|consen  173 ILVDVERGRTVKGW  186 (335)
T ss_pred             EEEEeccccccccc
Confidence            99999887655443

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

Probab=99.49  E-value=3.7e-13  Score=128.58  Aligned_cols=169  Identities=22%  Similarity=0.386  Sum_probs=122.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC--CCCcccEEEEEecCHHHHHHHHH-hCCcccC---CeeE
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA--DGRFKGYGHVEFASVEDAHKAIE-LNGQMLG---NRAI  486 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~--~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~---gr~i  486 (675)
                      .+.-|||||.+||.++.-.+|+.||..|---..+.|.+..  ..-.+-+|||.|.+...|..|+. |||..|+   +..|
T Consensus        31 ~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stL  110 (284)
T KOG1457|consen   31 PGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTL  110 (284)
T ss_pred             ccccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCcee
Confidence            3457999999999999999999999998777777666553  23366899999999999999997 9999995   7889


Q ss_pred             EEEeccccCCCCCCCCCCC----------CCC--------------------ccC-------------------------
Q 045516          487 RLDFARERGAYTPYSGGNE----------SNS--------------------FQK-------------------------  511 (675)
Q Consensus       487 ~V~~a~~~~~~~~~~~~~~----------~~~--------------------~~~-------------------------  511 (675)
                      +|++++.........+...          ..+                    ++.                         
T Consensus       111 hiElAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~~~l~a~~~~~  190 (284)
T KOG1457|consen  111 HIELAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTKSEALSAPDSKA  190 (284)
T ss_pred             EeeehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCccccccCCCccccchhhhhhhhhcC
Confidence            9999875432211111000          000                    000                         


Q ss_pred             -------------CCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHH
Q 045516          512 -------------GGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFN  578 (675)
Q Consensus       512 -------------~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~  578 (675)
                                   ........||||.||..+|++++    |+++|..|-....++|...  .|  ...|||.|.+.+.|.
T Consensus       191 P~a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~----l~~~~~~~~gf~~l~~~~~--~g--~~vaf~~~~~~~~at  262 (284)
T KOG1457|consen  191 PSANAHLEKSSQGGSGARACSTLFIANLGPNCTEDE----LKQLLSRYPGFHILKIRAR--GG--MPVAFADFEEIEQAT  262 (284)
T ss_pred             CcccchhhhhhcccccchhhhhHhhhccCCCCCHHH----HHHHHHhCCCceEEEEecC--CC--cceEeecHHHHHHHH
Confidence                         00112357999999999999999    5566666666555555432  12  457999999999999


Q ss_pred             HHHH-hCCceeC
Q 045516          579 KALE-MSGTEIG  589 (675)
Q Consensus       579 ~Al~-lng~~~~  589 (675)
                      .||. |.|..|-
T Consensus       263 ~am~~lqg~~~s  274 (284)
T KOG1457|consen  263 DAMNHLQGNLLS  274 (284)
T ss_pred             HHHHHhhcceec
Confidence            9998 9887763

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.48  E-value=1.4e-13  Score=112.43  Aligned_cols=69  Identities=43%  Similarity=0.775  Sum_probs=64.0

Q ss_pred             EEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEE
Q 045516          419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIR  487 (675)
Q Consensus       419 lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~  487 (675)
                      |||+|||+++++++|+++|..||.|..|+|..+..+.++|+|||+|.+.++|.+||. +++..|+|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            899999999999999999999999999999999888999999999999999999998 777999999885

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 ....

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

Probab=99.47  E-value=8.6e-14  Score=134.65  Aligned_cols=77  Identities=27%  Similarity=0.545  Sum_probs=73.0

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEeccc
Q 045516          417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       417 ~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a~~  493 (675)
                      +.||||||+|.+..+.|+++|++||+|+...|+.|+ +|+++||+||+|.+.+.|.+|+.--+-.|+||+..|.++.-
T Consensus        13 TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~piIdGR~aNcnlA~l   90 (247)
T KOG0149|consen   13 TKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPNPIIDGRKANCNLASL   90 (247)
T ss_pred             EEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCCCcccccccccchhhh
Confidence            589999999999999999999999999999999998 99999999999999999999999667789999999998865

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

Probab=99.46  E-value=1.8e-13  Score=132.78  Aligned_cols=81  Identities=30%  Similarity=0.482  Sum_probs=77.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      .+.++|-|.||+.++++.+|++||..||.|..|+|.+++ +|.++|||||.|.+.++|.+||. |||+-++...|+|.|+
T Consensus       187 ~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEws  266 (270)
T KOG0122|consen  187 DDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWS  266 (270)
T ss_pred             CccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEec
Confidence            467899999999999999999999999999999999998 99999999999999999999998 9999999999999999


Q ss_pred             ccc
Q 045516          492 RER  494 (675)
Q Consensus       492 ~~~  494 (675)
                      .++
T Consensus       267 kP~  269 (270)
T KOG0122|consen  267 KPS  269 (270)
T ss_pred             CCC
Confidence            764

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

Probab=99.46  E-value=6.5e-13  Score=122.86  Aligned_cols=79  Identities=20%  Similarity=0.423  Sum_probs=71.8

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~  596 (675)
                      .+.|||+||+..++..+    |+.+|..||.|..|.|...+     .|||||+|.++-+|..|+. |+|..|+|..|+|.
T Consensus        10 ~~kVYVGnL~~~a~k~e----LE~~F~~yG~lrsvWvArnP-----PGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE   80 (195)
T KOG0107|consen   10 NTKVYVGNLGSRATKRE----LERAFSKYGPLRSVWVARNP-----PGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVE   80 (195)
T ss_pred             CceEEeccCCCCcchHH----HHHHHHhcCcceeEEEeecC-----CCceEEeccCcccHHHHHhhcCCccccCceEEEE
Confidence            68999999999999998    88999999999999998864     7999999999999999998 99999999999999


Q ss_pred             ccccCCCCC
Q 045516          597 EAKQRGDFG  605 (675)
Q Consensus       597 ~a~~r~~~~  605 (675)
                      +...+....
T Consensus        81 ~S~G~~r~~   89 (195)
T KOG0107|consen   81 LSTGRPRGS   89 (195)
T ss_pred             eecCCcccc
Confidence            887655433

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

Probab=99.46  E-value=8.2e-14  Score=131.62  Aligned_cols=84  Identities=29%  Similarity=0.542  Sum_probs=79.8

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEE
Q 045516          410 TPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIR  487 (675)
Q Consensus       410 ~~~~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~  487 (675)
                      .|...+..+|.|-||.|.++.++|+.+|++||.|.+|+|+.+. ++.++|||||.|....+|+.||+ |+|.+|+|+.|+
T Consensus         7 PPdv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelr   86 (256)
T KOG4207|consen    7 PPDVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELR   86 (256)
T ss_pred             CCCcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceee
Confidence            4567789999999999999999999999999999999999998 99999999999999999999998 999999999999


Q ss_pred             EEeccc
Q 045516          488 LDFARE  493 (675)
Q Consensus       488 V~~a~~  493 (675)
                      |+++.-
T Consensus        87 Vq~ary   92 (256)
T KOG4207|consen   87 VQMARY   92 (256)
T ss_pred             ehhhhc
Confidence            999863

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.45  E-value=2.8e-13  Score=133.50  Aligned_cols=77  Identities=22%  Similarity=0.302  Sum_probs=71.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEeccc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a~~  493 (675)
                      ..++|||+||++.+|+++|++||+.||.|.+|+|+++  +...|||||+|.+++.+..||.|||..|.+++|.|.....
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D--~et~gfAfVtF~d~~aaetAllLnGa~l~d~~I~It~~~~   80 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRS--GEYACTAYVTFKDAYALETAVLLSGATIVDQRVCITRWGQ   80 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecC--CCcceEEEEEECCHHHHHHHHhcCCCeeCCceEEEEeCcc
Confidence            4689999999999999999999999999999999987  4556899999999999999999999999999999987654

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

Probab=99.43  E-value=1.7e-14  Score=133.63  Aligned_cols=81  Identities=28%  Similarity=0.562  Sum_probs=75.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      .++--||||||||.+|+.+|.-+|++||+|++|.|++|. ||+++||||+.|.+..+...|+. |||..|.||.|+|+..
T Consensus        33 kdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv  112 (219)
T KOG0126|consen   33 KDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHV  112 (219)
T ss_pred             ccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeec
Confidence            356789999999999999999999999999999999998 99999999999999999999997 9999999999999877


Q ss_pred             ccc
Q 045516          492 RER  494 (675)
Q Consensus       492 ~~~  494 (675)
                      ...
T Consensus       113 ~~Y  115 (219)
T KOG0126|consen  113 SNY  115 (219)
T ss_pred             ccc
Confidence            543

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

Probab=99.42  E-value=3e-13  Score=118.55  Aligned_cols=79  Identities=24%  Similarity=0.434  Sum_probs=75.3

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEE
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVV  595 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V  595 (675)
                      .+++|||+||.+.+++++    |.++|++||.|..|.|-.|+.+-.+-|||||+|.+.++|..||. ++|..|+.+.|+|
T Consensus        35 ~S~tvyVgNlSfyttEEq----iyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~  110 (153)
T KOG0121|consen   35 KSCTVYVGNLSFYTTEEQ----IYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRI  110 (153)
T ss_pred             hcceEEEeeeeeeecHHH----HHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceee
Confidence            379999999999999998    78999999999999999999999999999999999999999999 9999999999999


Q ss_pred             eccc
Q 045516          596 DEAK  599 (675)
Q Consensus       596 ~~a~  599 (675)
                      +|..
T Consensus       111 D~D~  114 (153)
T KOG0121|consen  111 DWDA  114 (153)
T ss_pred             eccc
Confidence            9864

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

Probab=99.42  E-value=6e-13  Score=123.63  Aligned_cols=76  Identities=20%  Similarity=0.386  Sum_probs=68.6

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~  596 (675)
                      .++|||+|||.++.+.+    |+++|-+||.|..|.|...+   .+-.||||+|.++-+|..||. -+|..|+|+.|+|.
T Consensus         6 ~~~iyvGNLP~diReke----ieDlFyKyg~i~~ieLK~r~---g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVE   78 (241)
T KOG0105|consen    6 SRRIYVGNLPGDIREKE----IEDLFYKYGRIREIELKNRP---GPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVE   78 (241)
T ss_pred             cceEEecCCCcchhhcc----HHHHHhhhcceEEEEeccCC---CCCCeeEEEecCccchhhhhhcccccccCcceEEEE
Confidence            68999999999999988    78999999999999886542   346899999999999999998 99999999999999


Q ss_pred             cccc
Q 045516          597 EAKQ  600 (675)
Q Consensus       597 ~a~~  600 (675)
                      |++.
T Consensus        79 fprg   82 (241)
T KOG0105|consen   79 FPRG   82 (241)
T ss_pred             eccC
Confidence            9863

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

Probab=99.39  E-value=1.8e-12  Score=109.54  Aligned_cols=80  Identities=21%  Similarity=0.458  Sum_probs=72.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ...++.|||+|||+.+|.+++.+||..||.|..|+|-..  ...+|.|||.|.+..+|.+|+. |+|..+.++.|.|-+.
T Consensus        15 pevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~--k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyy   92 (124)
T KOG0114|consen   15 PEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNT--KETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYY   92 (124)
T ss_pred             hhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCc--cCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEec
Confidence            356789999999999999999999999999999999764  3458999999999999999997 9999999999999887


Q ss_pred             ccc
Q 045516          492 RER  494 (675)
Q Consensus       492 ~~~  494 (675)
                      +..
T Consensus        93 q~~   95 (124)
T KOG0114|consen   93 QPE   95 (124)
T ss_pred             CHH
Confidence            643

>PLN03213 repressor of silencing 3; Provisional

Probab=99.39  E-value=8.9e-13  Score=138.31  Aligned_cols=76  Identities=28%  Similarity=0.450  Sum_probs=70.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCH--HHHHHHHH-hCCcccCCeeEEEEec
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASV--EDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~--e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ...+||||||+|.+++++|+.+|..||.|.+|.|++. +|  +|||||+|.+.  ..+.+||. |||..|+||.|+|..+
T Consensus         9 ~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE-TG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKA   85 (759)
T PLN03213          9 GGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT-KG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKA   85 (759)
T ss_pred             cceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc-cC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeec
Confidence            4579999999999999999999999999999999933 56  99999999987  78999998 9999999999999988


Q ss_pred             cc
Q 045516          492 RE  493 (675)
Q Consensus       492 ~~  493 (675)
                      ++
T Consensus        86 KP   87 (759)
T PLN03213         86 KE   87 (759)
T ss_pred             cH
Confidence            75

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

Probab=99.38  E-value=9.4e-13  Score=132.55  Aligned_cols=80  Identities=31%  Similarity=0.571  Sum_probs=74.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecc
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~  492 (675)
                      ...++|+|.||||...+-||+.+|.+||.|++|.|+.+..| +|||+||+|.+.++|.+|-+ |||..|.||.|.|..+.
T Consensus        94 ~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERG-SKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~AT  172 (376)
T KOG0125|consen   94 DTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERG-SKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNAT  172 (376)
T ss_pred             CCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCC-CCccceEEecChhhHHHHHHHhhcceeeceEEEEeccc
Confidence            45689999999999999999999999999999999987544 69999999999999999997 99999999999999998


Q ss_pred             cc
Q 045516          493 ER  494 (675)
Q Consensus       493 ~~  494 (675)
                      .+
T Consensus       173 ar  174 (376)
T KOG0125|consen  173 AR  174 (376)
T ss_pred             hh
Confidence            76

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

Probab=99.38  E-value=1.1e-11  Score=128.09  Aligned_cols=173  Identities=20%  Similarity=0.266  Sum_probs=135.4

Q ss_pred             CceEEEcCCC-CCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEeccc
Q 045516          416 SKTLFVGNLP-FSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       416 ~~tlfV~nLp-~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~  493 (675)
                      +..|.|.||. +.+|.+-|..+|.-||.|.+|.|++++    +-.|+|.|.+...|+.|+. |+|..|.|+.|+|.+++.
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nk----kd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH  372 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNK----KDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKH  372 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecC----CcceeeeecchhHHHHHHHHhhcceecCceEEEeeccC
Confidence            6899999995 678999999999999999999999875    4789999999999999998 999999999999999986


Q ss_pred             cCCCCCCCCCCC-----------CCCccC------CCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecc
Q 045516          494 RGAYTPYSGGNE-----------SNSFQK------GGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPK  556 (675)
Q Consensus       494 ~~~~~~~~~~~~-----------~~~~~~------~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~  556 (675)
                      .....+..+...           -..|..      ....+++.+|++.|+|..+++++    |+.+|..-|.......+.
T Consensus       373 ~~vqlp~egq~d~glT~dy~~spLhrfkkpgsKN~~ni~PpsatlHlsnip~svsee~----lk~~f~~~g~~vkafkff  448 (492)
T KOG1190|consen  373 TNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNYQNIFPPSATLHLSNIPPSVSEED----LKNLFQEPGGQVKAFKFF  448 (492)
T ss_pred             ccccCCCCCCccccccccCCCCchhhccCcccccccccCCchhheeeccCCcccchhH----HHHhhhcCCceEEeeeec
Confidence            554433322111           011111      12346788999999999999999    566666657554433322


Q ss_pred             cCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCe-eeEEecccc
Q 045516          557 DYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGY-SLVVDEAKQ  600 (675)
Q Consensus       557 d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr-~l~V~~a~~  600 (675)
                          +..+-++++.|.+.+.|..|+- +|++.+++. .|+|.|.+.
T Consensus       449 ----~kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSFSks  490 (492)
T KOG1190|consen  449 ----QKDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSFSKS  490 (492)
T ss_pred             ----CCCcceeecccCChhHhhhhccccccccCCCCceEEEEeecc
Confidence                2237799999999999999987 999999865 899998764

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

Probab=99.38  E-value=8.1e-13  Score=116.78  Aligned_cols=86  Identities=27%  Similarity=0.492  Sum_probs=80.2

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEE
Q 045516          410 TPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIR  487 (675)
Q Consensus       410 ~~~~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~  487 (675)
                      ++..-+...|||.|+...+++++|.+.|..||+|.+|+|-.++ +|..+|||+|+|.+...|+.||. |||..|+|+.|.
T Consensus        66 PqrSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~  145 (170)
T KOG0130|consen   66 PQRSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVS  145 (170)
T ss_pred             CccceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCcee
Confidence            3345688999999999999999999999999999999999998 99999999999999999999997 999999999999


Q ss_pred             EEeccccC
Q 045516          488 LDFARERG  495 (675)
Q Consensus       488 V~~a~~~~  495 (675)
                      |+|+-..+
T Consensus       146 VDw~Fv~g  153 (170)
T KOG0130|consen  146 VDWCFVKG  153 (170)
T ss_pred             EEEEEecC
Confidence            99997654

>smart00362 RRM_2 RNA recognition motif

Probab=99.36  E-value=3.2e-12  Score=103.34  Aligned_cols=71  Identities=49%  Similarity=0.844  Sum_probs=66.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEE
Q 045516          418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLD  489 (675)
Q Consensus       418 tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~  489 (675)
                      +|||+|||..++.++|+++|..||.|..|++..+. +.++|||||+|.+.+.|..|+. +++..|.|+.|.|.
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~-~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT-GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC-CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            69999999999999999999999999999999877 7789999999999999999998 99999999999873

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

Probab=99.36  E-value=4.9e-12  Score=136.10  Aligned_cols=76  Identities=22%  Similarity=0.424  Sum_probs=66.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEec
Q 045516          416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFA  491 (675)
Q Consensus       416 ~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a  491 (675)
                      ..+|||+|||++++..+|+++|..||.|...+|.... .+....||||+|.+...++.||..+-..|+++.|.|..-
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~Asp~~ig~~kl~Veek  364 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEASPLEIGGRKLNVEEK  364 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcCccccCCeeEEEEec
Confidence            3459999999999999999999999999999987654 455559999999999999999998888888898888654

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

Probab=99.34  E-value=1.3e-11  Score=131.72  Aligned_cols=182  Identities=15%  Similarity=0.257  Sum_probs=124.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-C--CCccc---EEEEEecCHHHHHHHHHhCCcccCCeeEE
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-D--GRFKG---YGHVEFASVEDAHKAIELNGQMLGNRAIR  487 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~--g~~kG---~afV~F~~~e~A~~Al~l~g~~~~gr~i~  487 (675)
                      .-++.||||+||+.++++.|...|..||.|.-=+-.+.. .  -..+|   |+|+.|.++..+...|.-.-..-.+..|.
T Consensus       257 ~~S~KVFvGGlp~dise~~i~~~F~~FGs~~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~~~~~~yf~  336 (520)
T KOG0129|consen  257 RYSRKVFVGGLPWDITEAQINASFGQFGSVKVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSEGEGNYYFK  336 (520)
T ss_pred             ccccceeecCCCccccHHHHHhhcccccceEeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhhcccceEEE
Confidence            457899999999999999999999999987654443221 1  22466   99999999999998885111122223333


Q ss_pred             EEeccccCC---CCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCee
Q 045516          488 LDFARERGA---YTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVK  564 (675)
Q Consensus       488 V~~a~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~r  564 (675)
                      |...+-+..   ..++................+.+||||++||.-++..+|-.+|.++   ||.|.++-|-+|.+-..++
T Consensus       337 vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~l---yGgV~yaGIDtD~k~KYPk  413 (520)
T KOG0129|consen  337 VSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDL---FGGVLYVGIDTDPKLKYPK  413 (520)
T ss_pred             EecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHh---cCceEEEEeccCcccCCCC
Confidence            332222211   1122211111111122344568999999999999999976666666   5899999999999899999


Q ss_pred             eEEEEEeCCHHHHHHHHHhCCceeCC----eeeEEecc
Q 045516          565 GIAYLDFTDADSFNKALEMSGTEIGG----YSLVVDEA  598 (675)
Q Consensus       565 G~afV~F~~~e~A~~Al~lng~~~~G----r~l~V~~a  598 (675)
                      |-|-|.|.+.....+||...-..|+.    .+|.|...
T Consensus       414 GaGRVtFsnqqsYi~AIsarFvql~h~d~~KRVEIkPY  451 (520)
T KOG0129|consen  414 GAGRVTFSNQQAYIKAISARFVQLDHTDIDKRVEIKPY  451 (520)
T ss_pred             CcceeeecccHHHHHHHhhheEEEeccccceeeeecce
Confidence            99999999999999999744444432    35555533

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

Probab=99.33  E-value=4.2e-12  Score=129.83  Aligned_cols=181  Identities=20%  Similarity=0.231  Sum_probs=134.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhC----CCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEe
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEV----AEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDF  490 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~----G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~  490 (675)
                      ..-.|.+++|||+++..+|.+||..-    |-+..|.|++..+|+..|-|||.|.++++|+.||..|...|+.|.|.|..
T Consensus       160 ~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~khrq~iGqRYIElFR  239 (508)
T KOG1365|consen  160 NQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALRKHRQNIGQRYIELFR  239 (508)
T ss_pred             cceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHHHHHHHHHHHHHhHHHHHHHH
Confidence            34568899999999999999999742    35678888888899999999999999999999999888888888887754


Q ss_pred             cccc--------CCCCCCCCCCCC-----CCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEE--EEec
Q 045516          491 ARER--------GAYTPYSGGNES-----NSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITR--ISVP  555 (675)
Q Consensus       491 a~~~--------~~~~~~~~~~~~-----~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~--v~i~  555 (675)
                      ++..        ....+..++...     ....-........+|.+++||+..+.++|..+|.++--   .|..  |++.
T Consensus       240 STaaEvqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~---~i~f~gVHmv  316 (508)
T KOG1365|consen  240 STAAEVQQVLNREVSEPLIPGLTSPLLPGGPARLVPPTRSKDCVRLRGLPYEATVEDILDFLGDFAT---DIRFQGVHMV  316 (508)
T ss_pred             HhHHHHHHHHHhhccccccCCCCCCCCCCCccccCCCCCCCCeeEecCCChhhhHHHHHHHHHHHhh---hcccceeEEE
Confidence            4321        110011110000     01111112233678999999999999998887776531   3333  7777


Q ss_pred             ccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEeccc
Q 045516          556 KDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVDEAK  599 (675)
Q Consensus       556 ~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~~a~  599 (675)
                      .+. .|++.|-|||+|.+.+.|..|+. .|.+.+..|.|.|..+.
T Consensus       317 ~N~-qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~S  360 (508)
T KOG1365|consen  317 LNG-QGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPCS  360 (508)
T ss_pred             EcC-CCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeecc
Confidence            764 49999999999999999999998 77777779999887664

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

Probab=99.33  E-value=3e-12  Score=124.37  Aligned_cols=80  Identities=30%  Similarity=0.494  Sum_probs=77.3

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~  596 (675)
                      .++|.|.||+.++++.+    |+++|..||.|.+|.|.+|..||.++|||||.|.+.++|.+||. |||+-+++-.|+|.
T Consensus       189 ~~tvRvtNLsed~~E~d----L~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvE  264 (270)
T KOG0122|consen  189 EATVRVTNLSEDMREDD----LEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVE  264 (270)
T ss_pred             cceeEEecCccccChhH----HHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEE
Confidence            68999999999999999    78899999999999999999999999999999999999999999 99999999999999


Q ss_pred             ccccC
Q 045516          597 EAKQR  601 (675)
Q Consensus       597 ~a~~r  601 (675)
                      |++|+
T Consensus       265 wskP~  269 (270)
T KOG0122|consen  265 WSKPS  269 (270)
T ss_pred             ecCCC
Confidence            99986

>PF00076 RRM_1: RNA recognition motif

Probab=99.32  E-value=8e-12  Score=101.54  Aligned_cols=69  Identities=29%  Similarity=0.633  Sum_probs=65.3

Q ss_pred             EEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          521 IFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       521 lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      |||+|||..+++.+    |+++|..||.|..+.+..+ .++..++||||+|.+.++|..|+. |||..|+|+.|+
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 LYVGNLPPDVTEEE----LRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHH----HHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHH----HHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            79999999999998    7788999999999999998 779999999999999999999999 999999999986

(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 ....

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

Probab=99.30  E-value=1.1e-11  Score=133.27  Aligned_cols=82  Identities=27%  Similarity=0.391  Sum_probs=69.6

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEec
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDE  597 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~~  597 (675)
                      ..+|||.|||.+++..+    |+++|..||.|...+|......+...+||||+|.+...+..||+.+-..|++++|.|..
T Consensus       288 ~~~i~V~nlP~da~~~~----l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~Asp~~ig~~kl~Vee  363 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAE----LEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEASPLEIGGRKLNVEE  363 (419)
T ss_pred             ccceEeecCCCCCCHHH----HHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcCccccCCeeEEEEe
Confidence            34599999999999998    88899999999999888754233334999999999999999999889999999999998


Q ss_pred             cccCCC
Q 045516          598 AKQRGD  603 (675)
Q Consensus       598 a~~r~~  603 (675)
                      -+++..
T Consensus       364 k~~~~~  369 (419)
T KOG0116|consen  364 KRPGFR  369 (419)
T ss_pred             cccccc
Confidence            776444

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

Probab=99.30  E-value=1.9e-10  Score=117.55  Aligned_cols=164  Identities=19%  Similarity=0.254  Sum_probs=128.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH---hCCcccCCeeEEEEe
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE---LNGQMLGNRAIRLDF  490 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~---l~g~~~~gr~i~V~~  490 (675)
                      ..+-.|.|+||-..+++.+|.+-++.||.|..|.++..     +..+.|+|.+.+.|..++.   -|...+.|+...+.+
T Consensus        29 ~~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P~-----~r~alvefedi~~akn~Vnfaa~n~i~i~gq~Al~Ny  103 (494)
T KOG1456|consen   29 NPSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMPH-----KRQALVEFEDIEGAKNCVNFAADNQIYIAGQQALFNY  103 (494)
T ss_pred             CCCceEEEeccccccchhHHHHHHhcCCceEEEEeccc-----cceeeeeeccccchhhheehhccCcccccCchhhccc
Confidence            44568999999999999999999999999999887754     6789999999999999996   466778888888888


Q ss_pred             ccccCCCCCCCCCCCCCCccCCCCCCCceEEEEecCC--CCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEE
Q 045516          491 ARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFD--SSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAY  568 (675)
Q Consensus       491 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp--~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~af  568 (675)
                      +.......+..           ....+...|.+.-|+  +.++-+-    |..++..+|.|.+|.|++..     --.|.
T Consensus       104 Stsq~i~R~g~-----------es~~pN~VLl~TIlNp~YpItvDV----ly~Icnp~GkVlRIvIfkkn-----gVQAm  163 (494)
T KOG1456|consen  104 STSQCIERPGD-----------ESATPNKVLLFTILNPQYPITVDV----LYTICNPQGKVLRIVIFKKN-----GVQAM  163 (494)
T ss_pred             chhhhhccCCC-----------CCCCCCeEEEEEeecCccccchhh----hhhhcCCCCceEEEEEEecc-----ceeeE
Confidence            76544322211           112235566655554  5566554    89999999999999998862     34699


Q ss_pred             EEeCCHHHHHHHHH-hCCceeC-C-eeeEEeccccCC
Q 045516          569 LDFTDADSFNKALE-MSGTEIG-G-YSLVVDEAKQRG  602 (675)
Q Consensus       569 V~F~~~e~A~~Al~-lng~~~~-G-r~l~V~~a~~r~  602 (675)
                      |+|.+.+.|++|.. |||..|. | +.|.|+|++|-+
T Consensus       164 VEFdsv~~AqrAk~alNGADIYsGCCTLKIeyAkP~r  200 (494)
T KOG1456|consen  164 VEFDSVEVAQRAKAALNGADIYSGCCTLKIEYAKPTR  200 (494)
T ss_pred             EeechhHHHHHHHhhcccccccccceeEEEEecCcce
Confidence            99999999999998 9999885 3 578999998743

>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=99.29  E-value=1.9e-11  Score=99.34  Aligned_cols=73  Identities=49%  Similarity=0.836  Sum_probs=68.8

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       418 tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      +|||+|||+.+++++|+++|..||.|..+.|..+..+.++|+|||+|.+.+.|..|+. +++..|.|+.|.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            5899999999999999999999999999999998866889999999999999999998 999999999999864

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).

>PF03546 Treacle: Treacher Collins syndrome protein Treacle; InterPro: IPR003993 Treacher Collins Syndrome (TCS) is an autosomal dominant disorder of craniofacial development, the features of which include conductive hearing loss and cleft palate [, ]; it is the most common of the human mandibulo-facial dysostosis disorders []

Probab=99.29  E-value=7.4e-11  Score=125.68  Aligned_cols=35  Identities=43%  Similarity=0.558  Sum_probs=24.8

Q ss_pred             CccccCcccccccCCCCCCCCCCCCCCCCCCccCCC
Q 045516          209 STAKKGTVAATKKSTGSSDDDSSSSEDSSESEEDNG  244 (675)
Q Consensus       209 ~~~k~~~~~~~~~~~~~~~~~sssse~~s~~e~~~~  244 (675)
                      ++.|.++++++.+.. ....+|+|||++|+++++..
T Consensus       199 ppqk~gpvatq~k~~-~~~~~SeSSEesS~SeeEa~  233 (519)
T PF03546_consen  199 PPQKAGPVATQAKAE-RPKEDSESSEESSDSEEEAP  233 (519)
T ss_pred             CccccCccccccccc-cccccccccccccccccccc
Confidence            356889999988764 45555666777777777764

The TCS locus has been mapped to human chromosome 5q31.3-32 and the mutated gene identified (TCOF1) []. To date, 35 mutations have been reported in TCOF1, all but one of which result in the introduction of a premature-termination codon into the predicted protein, Treacle. The observed mutational spectrum supports the hypothesis that TCS results from haploinsufficiency. Treacle is a low complexity protein of 1,411 amino acids whose predicted protein structure contains a set of highly polar repeated motifs []. These motifs are common to nucleolar trafficking proteins in other species and are predicted to be phosphorylated by casein kinase. In concert with this observation, the full-length TCOF1 protein sequence also contains putative nuclear and nucleolar localisation signals []. Throughout the open reading frame are found mutations in TCS families and several polymorphisms. It has thus been suggested that TCS results from defects in a nucleolar trafficking protein that is critically required during human craniofacial development.

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

Probab=99.28  E-value=8.6e-12  Score=135.58  Aligned_cols=183  Identities=25%  Similarity=0.445  Sum_probs=145.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhC-----------CC-eEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcc
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEV-----------AE-VVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQM  480 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~-----------G~-I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~  480 (675)
                      ....+.+||+|||+.++++.+..||..-           |+ |+.|.|-.     .++||||+|.+.+.|..|+.+++..
T Consensus       172 t~q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~n~-----~~nfa~ie~~s~~~at~~~~~~~~~  246 (500)
T KOG0120|consen  172 TRQARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQLNL-----EKNFAFIEFRSISEATEAMALDGII  246 (500)
T ss_pred             hhhhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeeecc-----cccceeEEecCCCchhhhhcccchh
Confidence            5678999999999999999999999863           22 56666543     4899999999999999999999999


Q ss_pred             cCCeeEEEEeccccCCCCCCCCC-----CCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEec
Q 045516          481 LGNRAIRLDFARERGAYTPYSGG-----NESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVP  555 (675)
Q Consensus       481 ~~gr~i~V~~a~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~  555 (675)
                      |.|+.+++......+........     ...............+.|||+|||..+++..++++|.    .||.+....++
T Consensus       247 f~g~~~~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~----~fg~lk~f~lv  322 (500)
T KOG0120|consen  247 FEGRPLKIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLD----SFGPLKAFRLV  322 (500)
T ss_pred             hCCCCceecccccccCCccchhhhccccccCCcccccCcccccchhhhccCcCccCHHHHHHHHH----hcccchhheee
Confidence            99999998655443322211111     1112222233344578999999999999999665555    45999999999


Q ss_pred             ccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEeccccCCCC
Q 045516          556 KDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVDEAKQRGDF  604 (675)
Q Consensus       556 ~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~~a~~r~~~  604 (675)
                      .+..+|.++||||.+|.+......|+. |||..+++..|.|..+......
T Consensus       323 ~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~~~  372 (500)
T KOG0120|consen  323 KDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGASN  372 (500)
T ss_pred             cccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccchh
Confidence            999999999999999999999999999 9999999999999998765443

>smart00360 RRM RNA recognition motif

Probab=99.26  E-value=2.1e-11  Score=98.09  Aligned_cols=69  Identities=43%  Similarity=0.751  Sum_probs=65.0

Q ss_pred             EcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEE
Q 045516          421 VGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLD  489 (675)
Q Consensus       421 V~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~  489 (675)
                      |+|||+.++.++|+.+|..||.|..|.|..+. ++.++|||||+|.+.+.|..|+. |++..|.|+.|+|.
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            68999999999999999999999999999887 68999999999999999999997 99999999999873

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.26  E-value=1.5e-11  Score=123.47  Aligned_cols=76  Identities=24%  Similarity=0.404  Sum_probs=70.5

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEec
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDE  597 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~~  597 (675)
                      .++|||+||++.+++.+    |++||+.||.|.+|+|+++..   .+|||||+|.+.+.|..||.|||..|+|+.|+|.+
T Consensus         4 ~rtVfVgNLs~~tTE~d----LrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~AllLnG~~l~gr~V~Vt~   76 (260)
T PLN03120          4 VRTVKVSNVSLKATERD----IKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALLLSGATIVDQSVTITP   76 (260)
T ss_pred             CCEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHHhcCCeeCCceEEEEe
Confidence            58999999999999998    789999999999999998853   47999999999999999999999999999999998


Q ss_pred             ccc
Q 045516          598 AKQ  600 (675)
Q Consensus       598 a~~  600 (675)
                      +..
T Consensus        77 a~~   79 (260)
T PLN03120         77 AED   79 (260)
T ss_pred             ccC
Confidence            753

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

Probab=99.26  E-value=3.9e-12  Score=121.23  Aligned_cols=83  Identities=30%  Similarity=0.534  Sum_probs=78.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      ...-|||||++|...+++.-|...|-.||.|.+|.|+.|. +++++||+||+|.-.++|..||. ||+..|.||.|+|.|
T Consensus         7 a~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~   86 (298)
T KOG0111|consen    7 ANQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNL   86 (298)
T ss_pred             cccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEee
Confidence            4556899999999999999999999999999999999998 89999999999999999999997 999999999999999


Q ss_pred             ccccC
Q 045516          491 ARERG  495 (675)
Q Consensus       491 a~~~~  495 (675)
                      +.+..
T Consensus        87 AkP~k   91 (298)
T KOG0111|consen   87 AKPEK   91 (298)
T ss_pred             cCCcc
Confidence            98653

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

Probab=99.24  E-value=2.5e-11  Score=117.69  Aligned_cols=79  Identities=27%  Similarity=0.386  Sum_probs=74.3

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEec
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDE  597 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~~  597 (675)
                      -..|||+||++.+..+.    |+++|.+||+|....|+.|+.+|+++||+||+|.+.+.|.+|+.--+-.|+||+..|.+
T Consensus        12 ~TKifVggL~w~T~~~~----l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~piIdGR~aNcnl   87 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKET----LRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPNPIIDGRKANCNL   87 (247)
T ss_pred             EEEEEEcCcccccchHH----HHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCCCcccccccccch
Confidence            57899999999999888    88999999999999999999999999999999999999999999778899999999998


Q ss_pred             ccc
Q 045516          598 AKQ  600 (675)
Q Consensus       598 a~~  600 (675)
                      +..
T Consensus        88 A~l   90 (247)
T KOG0149|consen   88 ASL   90 (247)
T ss_pred             hhh
Confidence            865

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

Probab=99.22  E-value=2e-11  Score=132.24  Aligned_cols=78  Identities=37%  Similarity=0.707  Sum_probs=75.7

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecccc
Q 045516          417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARER  494 (675)
Q Consensus       417 ~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~~  494 (675)
                      +.||||||||.+++++|..+|+.+|.|.+++|++|+ +|+++||||++|.+.+.+..|+. |||..|.||.|+|.|+...
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~   98 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNR   98 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccccc
Confidence            899999999999999999999999999999999998 99999999999999999999998 9999999999999998754

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.21  E-value=8.1e-11  Score=96.06  Aligned_cols=69  Identities=29%  Similarity=0.641  Sum_probs=62.6

Q ss_pred             EEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          521 IFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       521 lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      |||+|||+.++.++    |..+|..||.|..|.+..+.. |..+|+|||+|.+.+.|..|+. +++..|+|+.|+
T Consensus         1 v~i~nlp~~~~~~~----l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEED----LRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHH----HHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHH----HHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            79999999999988    778899999999999999977 9999999999999999999999 888999999885

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 ....

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

Probab=99.21  E-value=3.3e-11  Score=106.71  Aligned_cols=87  Identities=26%  Similarity=0.459  Sum_probs=80.1

Q ss_pred             CCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeee
Q 045516          515 GQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSL  593 (675)
Q Consensus       515 ~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l  593 (675)
                      .....+|||.++....++++    +.+.|..||.|..|+|-.|+.||..+|||+|+|.+...|+.||. |||..|.|+.|
T Consensus        69 SVEGwIi~VtgvHeEatEed----i~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v  144 (170)
T KOG0130|consen   69 SVEGWIIFVTGVHEEATEED----IHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNV  144 (170)
T ss_pred             ceeeEEEEEeccCcchhHHH----HHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCce
Confidence            34478999999999999998    78889999999999999999999999999999999999999998 99999999999


Q ss_pred             EEeccccCCCCC
Q 045516          594 VVDEAKQRGDFG  605 (675)
Q Consensus       594 ~V~~a~~r~~~~  605 (675)
                      .|+|+..++..+
T Consensus       145 ~VDw~Fv~gp~~  156 (170)
T KOG0130|consen  145 SVDWCFVKGPER  156 (170)
T ss_pred             eEEEEEecCCcc
Confidence            999998766543

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

Probab=99.17  E-value=8.8e-11  Score=99.45  Aligned_cols=77  Identities=22%  Similarity=0.410  Sum_probs=71.1

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~  596 (675)
                      .+.|||+|||+.++.++    +.++|++||.|..|+|-....|   +|.|||.|.+..+|.+|+. |+|..+.++.|.|-
T Consensus        18 nriLyirNLp~~ITsee----mydlFGkyg~IrQIRiG~~k~T---rGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vl   90 (124)
T KOG0114|consen   18 NRILYIRNLPFKITSEE----MYDLFGKYGTIRQIRIGNTKET---RGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVL   90 (124)
T ss_pred             heeEEEecCCccccHHH----HHHHhhcccceEEEEecCccCc---CceEEEEehHhhhHHHHHHHhcccccCCceEEEE
Confidence            68999999999999998    8899999999999999877654   8999999999999999998 99999999999998


Q ss_pred             ccccC
Q 045516          597 EAKQR  601 (675)
Q Consensus       597 ~a~~r  601 (675)
                      +..+-
T Consensus        91 yyq~~   95 (124)
T KOG0114|consen   91 YYQPE   95 (124)
T ss_pred             ecCHH
Confidence            87653

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

Probab=99.17  E-value=6.2e-12  Score=120.03  Aligned_cols=147  Identities=22%  Similarity=0.306  Sum_probs=119.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ....+||||+||-..++++-|.++|-+.|+|..|.|+.+.++..+ ||||.|.++-.+.-|++ +||..|.++.|.|.+-
T Consensus         6 ae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r   84 (267)
T KOG4454|consen    6 AEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLR   84 (267)
T ss_pred             cchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCc-eeeeecccccchhhhhhhcccchhccchhhcccc
Confidence            345689999999999999999999999999999999999888877 99999999999999999 8999999999998764


Q ss_pred             cccCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEe
Q 045516          492 RERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDF  571 (675)
Q Consensus       492 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F  571 (675)
                      .....                      .-     |...++.+    ++...|...|.|..+++.++++ |+.+.++||.+
T Consensus        85 ~G~sh----------------------ap-----ld~r~~~e----i~~~v~s~a~p~~~~R~~~~~d-~rnrn~~~~~~  132 (267)
T KOG4454|consen   85 CGNSH----------------------AP-----LDERVTEE----ILYEVFSQAGPIEGVRIPTDND-GRNRNFGFVTY  132 (267)
T ss_pred             cCCCc----------------------ch-----hhhhcchh----hheeeecccCCCCCcccccccc-CCccCccchhh
Confidence            32110                      00     22234443    3778899999999999999977 89999999998


Q ss_pred             CCHHHHHHHHH-hCCceeCCee
Q 045516          572 TDADSFNKALE-MSGTEIGGYS  592 (675)
Q Consensus       572 ~~~e~A~~Al~-lng~~~~Gr~  592 (675)
                      ......-.++. ..+..+.-+.
T Consensus       133 qr~~~~P~~~~~y~~l~~~~~~  154 (267)
T KOG4454|consen  133 QRLCAVPFALDLYQGLELFQKK  154 (267)
T ss_pred             hhhhcCcHHhhhhcccCcCCCC
Confidence            88777777776 5555444333

>PF03546 Treacle: Treacher Collins syndrome protein Treacle; InterPro: IPR003993 Treacher Collins Syndrome (TCS) is an autosomal dominant disorder of craniofacial development, the features of which include conductive hearing loss and cleft palate [, ]; it is the most common of the human mandibulo-facial dysostosis disorders []

Probab=99.17  E-value=2.5e-10  Score=121.66  Aligned_cols=37  Identities=35%  Similarity=0.610  Sum_probs=31.9

Q ss_pred             cccccccchhhccCCCCCCCCCCCCCCCCCCCCCCcc
Q 045516          119 VAAKNGAVAATAKKSKPDSSSSDSSDDDSDEDEVPTS  155 (675)
Q Consensus       119 ~~~k~~~~~~~~~~~k~~~~s~~ss~~~s~e~e~~~~  155 (675)
                      .+.|.++++.+++.++++.+|++|+|++++|+|.|++
T Consensus         4 ~pgk~gp~a~qaka~kpeedseSSsEeSdSe~E~pa~   40 (519)
T PF03546_consen    4 PPGKTGPLATQAKAGKPEEDSESSSEESDSEEEAPAA   40 (519)
T ss_pred             CCCCcCccccccccccccccccccccccccccccccc
Confidence            4678899999999999999999999988888887763

The TCS locus has been mapped to human chromosome 5q31.3-32 and the mutated gene identified (TCOF1) []. To date, 35 mutations have been reported in TCOF1, all but one of which result in the introduction of a premature-termination codon into the predicted protein, Treacle. The observed mutational spectrum supports the hypothesis that TCS results from haploinsufficiency. Treacle is a low complexity protein of 1,411 amino acids whose predicted protein structure contains a set of highly polar repeated motifs []. These motifs are common to nucleolar trafficking proteins in other species and are predicted to be phosphorylated by casein kinase. In concert with this observation, the full-length TCOF1 protein sequence also contains putative nuclear and nucleolar localisation signals []. Throughout the open reading frame are found mutations in TCS families and several polymorphisms. It has thus been suggested that TCS results from defects in a nucleolar trafficking protein that is critically required during human craniofacial development.

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

Probab=99.17  E-value=1.7e-11  Score=116.93  Aligned_cols=82  Identities=27%  Similarity=0.530  Sum_probs=76.8

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~  596 (675)
                      -++|||++|...+++.-    |...|-.||.|..|.|+.|+.++++|||+||+|.-.++|..||. ||+..|.||.|+|.
T Consensus        10 KrtlYVGGladeVtekv----LhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN   85 (298)
T KOG0111|consen   10 KRTLYVGGLADEVTEKV----LHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVN   85 (298)
T ss_pred             ceeEEeccchHHHHHHH----HHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEe
Confidence            68999999998888875    88999999999999999999999999999999999999999998 99999999999999


Q ss_pred             ccccCCC
Q 045516          597 EAKQRGD  603 (675)
Q Consensus       597 ~a~~r~~  603 (675)
                      +++|-.-
T Consensus        86 ~AkP~ki   92 (298)
T KOG0111|consen   86 LAKPEKI   92 (298)
T ss_pred             ecCCccc
Confidence            9987543

>PLN03213 repressor of silencing 3; Provisional

Probab=99.16  E-value=7e-11  Score=124.28  Aligned_cols=75  Identities=27%  Similarity=0.507  Sum_probs=69.3

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCH--HHHHHHHH-hCCceeCCeeeE
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDA--DSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~--e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      ..+|||+||.+.+++++    |+.+|..||.|.+|.|+  +.+|  ||||||+|.+.  ..+.+||. |||..|.||.|+
T Consensus        10 gMRIYVGNLSydVTEDD----LravFSeFGsVkdVEIp--RETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LK   81 (759)
T PLN03213         10 GVRLHVGGLGESVGRDD----LLKIFSPMGTVDAVEFV--RTKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLR   81 (759)
T ss_pred             ceEEEEeCCCCCCCHHH----HHHHHHhcCCeeEEEEe--cccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeE
Confidence            68999999999999999    78889999999999999  4567  99999999987  78999998 999999999999


Q ss_pred             Eecccc
Q 045516          595 VDEAKQ  600 (675)
Q Consensus       595 V~~a~~  600 (675)
                      |..|++
T Consensus        82 VNKAKP   87 (759)
T PLN03213         82 LEKAKE   87 (759)
T ss_pred             EeeccH
Confidence            999865

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

Probab=99.16  E-value=7.9e-12  Score=116.15  Aligned_cols=77  Identities=31%  Similarity=0.488  Sum_probs=72.8

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~  596 (675)
                      +..|||+|||+.+++.+    |--+|++||+|..|.|++|..||.++||||+.|.+..+-..|+. |||..|.||.|+|+
T Consensus        35 sA~Iyiggl~~~LtEgD----il~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVD  110 (219)
T KOG0126|consen   35 SAYIYIGGLPYELTEGD----ILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVD  110 (219)
T ss_pred             ceEEEECCCcccccCCc----EEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEee
Confidence            67899999999999998    67899999999999999999999999999999999999999997 99999999999998


Q ss_pred             cc
Q 045516          597 EA  598 (675)
Q Consensus       597 ~a  598 (675)
                      ..
T Consensus       111 Hv  112 (219)
T KOG0126|consen  111 HV  112 (219)
T ss_pred             ec
Confidence            54

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.14  E-value=1.6e-10  Score=114.23  Aligned_cols=75  Identities=21%  Similarity=0.394  Sum_probs=69.4

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEec
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDE  597 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~~  597 (675)
                      ..+|||+||++.+++.+    |++||+.||.|.+|+|+++   +...+||||+|.+.+.+..||.|||..|.++.|.|..
T Consensus         5 g~TV~V~NLS~~tTE~d----LrefFS~~G~I~~V~I~~D---~et~gfAfVtF~d~~aaetAllLnGa~l~d~~I~It~   77 (243)
T PLN03121          5 GYTAEVTNLSPKATEKD----VYDFFSHCGAIEHVEIIRS---GEYACTAYVTFKDAYALETAVLLSGATIVDQRVCITR   77 (243)
T ss_pred             ceEEEEecCCCCCCHHH----HHHHHHhcCCeEEEEEecC---CCcceEEEEEECCHHHHHHHHhcCCCeeCCceEEEEe
Confidence            68999999999999998    8899999999999999998   4556899999999999999999999999999999986


Q ss_pred             cc
Q 045516          598 AK  599 (675)
Q Consensus       598 a~  599 (675)
                      ..
T Consensus        78 ~~   79 (243)
T PLN03121         78 WG   79 (243)
T ss_pred             Cc
Confidence            53

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

Probab=99.14  E-value=6.8e-10  Score=114.95  Aligned_cols=172  Identities=23%  Similarity=0.341  Sum_probs=126.5

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCccc-EEEEEecCHHHHHHHHH-hCCcccCC--eeEEEEec
Q 045516          416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKG-YGHVEFASVEDAHKAIE-LNGQMLGN--RAIRLDFA  491 (675)
Q Consensus       416 ~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG-~afV~F~~~e~A~~Al~-l~g~~~~g--r~i~V~~a  491 (675)
                      --+++|.|+-+-++.+-|..+|+.||.|..|.....    +.| .|+|.|.+...|+.|.. |+|..|..  ..|+|+|+
T Consensus       150 vLr~iie~m~ypVslDVLHqvFS~fG~VlKIiTF~K----nn~FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~S  225 (492)
T KOG1190|consen  150 VLRTIIENMFYPVSLDVLHQVFSKFGFVLKIITFTK----NNGFQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFS  225 (492)
T ss_pred             eEEEEeccceeeeEHHHHHHHHhhcceeEEEEEEec----ccchhhhhhccchhhHHHHHHhccCCcccCceeEEEeehh
Confidence            357899999999999999999999999988865542    234 48999999999999986 99998854  44666665


Q ss_pred             cccCC-----------CC-CCC-CC-----------------------CC--CCC-----ccCCCCCC--CceEEEEecC
Q 045516          492 RERGA-----------YT-PYS-GG-----------------------NE--SNS-----FQKGGRGQ--AAHTIFIKGF  526 (675)
Q Consensus       492 ~~~~~-----------~~-~~~-~~-----------------------~~--~~~-----~~~~~~~~--~~~~lfV~nL  526 (675)
                      .-...           ++ +.. .+                       +.  ...     ...+....  ....|.|.||
T Consensus       226 klt~LnvKynndkSRDyTnp~LP~gd~~p~l~~~~~aa~~~~~~~~g~p~aip~~~~~a~~a~~~~~~~~~n~vllvsnl  305 (492)
T KOG1190|consen  226 KLTDLNVKYNNDKSRDYTNPDLPVGDGQPSLDQLMAAAFGSVPAVHGAPLAIPSGAAGANAADGKIESPSANVVLLVSNL  305 (492)
T ss_pred             hcccceeeccccccccccCCCCCCCccccccchhhhccccccccccCCcccCCccchhhcccccccccCCCceEEEEecC
Confidence            42110           00 000 00                       00  000     00000111  2578888998


Q ss_pred             CC-CcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEecccc
Q 045516          527 DS-SVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVDEAKQ  600 (675)
Q Consensus       527 p~-~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~~a~~  600 (675)
                      .. .+|.+-    |..+|+-||.|.+|.|+.+.     +-.|+|+|.+...|..|+. |+|+.|.|+.|+|.+.+-
T Consensus       306 n~~~VT~d~----LftlFgvYGdVqRVkil~nk-----kd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH  372 (492)
T KOG1190|consen  306 NEEAVTPDV----LFTLFGVYGDVQRVKILYNK-----KDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKH  372 (492)
T ss_pred             chhccchhH----HHHHHhhhcceEEEEeeecC-----CcceeeeecchhHHHHHHHHhhcceecCceEEEeeccC
Confidence            65 466665    88999999999999999875     3579999999999999999 999999999999999864

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

Probab=99.14  E-value=7.5e-11  Score=118.99  Aligned_cols=81  Identities=15%  Similarity=0.318  Sum_probs=74.0

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEE
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVV  595 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V  595 (675)
                      ..++|+|.|||+.+.+.+    |+.+|.+||.|.+|.|+.+.  .-++||+||+|.+.++|.+|.+ |||..+.||.|.|
T Consensus        95 ~pkRLhVSNIPFrFRdpD----L~aMF~kfG~VldVEIIfNE--RGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEV  168 (376)
T KOG0125|consen   95 TPKRLHVSNIPFRFRDPD----LRAMFEKFGKVLDVEIIFNE--RGSKGFGFVTMENPADADRARAELHGTVVEGRKIEV  168 (376)
T ss_pred             CCceeEeecCCccccCcc----HHHHHHhhCceeeEEEEecc--CCCCccceEEecChhhHHHHHHHhhcceeeceEEEE
Confidence            468999999999999998    78899999999999999873  4579999999999999999998 9999999999999


Q ss_pred             eccccCCC
Q 045516          596 DEAKQRGD  603 (675)
Q Consensus       596 ~~a~~r~~  603 (675)
                      ..+..|-.
T Consensus       169 n~ATarV~  176 (376)
T KOG0125|consen  169 NNATARVH  176 (376)
T ss_pred             eccchhhc
Confidence            99987744

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

Probab=99.14  E-value=3.6e-10  Score=117.52  Aligned_cols=80  Identities=26%  Similarity=0.492  Sum_probs=72.0

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEE
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVV  595 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V  595 (675)
                      ..+.+||.||||++.|++|++++++.   .|+|++|.|+.| ..|++||+|.|+|.+++.+++|++ ||.+.+.||.|.|
T Consensus        43 r~R~vfItNIpyd~rWqdLKdLvrek---vGev~yveLl~D-~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~v  118 (608)
T KOG4212|consen   43 RDRSVFITNIPYDYRWQDLKDLVREK---VGEVEYVELLFD-ESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVV  118 (608)
T ss_pred             ccceEEEecCcchhhhHhHHHHHHHh---cCceEeeeeecc-cCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEE
Confidence            35679999999999999977776664   699999999999 469999999999999999999999 9999999999999


Q ss_pred             ecccc
Q 045516          596 DEAKQ  600 (675)
Q Consensus       596 ~~a~~  600 (675)
                      .....
T Consensus       119 KEd~d  123 (608)
T KOG4212|consen  119 KEDHD  123 (608)
T ss_pred             eccCc
Confidence            87754

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

Probab=99.08  E-value=3e-10  Score=108.34  Aligned_cols=81  Identities=27%  Similarity=0.433  Sum_probs=74.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhC-CCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEV-AEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~-G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      .....+||..||+.+.+.+|..+|.+| |.|..++|.+++ ||.++|||||+|.+++.|.-|.+ ||++.|+|+.|.|.+
T Consensus        47 ~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~v  126 (214)
T KOG4208|consen   47 EIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHV  126 (214)
T ss_pred             CCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEE
Confidence            445789999999999999999999998 788999997776 99999999999999999999998 999999999999999


Q ss_pred             cccc
Q 045516          491 ARER  494 (675)
Q Consensus       491 a~~~  494 (675)
                      ..+.
T Consensus       127 mppe  130 (214)
T KOG4208|consen  127 MPPE  130 (214)
T ss_pred             eCch
Confidence            8654

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

Probab=99.06  E-value=6.2e-10  Score=115.83  Aligned_cols=85  Identities=24%  Similarity=0.430  Sum_probs=79.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEeccc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a~~  493 (675)
                      ..+.|||++||.++++.+|+++|.+||.|..+.|+++. +.+.+||+||.|.+.+.+.+++.+..+.|.|+.+.|..+.+
T Consensus        96 ~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~~~f~~~~gk~vevkrA~p  175 (311)
T KOG4205|consen   96 RTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTLQKFHDFNGKKVEVKRAIP  175 (311)
T ss_pred             ceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecccceeeecCceeeEeeccc
Confidence            46799999999999999999999999999999999998 89999999999999999999999999999999999999988


Q ss_pred             cCCCCC
Q 045516          494 RGAYTP  499 (675)
Q Consensus       494 ~~~~~~  499 (675)
                      +.....
T Consensus       176 k~~~~~  181 (311)
T KOG4205|consen  176 KEVMQS  181 (311)
T ss_pred             hhhccc
Confidence            765443

>PF13893 RRM_5: RNA recognition motif

Probab=99.05  E-value=6.4e-10  Score=86.71  Aligned_cols=55  Identities=42%  Similarity=0.761  Sum_probs=50.2

Q ss_pred             HHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          433 VQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       433 L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      |+++|++||.|..|.+....    +++|||+|.+.++|..|+. |||..|.|++|+|.|+
T Consensus         1 L~~~f~~fG~V~~i~~~~~~----~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK----RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS----TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            78999999999999998653    6999999999999999998 9999999999999885

(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 ....

>smart00362 RRM_2 RNA recognition motif

Probab=99.05  E-value=7.9e-10  Score=89.15  Aligned_cols=71  Identities=37%  Similarity=0.733  Sum_probs=64.3

Q ss_pred             EEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEe
Q 045516          520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVD  596 (675)
Q Consensus       520 ~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~  596 (675)
                      +|||.|||..++.++    |+.+|..||.|..+.+..+.  +.++|+|||+|.+...|..|+. +++..|.|+.|+|.
T Consensus         1 ~v~i~~l~~~~~~~~----l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEED----LKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHH----HHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            589999999999988    66777888999999999876  7789999999999999999998 99999999999874

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

Probab=99.03  E-value=4.3e-10  Score=115.50  Aligned_cols=79  Identities=32%  Similarity=0.622  Sum_probs=75.0

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~  596 (675)
                      .++|||+||++.+++++    |..+|..||.|..|+|..+..+|.++|||||.|.+.+.+..|+. |++..|.|+.|.|.
T Consensus       115 ~~~l~v~nL~~~~~~~~----l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~  190 (306)
T COG0724         115 NNTLFVGNLPYDVTEED----LRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQ  190 (306)
T ss_pred             CceEEEeCCCCCCCHHH----HHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEee
Confidence            59999999999999998    78899999999999999999999999999999999999999998 99999999999999


Q ss_pred             cccc
Q 045516          597 EAKQ  600 (675)
Q Consensus       597 ~a~~  600 (675)
                      +...
T Consensus       191 ~~~~  194 (306)
T COG0724         191 KAQP  194 (306)
T ss_pred             cccc
Confidence            9653

>smart00361 RRM_1 RNA recognition motif

Probab=99.03  E-value=8.9e-10  Score=90.15  Aligned_cols=59  Identities=29%  Similarity=0.432  Sum_probs=53.3

Q ss_pred             HHHHHHHhh----hCCCeEEEE-EeeCC-C--CCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEE
Q 045516          430 QADVQNFFS----EVAEVVDVR-LSSDA-D--GRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRL  488 (675)
Q Consensus       430 e~~L~~~F~----~~G~I~~v~-i~~~~-~--g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V  488 (675)
                      +++|+++|.    .||.|..|. |+.+. +  ++++|||||.|.+.++|.+||. |||..|.||.|++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            578999999    999999996 66655 4  8899999999999999999998 9999999999986

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

Probab=99.02  E-value=2.6e-10  Score=111.80  Aligned_cols=83  Identities=24%  Similarity=0.452  Sum_probs=79.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      .+.|.|||-.||....+.+|..+|-.||.|++.++..|+ ++.++.|+||.|.++..++.||. |||+.|+-++|+|.+.
T Consensus       283 PeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQLK  362 (371)
T KOG0146|consen  283 PEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQLK  362 (371)
T ss_pred             CCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhhhc
Confidence            478999999999999999999999999999999999999 99999999999999999999998 9999999999999998


Q ss_pred             cccCC
Q 045516          492 RERGA  496 (675)
Q Consensus       492 ~~~~~  496 (675)
                      +++..
T Consensus       363 RPkda  367 (371)
T KOG0146|consen  363 RPKDA  367 (371)
T ss_pred             Ccccc
Confidence            87754

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

Probab=99.00  E-value=2.2e-10  Score=128.82  Aligned_cols=159  Identities=21%  Similarity=0.350  Sum_probs=133.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ...++|||++||...+++.+|+..|..||.|..|.|-.-.-++-.-|+||.|.+...+..|+. +.+..|....+++.+.
T Consensus       369 ~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG  448 (975)
T KOG0112|consen  369 FRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLG  448 (975)
T ss_pred             hhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhhcCCccccCccccccc
Confidence            356799999999999999999999999999999999877667777899999999999999885 8888886666666554


Q ss_pred             cccCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEe
Q 045516          492 RERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDF  571 (675)
Q Consensus       492 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F  571 (675)
                      ...                    ..+.+.+||++|..-+....    |...|..||.|..|.|...      .-|+||.|
T Consensus       449 ~~k--------------------st~ttr~~sgglg~w~p~~~----l~r~fd~fGpir~Idy~hg------q~yayi~y  498 (975)
T KOG0112|consen  449 QPK--------------------STPTTRLQSGGLGPWSPVSR----LNREFDRFGPIRIIDYRHG------QPYAYIQY  498 (975)
T ss_pred             ccc--------------------cccceeeccCCCCCCChHHH----HHHHhhccCcceeeecccC------Ccceeeec
Confidence            321                    22368899999998887765    8899999999999877543      46999999


Q ss_pred             CCHHHHHHHHH-hCCceeCC--eeeEEeccccC
Q 045516          572 TDADSFNKALE-MSGTEIGG--YSLVVDEAKQR  601 (675)
Q Consensus       572 ~~~e~A~~Al~-lng~~~~G--r~l~V~~a~~r  601 (675)
                      .+...+..|+. |.|..|+|  +.|+|.|+.+-
T Consensus       499 es~~~aq~a~~~~rgap~G~P~~r~rvdla~~~  531 (975)
T KOG0112|consen  499 ESPPAAQAATHDMRGAPLGGPPRRLRVDLASPP  531 (975)
T ss_pred             ccCccchhhHHHHhcCcCCCCCcccccccccCC
Confidence            99999999998 99999986  67999988643

>smart00361 RRM_1 RNA recognition motif

Probab=98.99  E-value=1.5e-09  Score=88.86  Aligned_cols=65  Identities=17%  Similarity=0.360  Sum_probs=55.5

Q ss_pred             HHHHHHHHHhhhcccCcEEEEE-ecccCCC--CCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEe
Q 045516          532 EDQVRASLEEHFGSCGEITRIS-VPKDYDT--GSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVD  596 (675)
Q Consensus       532 e~~i~~~L~~~F~~~G~I~~v~-i~~d~~t--G~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~  596 (675)
                      +++|+++|...+..||.|..|. |+.+..+  +.++|||||.|.+.++|..|+. |||..|.|+.|++.
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~~   70 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKAE   70 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEeC
Confidence            3566666666666999999996 7776666  9999999999999999999998 99999999999873

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

Probab=98.99  E-value=4e-10  Score=105.18  Aligned_cols=80  Identities=23%  Similarity=0.433  Sum_probs=74.9

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~  596 (675)
                      ..+|||+||+..++++.    |+++|-++|.|.+|+|++|+.+..++|||||+|.+.++|.-|+. ||...|.|++|+|.
T Consensus         9 d~tiyvgnld~kvs~~~----l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~   84 (203)
T KOG0131|consen    9 DATLYVGNLDEKVSEEL----LYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVN   84 (203)
T ss_pred             CceEEEecCCHHHHHHH----HHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEE
Confidence            68999999999998876    78889999999999999999999999999999999999999999 99999999999999


Q ss_pred             ccccC
Q 045516          597 EAKQR  601 (675)
Q Consensus       597 ~a~~r  601 (675)
                      .+...
T Consensus        85 kas~~   89 (203)
T KOG0131|consen   85 KASAH   89 (203)
T ss_pred             ecccc
Confidence            88743

>smart00360 RRM RNA recognition motif

Probab=98.98  E-value=1.4e-09  Score=87.30  Aligned_cols=70  Identities=34%  Similarity=0.638  Sum_probs=63.6

Q ss_pred             EecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEe
Q 045516          523 IKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVD  596 (675)
Q Consensus       523 V~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~  596 (675)
                      |+|||..+++++    |+.+|..||.|..|.|..+..++.++|||||+|.+.+.|..|+. |++..|+|+.|+|.
T Consensus         1 i~~l~~~~~~~~----l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEE----LRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHH----HHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            578999999988    66777888999999999988889999999999999999999998 99999999999874

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

Probab=98.97  E-value=8e-11  Score=131.92  Aligned_cols=148  Identities=19%  Similarity=0.244  Sum_probs=127.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEecc
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a~  492 (675)
                      .+..++||.||+..+.+.+|..+|..||.|..|+|.... +++++|+|||+|..++++.+||.++...|.|         
T Consensus       665 R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g---------  735 (881)
T KOG0128|consen  665 RDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG---------  735 (881)
T ss_pred             HHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhh---------
Confidence            456799999999999999999999999999888887444 7999999999999999999999976666655         


Q ss_pred             ccCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeC
Q 045516          493 ERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFT  572 (675)
Q Consensus       493 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~  572 (675)
                                               ...|||.|+|+..|.++    |+.+|..+|.+..++++..+. |.++|.+||.|.
T Consensus       736 -------------------------K~~v~i~g~pf~gt~e~----~k~l~~~~gn~~~~~~vt~r~-gkpkg~a~v~y~  785 (881)
T KOG0128|consen  736 -------------------------KISVAISGPPFQGTKEE----LKSLASKTGNVTSLRLVTVRA-GKPKGKARVDYN  785 (881)
T ss_pred             -------------------------hhhhheeCCCCCCchHH----HHhhccccCCccccchhhhhc-cccccceeccCC
Confidence                                     14578999999999987    788999999999999887754 999999999999


Q ss_pred             CHHHHHHHHH-hCCceeCCeeeEEecccc
Q 045516          573 DADSFNKALE-MSGTEIGGYSLVVDEAKQ  600 (675)
Q Consensus       573 ~~e~A~~Al~-lng~~~~Gr~l~V~~a~~  600 (675)
                      +..++.+++. ++...+.-+.+.|....|
T Consensus       786 ~ea~~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  786 TEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             CcchhhhhcccchhhhhhhcCccccccCC
Confidence            9999999987 877777766666666444

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

Probab=98.97  E-value=9.1e-10  Score=119.42  Aligned_cols=84  Identities=26%  Similarity=0.474  Sum_probs=78.7

Q ss_pred             eEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEec
Q 045516          519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVDE  597 (675)
Q Consensus       519 ~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~~  597 (675)
                      +.|||+|+|+.+++++    |..+|...|.|..++++.|++||.++||||++|.+.+.|..|+. |||..|+||.|+|.|
T Consensus        19 ~~v~vgnip~~~se~~----l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~   94 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQ----LLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNY   94 (435)
T ss_pred             cceEecCCCCcccHHH----HHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeec
Confidence            8999999999999998    77888899999999999999999999999999999999999998 999999999999999


Q ss_pred             cccCCCCCC
Q 045516          598 AKQRGDFGS  606 (675)
Q Consensus       598 a~~r~~~~~  606 (675)
                      +..+....+
T Consensus        95 ~~~~~~~~~  103 (435)
T KOG0108|consen   95 ASNRKNAER  103 (435)
T ss_pred             ccccchhHH
Confidence            987666543

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

Probab=98.94  E-value=1.2e-09  Score=108.78  Aligned_cols=80  Identities=24%  Similarity=0.413  Sum_probs=73.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecc
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~  492 (675)
                      ..+.+|||+||.+.++..+|+..|..||+|..|.|+       ++|+||.|...++|..||. |||..|+|++|+|+++.
T Consensus        76 k~stkl~vgNis~tctn~ElRa~fe~ygpviecdiv-------kdy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~st  148 (346)
T KOG0109|consen   76 KASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIV-------KDYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLST  148 (346)
T ss_pred             CCccccccCCCCccccCHHHhhhhcccCCceeeeee-------cceeEEEEeeccchHHHHhcccccccccceeeeeeec
Confidence            346799999999999999999999999999999999       6799999999999999997 99999999999999998


Q ss_pred             ccCCCCCC
Q 045516          493 ERGAYTPY  500 (675)
Q Consensus       493 ~~~~~~~~  500 (675)
                      .+-...+.
T Consensus       149 srlrtapg  156 (346)
T KOG0109|consen  149 SRLRTAPG  156 (346)
T ss_pred             cccccCCC
Confidence            87554443

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

Probab=98.94  E-value=3.9e-08  Score=100.93  Aligned_cols=169  Identities=17%  Similarity=0.171  Sum_probs=126.1

Q ss_pred             CCCCceEEEcCCC-CCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          413 SGGSKTLFVGNLP-FSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       413 ~~~~~tlfV~nLp-~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      ....+.+.|-+|. -.++.+.|.++|-.||.|..|.|++.+    .|.|+|++.+...+++||. ||+..|.|..|.|.+
T Consensus       284 ~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk----~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~  359 (494)
T KOG1456|consen  284 GAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK----PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCV  359 (494)
T ss_pred             CCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc----cceeEEEcCcHHHHHHHHHHhccCccccceEEEee
Confidence            4578899999996 568899999999999999999999875    6789999999999999998 999999999999988


Q ss_pred             ccccCCCCC--C---CC--------CCCCCCccCC------CCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEE
Q 045516          491 ARERGAYTP--Y---SG--------GNESNSFQKG------GRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITR  551 (675)
Q Consensus       491 a~~~~~~~~--~---~~--------~~~~~~~~~~------~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~  551 (675)
                      +........  .   .+        +..++.|...      ...+++++|+.-|.|..++++.+..++.+.--   ....
T Consensus       360 SkQ~~v~~~~pflLpDgSpSfKdys~SkNnRFssp~qAsKNrIq~Ps~vLHffNaP~~vtEe~l~~i~nek~v---~~~s  436 (494)
T KOG1456|consen  360 SKQNFVSPVQPFLLPDGSPSFKDYSGSKNNRFSSPEQASKNRIQPPSNVLHFFNAPLGVTEEQLIGICNEKDV---PPTS  436 (494)
T ss_pred             ccccccccCCceecCCCCcchhhcccccccccCChhHhhcccccCCcceeEEecCCCccCHHHHHHHhhhcCC---Ccce
Confidence            865421110  0   00        1112222211      13457999999999999999985544443311   2455


Q ss_pred             EEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCC
Q 045516          552 ISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGG  590 (675)
Q Consensus       552 v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~G  590 (675)
                      |+|+..+  ....--++++|.+..+|..||. +|...|.+
T Consensus       437 vkvFp~k--serSssGllEfe~~s~Aveal~~~NH~pi~~  474 (494)
T KOG1456|consen  437 VKVFPLK--SERSSSGLLEFENKSDAVEALMKLNHYPIEG  474 (494)
T ss_pred             EEeeccc--ccccccceeeeehHHHHHHHHHHhccccccC
Confidence            6666543  2234568999999999999998 88888865

>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=98.92  E-value=5.9e-09  Score=84.46  Aligned_cols=73  Identities=36%  Similarity=0.675  Sum_probs=65.0

Q ss_pred             EEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEec
Q 045516          520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVDE  597 (675)
Q Consensus       520 ~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~~  597 (675)
                      +|+|+|||..+++++    |.++|..||.|..+.+..+..+ .++|+|||.|.+.+.|..|+. +++..|+|+.|.|.+
T Consensus         1 ~i~i~~l~~~~~~~~----i~~~~~~~g~i~~~~~~~~~~~-~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEED----LRELFSKFGKVESVRIVRDKDT-KSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHH----HHHHHHhcCCEEEEEEeeCCCC-CcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            489999999999988    6667777799999999987654 779999999999999999998 999999999999874

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).

>PF13893 RRM_5: RNA recognition motif

Probab=98.91  E-value=4.1e-09  Score=82.10  Aligned_cols=55  Identities=31%  Similarity=0.587  Sum_probs=50.0

Q ss_pred             HHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEecc
Q 045516          539 LEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVDEA  598 (675)
Q Consensus       539 L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~~a  598 (675)
                      |..+|++||.|..|.+....     +++|||+|.+.++|..|+. |||..|+|+.|+|.|+
T Consensus         1 L~~~f~~fG~V~~i~~~~~~-----~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK-----RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-----TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            67899999999999998863     5999999999999999998 9999999999999985

(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 ....

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

Probab=98.89  E-value=4.9e-09  Score=107.67  Aligned_cols=183  Identities=17%  Similarity=0.178  Sum_probs=130.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEE-EEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDV-RLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v-~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a  491 (675)
                      ..++..|..++|||..+..+|-.||.-.-...-. -|..+..|+..|.+.|.|.+.+.-..|++-+.+.+++|.|.|..+
T Consensus        57 ~~~~vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~RdlalkRhkhh~g~ryievYka  136 (508)
T KOG1365|consen   57 ADDNVVVRARGLPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALKRHKHHMGTRYIEVYKA  136 (508)
T ss_pred             cCcceEEEecCCCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhHhhhhhccCCceeeecc
Confidence            3456778899999999999999999865322222 223333688899999999999999999998889999999999766


Q ss_pred             cccCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEe
Q 045516          492 RERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDF  571 (675)
Q Consensus       492 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F  571 (675)
                      ....-..-.. +. .+...........-.|.+++||++++..++..+|...+---|.+..|.+++. ..|++.|-|||.|
T Consensus       137 ~ge~f~~iag-g~-s~e~~~flsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~r-pdgrpTGdAFvlf  213 (508)
T KOG1365|consen  137 TGEEFLKIAG-GT-SNEAAPFLSKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTR-PDGRPTGDAFVLF  213 (508)
T ss_pred             CchhheEecC-Cc-cccCCCCCCcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEEC-CCCCcccceEEEe
Confidence            5432111111 10 0000011111225678899999999999966555433333345556655554 3499999999999


Q ss_pred             CCHHHHHHHHHhCCceeCCeeeEEecc
Q 045516          572 TDADSFNKALEMSGTEIGGYSLVVDEA  598 (675)
Q Consensus       572 ~~~e~A~~Al~lng~~~~Gr~l~V~~a  598 (675)
                      .+.+.|..||..|...|+-|+|.+...
T Consensus       214 a~ee~aq~aL~khrq~iGqRYIElFRS  240 (508)
T KOG1365|consen  214 ACEEDAQFALRKHRQNIGQRYIELFRS  240 (508)
T ss_pred             cCHHHHHHHHHHHHHHHhHHHHHHHHH
Confidence            999999999999999999998877654

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

Probab=98.89  E-value=2.4e-09  Score=108.95  Aligned_cols=82  Identities=23%  Similarity=0.434  Sum_probs=76.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHH-HhCCcccCCeeEEEEecc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAI-ELNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al-~l~g~~~~gr~i~V~~a~  492 (675)
                      ..+.|||--|++-++.++|.-+|+.||.|..|.++++. +|-+..||||+|.+.+++++|+ .|++..|+.|+|+|.|++
T Consensus       238 PeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFSQ  317 (479)
T KOG0415|consen  238 PENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFSQ  317 (479)
T ss_pred             CcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeehhh
Confidence            35799999999999999999999999999999999998 9999999999999999999999 599999999999999997


Q ss_pred             ccCC
Q 045516          493 ERGA  496 (675)
Q Consensus       493 ~~~~  496 (675)
                      .-..
T Consensus       318 SVsk  321 (479)
T KOG0415|consen  318 SVSK  321 (479)
T ss_pred             hhhh
Confidence            6443

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

Probab=98.87  E-value=4.2e-09  Score=102.26  Aligned_cols=84  Identities=25%  Similarity=0.434  Sum_probs=77.6

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~  596 (675)
                      ..||||.||+..+..++++..|+.+|++||.|..|.....   ...||.|||.|.+.+.|..|+. |+|..|.|..|+|.
T Consensus         9 n~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt---~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriq   85 (221)
T KOG4206|consen    9 NGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKT---PKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQ   85 (221)
T ss_pred             CceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCC---CCccCceEEEecChhHHHHHHHHhcCCcccCchhhee
Confidence            4599999999999999999999999999999999988764   6789999999999999999998 99999999999999


Q ss_pred             ccccCCCC
Q 045516          597 EAKQRGDF  604 (675)
Q Consensus       597 ~a~~r~~~  604 (675)
                      |++.....
T Consensus        86 yA~s~sdi   93 (221)
T KOG4206|consen   86 YAKSDSDI   93 (221)
T ss_pred             cccCccch
Confidence            99876544

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

Probab=98.86  E-value=5.2e-09  Score=106.79  Aligned_cols=76  Identities=28%  Similarity=0.489  Sum_probs=70.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH--hCCcccCCeeEEEEe
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE--LNGQMLGNRAIRLDF  490 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~--l~g~~~~gr~i~V~~  490 (675)
                      ....++|||+||...+++.+|+++|.+||+|..|++...     +++|||+|.+...|+.|.+  +|...|.|++|.|.|
T Consensus       225 D~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~-----~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~W  299 (377)
T KOG0153|consen  225 DTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR-----KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKW  299 (377)
T ss_pred             ccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc-----cccceeeehhhHHHHHHHHhhcceeeecceEEEEEe
Confidence            456789999999999999999999999999999999865     7899999999999999996  898899999999999


Q ss_pred             ccc
Q 045516          491 ARE  493 (675)
Q Consensus       491 a~~  493 (675)
                      ..+
T Consensus       300 g~~  302 (377)
T KOG0153|consen  300 GRP  302 (377)
T ss_pred             CCC
Confidence            876

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

Probab=98.85  E-value=5.3e-09  Score=116.12  Aligned_cols=80  Identities=28%  Similarity=0.537  Sum_probs=74.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecc
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~  492 (675)
                      --++|||||+|+.++++.+|..+|+.||.|.+|.|+..     +|||||.+.+..+|.+||. |++..|.++.|+|.|+.
T Consensus       419 V~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~-----R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~  493 (894)
T KOG0132|consen  419 VCSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP-----RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAV  493 (894)
T ss_pred             EeeeeeeeccccchhhHHHHHHHHHhcccceeEeeccC-----CceeEEEEeehhHHHHHHHHHhcccccceeeEEeeec
Confidence            35799999999999999999999999999999999854     8999999999999999997 99999999999999998


Q ss_pred             ccCCCC
Q 045516          493 ERGAYT  498 (675)
Q Consensus       493 ~~~~~~  498 (675)
                      ..+...
T Consensus       494 g~G~ks  499 (894)
T KOG0132|consen  494 GKGPKS  499 (894)
T ss_pred             cCCcch
Confidence            876544

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

Probab=98.80  E-value=1.4e-08  Score=101.87  Aligned_cols=79  Identities=32%  Similarity=0.550  Sum_probs=75.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecccc
Q 045516          416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARER  494 (675)
Q Consensus       416 ~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~~  494 (675)
                      ..+|+|.|||+.+++.+|++||..||.+..+-|.+++.|++.|.|-|.|...++|..||+ |||..|+|+.|.|.+....
T Consensus        83 ~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~~  162 (243)
T KOG0533|consen   83 STKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISSP  162 (243)
T ss_pred             cceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEecCc
Confidence            468999999999999999999999999999999999999999999999999999999998 9999999999999887644

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

Probab=98.73  E-value=3.9e-08  Score=98.90  Aligned_cols=81  Identities=33%  Similarity=0.589  Sum_probs=76.7

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEe
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVD  596 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~  596 (675)
                      ....+||+|+.+.++.+.    ++.+|..||.|..|.|+.++.+|.++||+||+|.+.+.+..+|.||+..|.|+.|.|.
T Consensus       100 d~~sv~v~nvd~~~t~~~----~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~l~gs~i~~~~i~vt  175 (231)
T KOG4209|consen  100 DAPSVWVGNVDFLVTLTK----IELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYKLDGSEIPGPAIEVT  175 (231)
T ss_pred             CCceEEEeccccccccch----hhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhhcCCcccccccceee
Confidence            478999999999999887    8899999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccC
Q 045516          597 EAKQR  601 (675)
Q Consensus       597 ~a~~r  601 (675)
                      +.+-+
T Consensus       176 ~~r~~  180 (231)
T KOG4209|consen  176 LKRTN  180 (231)
T ss_pred             eeeee
Confidence            88766

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

Probab=98.70  E-value=2.1e-08  Score=102.10  Aligned_cols=83  Identities=22%  Similarity=0.349  Sum_probs=77.8

Q ss_pred             CCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCee
Q 045516          514 RGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYS  592 (675)
Q Consensus       514 ~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~  592 (675)
                      ..++.+.|||--|++-++.++    |.-+|+.||.|..|.|++|+.||.+-.||||+|.+.++|.+|+= |++..|+.++
T Consensus       235 ~~PPeNVLFVCKLNPVTtDeD----LeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrR  310 (479)
T KOG0415|consen  235 VKPPENVLFVCKLNPVTTDED----LEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRR  310 (479)
T ss_pred             cCCCcceEEEEecCCcccccc----hhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccce
Confidence            456789999999999999888    88999999999999999999999999999999999999999975 9999999999


Q ss_pred             eEEecccc
Q 045516          593 LVVDEAKQ  600 (675)
Q Consensus       593 l~V~~a~~  600 (675)
                      |+|+|...
T Consensus       311 IHVDFSQS  318 (479)
T KOG0415|consen  311 IHVDFSQS  318 (479)
T ss_pred             EEeehhhh
Confidence            99999864

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

Probab=98.68  E-value=3.6e-08  Score=94.27  Aligned_cols=81  Identities=19%  Similarity=0.292  Sum_probs=71.9

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhccc-CcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSC-GEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~-G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      ....++|..+|..+.+.+|    ..+|.+| |.|.++++.++..||.++|||||+|.+.+.|.-|.+ ||+..|.|+.|.
T Consensus        48 ~~g~~~~~~~p~g~~e~~~----~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~  123 (214)
T KOG4208|consen   48 IEGVVYVDHIPHGFFETEI----LNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLE  123 (214)
T ss_pred             CccceeecccccchhHHHH----hhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheee
Confidence            3678999999999998884    4455555 899999999999999999999999999999999999 999999999999


Q ss_pred             EeccccC
Q 045516          595 VDEAKQR  601 (675)
Q Consensus       595 V~~a~~r  601 (675)
                      |.+-.+.
T Consensus       124 c~vmppe  130 (214)
T KOG4208|consen  124 CHVMPPE  130 (214)
T ss_pred             eEEeCch
Confidence            9988765

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

Probab=98.67  E-value=1.6e-08  Score=99.17  Aligned_cols=168  Identities=20%  Similarity=0.327  Sum_probs=129.7

Q ss_pred             CCceEEEcCCCCCCCHHH-H--HHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          415 GSKTLFVGNLPFSVEQAD-V--QNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~-L--~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      ....+|++|+-..+..+- |  ...|.-|-.++...++++..+.-++++|+.|.......++-. -+++.+.-++|++.-
T Consensus        95 ~vf~p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~  174 (290)
T KOG0226|consen   95 AVFRPFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDRPQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAA  174 (290)
T ss_pred             ccccccccccccccCCCCCCcchhhhccchhhhhhhhhhcCCCccCcccccCcchhhhhhhhccccccccccCcceeecc
Confidence            346778888876666555 3  678888877888888888888889999999998877777775 677777777755533


Q ss_pred             ccccCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEE
Q 045516          491 ARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLD  570 (675)
Q Consensus       491 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~  570 (675)
                      .+.-..  +.        +.  .-.....+||.+.|.-.++.+.    |...|.+|-.....+++++..||+++||+||.
T Consensus       175 gtswed--Ps--------l~--ew~~~DfRIfcgdlgNevnd~v----l~raf~Kfpsf~~akviRdkRTgKSkgygfVS  238 (290)
T KOG0226|consen  175 GTSWED--PS--------LA--EWDEDDFRIFCGDLGNEVNDDV----LARAFKKFPSFQKAKVIRDKRTGKSKGYGFVS  238 (290)
T ss_pred             ccccCC--cc--------cc--cCccccceeecccccccccHHH----HHHHHHhccchhhccccccccccccccceeee
Confidence            322110  00        00  0112267899998888888876    78888888999999999999999999999999


Q ss_pred             eCCHHHHHHHHH-hCCceeCCeeeEEecc
Q 045516          571 FTDADSFNKALE-MSGTEIGGYSLVVDEA  598 (675)
Q Consensus       571 F~~~e~A~~Al~-lng~~~~Gr~l~V~~a  598 (675)
                      |.++.++.+||. |+|.+++.|.|.++-.
T Consensus       239 f~~pad~~rAmrem~gkyVgsrpiklRkS  267 (290)
T KOG0226|consen  239 FRDPADYVRAMREMNGKYVGSRPIKLRKS  267 (290)
T ss_pred             ecCHHHHHHHHHhhcccccccchhHhhhh
Confidence            999999999998 9999999999987643

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

Probab=98.67  E-value=4e-08  Score=105.34  Aligned_cols=81  Identities=28%  Similarity=0.457  Sum_probs=73.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      ..-.+.|||.+|...+...+|+.||++||.|+-..++.+. +---+.|+||+|.+.+.|.+||+ |+.+.|.|+.|.|..
T Consensus       402 s~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEk  481 (940)
T KOG4661|consen  402 STLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEK  481 (940)
T ss_pred             cccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeee
Confidence            4557899999999999999999999999999999999885 44458999999999999999998 999999999999988


Q ss_pred             ccc
Q 045516          491 ARE  493 (675)
Q Consensus       491 a~~  493 (675)
                      +..
T Consensus       482 aKN  484 (940)
T KOG4661|consen  482 AKN  484 (940)
T ss_pred             ccc
Confidence            764

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

Probab=98.67  E-value=1.3e-08  Score=105.00  Aligned_cols=166  Identities=18%  Similarity=0.184  Sum_probs=119.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCC----CCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEec
Q 045516          416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD----GRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFA  491 (675)
Q Consensus       416 ~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~----g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a  491 (675)
                      .+.|.|.||.++++.++|+.||..+|.|..++|+.+..    ......|||-|.+...+..|..|.++.|-++.|.|...
T Consensus         7 ~~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQhLtntvfvdraliv~p~   86 (479)
T KOG4676|consen    7 LGVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQHLTNTVFVDRALIVRPY   86 (479)
T ss_pred             CceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhhhccceeeeeeEEEEec
Confidence            35899999999999999999999999999999987642    33567999999999999999999999998888888655


Q ss_pred             cccCCCC-------------CC---CCCCCC--CCccCCC--------------------CCCCceEEEEecCCCCcCHH
Q 045516          492 RERGAYT-------------PY---SGGNES--NSFQKGG--------------------RGQAAHTIFIKGFDSSVGED  533 (675)
Q Consensus       492 ~~~~~~~-------------~~---~~~~~~--~~~~~~~--------------------~~~~~~~lfV~nLp~~~te~  533 (675)
                      .......             +.   ..+...  ..+...+                    .....++|+|.+|+..+...
T Consensus        87 ~~~~~p~r~af~~l~~~navprll~pdg~Lp~~~~lt~~nh~p~ailktP~Lp~~~~A~kleeirRt~~v~sl~~~~~l~  166 (479)
T KOG4676|consen   87 GDEVIPDRFAFVELADQNAVPRLLPPDGVLPGDRPLTKINHSPNAILKTPELPPQAAAKKLEEIRRTREVQSLISAAILP  166 (479)
T ss_pred             CCCCCccHHHHHhcCcccccccccCCCCccCCCCccccccCCccceecCCCCChHhhhhhhHHHHhhhhhhcchhhhcch
Confidence            4321000             00   000000  0000000                    00123567777777666655


Q ss_pred             HHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeC
Q 045516          534 QVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIG  589 (675)
Q Consensus       534 ~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~  589 (675)
                      +    |-.+|..||.|.+.++.-.    ...-+|.|.|........|+.++|+.|.
T Consensus       167 e----~~e~f~r~Gev~ya~~ask----~~s~~c~~sf~~qts~~halr~~gre~k  214 (479)
T KOG4676|consen  167 E----SGESFERKGEVSYAHTASK----SRSSSCSHSFRKQTSSKHALRSHGRERK  214 (479)
T ss_pred             h----hhhhhhhcchhhhhhhhcc----CCCcchhhhHhhhhhHHHHHHhcchhhh
Confidence            5    7788999999998877653    3366788999999999999999888775

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

Probab=98.65  E-value=5.3e-09  Score=108.58  Aligned_cols=154  Identities=17%  Similarity=0.311  Sum_probs=119.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCc-ccCCeeEEEEecccc
Q 045516          417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQ-MLGNRAIRLDFARER  494 (675)
Q Consensus       417 ~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~-~~~gr~i~V~~a~~~  494 (675)
                      ..|||+||...++-.+|..+|...-.-..-.|+.     -.||+||.+.+..-|.+|++ |+|. .+.|.++.|....++
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~-----k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~k   76 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV-----KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPK   76 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceee-----ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhH
Confidence            4799999999999999999998652111111221     16999999999999999998 8776 689999999887665


Q ss_pred             CCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEeccc-CCCCCeeeEEEEEeCC
Q 045516          495 GAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKD-YDTGSVKGIAYLDFTD  573 (675)
Q Consensus       495 ~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d-~~tG~~rG~afV~F~~  573 (675)
                      ...                    ++.+-|+|+|..+.|+.    |..+...||.|..|..... .+    .-..-|+|..
T Consensus        77 kqr--------------------srk~Qirnippql~wev----ld~Ll~qyg~ve~~eqvnt~~e----tavvnvty~~  128 (584)
T KOG2193|consen   77 KQR--------------------SRKIQIRNIPPQLQWEV----LDSLLAQYGTVENCEQVNTDSE----TAVVNVTYSA  128 (584)
T ss_pred             HHH--------------------hhhhhHhcCCHHHHHHH----HHHHHhccCCHhHhhhhccchH----HHHHHHHHHH
Confidence            321                    56789999999998887    7778888899999876432 22    2234467889


Q ss_pred             HHHHHHHHH-hCCceeCCeeeEEeccccCCC
Q 045516          574 ADSFNKALE-MSGTEIGGYSLVVDEAKQRGD  603 (675)
Q Consensus       574 ~e~A~~Al~-lng~~~~Gr~l~V~~a~~r~~  603 (675)
                      .+.+..||. |+|..|....+.|.|-.....
T Consensus       129 ~~~~~~ai~kl~g~Q~en~~~k~~YiPdeq~  159 (584)
T KOG2193|consen  129 QQQHRQAIHKLNGPQLENQHLKVGYIPDEQN  159 (584)
T ss_pred             HHHHHHHHHhhcchHhhhhhhhcccCchhhh
Confidence            999999998 999999999999988754433

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

Probab=98.60  E-value=1e-07  Score=95.91  Aligned_cols=82  Identities=27%  Similarity=0.447  Sum_probs=76.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a  491 (675)
                      .-+.+.|||+||.+.+|.++|..+|+.||.|..|.|..+. .++++||+||+|.+.+.+..+|.||+..|.|+.|.|.+.
T Consensus        98 ~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~l~gs~i~~~~i~vt~~  177 (231)
T KOG4209|consen   98 EVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYKLDGSEIPGPAIEVTLK  177 (231)
T ss_pred             ccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhhcCCcccccccceeeee
Confidence            4466899999999999999999999999999999999998 678999999999999999999999999999999999888


Q ss_pred             ccc
Q 045516          492 RER  494 (675)
Q Consensus       492 ~~~  494 (675)
                      +.+
T Consensus       178 r~~  180 (231)
T KOG4209|consen  178 RTN  180 (231)
T ss_pred             eee
Confidence            765

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

Probab=98.58  E-value=1.6e-07  Score=96.88  Aligned_cols=84  Identities=31%  Similarity=0.510  Sum_probs=75.9

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEE--------EEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCce
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEIT--------RISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTE  587 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~--------~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~  587 (675)
                      ...+|||.+|+..++..+    |..+|.+||.|.        .|.|.++.+|+.++|-|.|.|.+...|+.||. +++..
T Consensus        65 ~~~ti~v~g~~d~~~~~~----~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkd  140 (351)
T KOG1995|consen   65 DNETIFVWGCPDSVCEND----NADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKD  140 (351)
T ss_pred             ccccceeeccCccchHHH----HHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhcccc
Confidence            467999999999999987    778888889874        47888999999999999999999999999998 99999


Q ss_pred             eCCeeeEEeccccCCCC
Q 045516          588 IGGYSLVVDEAKQRGDF  604 (675)
Q Consensus       588 ~~Gr~l~V~~a~~r~~~  604 (675)
                      |.|..|.|.++..+...
T Consensus       141 f~gn~ikvs~a~~r~~v  157 (351)
T KOG1995|consen  141 FCGNTIKVSLAERRTGV  157 (351)
T ss_pred             ccCCCchhhhhhhccCc
Confidence            99999999999887753

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

Probab=98.55  E-value=1.4e-07  Score=96.42  Aligned_cols=75  Identities=29%  Similarity=0.526  Sum_probs=68.4

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH--hCCceeCCeee
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE--MSGTEIGGYSL  593 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~--lng~~~~Gr~l  593 (675)
                      ....+|||+||...+++.+    |++||.+||.|+.|++...      +++|||+|.+...|..|..  +|...|+|++|
T Consensus       226 ~~I~tLyIg~l~d~v~e~d----IrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl  295 (377)
T KOG0153|consen  226 TSIKTLYIGGLNDEVLEQD----IRDHFYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNKLVINGFRL  295 (377)
T ss_pred             cceeEEEecccccchhHHH----HHHHHhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcceeeecceEE
Confidence            3478999999999999888    6789999999999999886      6799999999999999986  89889999999


Q ss_pred             EEecccc
Q 045516          594 VVDEAKQ  600 (675)
Q Consensus       594 ~V~~a~~  600 (675)
                      .|.|..+
T Consensus       296 ~i~Wg~~  302 (377)
T KOG0153|consen  296 KIKWGRP  302 (377)
T ss_pred             EEEeCCC
Confidence            9999988

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

Probab=98.55  E-value=4.4e-07  Score=91.09  Aligned_cols=81  Identities=21%  Similarity=0.393  Sum_probs=72.1

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~  596 (675)
                      ...|+|.||++.+...+    |+++|..||.+..+.|.+++ .|++.|.|-|.|...++|.+|+. |||..|+|+.|.+.
T Consensus        83 ~~~v~v~NL~~~V~~~D----l~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~  157 (243)
T KOG0533|consen   83 STKVNVSNLPYGVIDAD----LKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIE  157 (243)
T ss_pred             cceeeeecCCcCcchHH----HHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeE
Confidence            57899999999999998    77888888999999999884 59999999999999999999998 99999999999888


Q ss_pred             ccccCCC
Q 045516          597 EAKQRGD  603 (675)
Q Consensus       597 ~a~~r~~  603 (675)
                      ...+...
T Consensus       158 ~i~~~~~  164 (243)
T KOG0533|consen  158 IISSPSQ  164 (243)
T ss_pred             EecCccc
Confidence            7654433

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

Probab=98.55  E-value=3.8e-08  Score=106.46  Aligned_cols=172  Identities=23%  Similarity=0.243  Sum_probs=109.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      .-.+++|+|-|||..++.++|+++|+.||+|..|++.+.    .+|++||+|.+..+|++||. ||+..|.|++|.....
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~----~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k~~~~  147 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPN----KRGIVFVEFYDVRDAERALKALNRREIAGKRIKRPGG  147 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccc----cCceEEEEEeehHhHHHHHHHHHHHHhhhhhhcCCCc
Confidence            346799999999999999999999999999999888765    38999999999999999997 9999999999882211


Q ss_pred             cccCCCCCCCCCCCCCCccC-----CCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeE
Q 045516          492 RERGAYTPYSGGNESNSFQK-----GGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGI  566 (675)
Q Consensus       492 ~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~  566 (675)
                      ..+.... ..+...-..+..     ...+-+...+|+- |.+....    .++..+|..+|.+.. +..     +...-.
T Consensus       148 ~~~~~~~-~~~~~~~~~~~~p~a~s~pgg~~~~~~~g~-l~P~~s~----~~~~~~~~~~~~~~~-~~~-----~~~~hq  215 (549)
T KOG4660|consen  148 ARRAMGL-QSGTSFLNHFGSPLANSPPGGWPRGQLFGM-LSPTRSS----ILLEHISSVDGSSPG-RET-----PLLNHQ  215 (549)
T ss_pred             ccccchh-cccchhhhhccchhhcCCCCCCcCCcceee-eccchhh----hhhhcchhccCcccc-ccc-----cchhhh
Confidence            1111000 000000000000     0000112233333 6665555    236667777777655 322     222336


Q ss_pred             EEEEeCCHHHHHHHHHhCCceeCCeeeEEecccc
Q 045516          567 AYLDFTDADSFNKALEMSGTEIGGYSLVVDEAKQ  600 (675)
Q Consensus       567 afV~F~~~e~A~~Al~lng~~~~Gr~l~V~~a~~  600 (675)
                      -|+.|.+..++..++.-.|..+.+....+.+..+
T Consensus       216 ~~~~~~~~~s~a~~~~~~G~~~s~~~~v~t~S~~  249 (549)
T KOG4660|consen  216 RFVEFADNRSYAFSEPRGGFLISNSSGVITFSGP  249 (549)
T ss_pred             hhhhhccccchhhcccCCceecCCCCceEEecCC
Confidence            7788888877755544226666666666666655

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

Probab=98.48  E-value=6.4e-07  Score=92.59  Aligned_cols=83  Identities=27%  Similarity=0.427  Sum_probs=75.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeE--------EEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccC
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVV--------DVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLG  482 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~--------~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~  482 (675)
                      ....-+|||-+||.++++.+|..||.+||.|.        .|+|.+++ |+..+|-|.|.|.+...|+.||. +++..|.
T Consensus        63 ~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~  142 (351)
T KOG1995|consen   63 KSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFC  142 (351)
T ss_pred             ccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhcccccc
Confidence            34567999999999999999999999999884        47788887 89999999999999999999998 9999999


Q ss_pred             CeeEEEEeccccC
Q 045516          483 NRAIRLDFARERG  495 (675)
Q Consensus       483 gr~i~V~~a~~~~  495 (675)
                      |..|.|.++..+.
T Consensus       143 gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  143 GNTIKVSLAERRT  155 (351)
T ss_pred             CCCchhhhhhhcc
Confidence            9999999987765

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

Probab=98.42  E-value=5.3e-07  Score=99.17  Aligned_cols=179  Identities=15%  Similarity=0.108  Sum_probs=128.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a  491 (675)
                      ..+.+.|-+.++++++...+++.||.-. .|..+.|..+. .+...|.+||.|.....+++|+.-|...+-.|.|.|...
T Consensus       308 v~d~~y~~~~gm~fn~~~nd~rkfF~g~-~~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~rn~~~~~~R~~q~~P~  386 (944)
T KOG4307|consen  308 VSDKYYNNYKGMEFNNDFNDGRKFFPGR-NAQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFTRNPSDDVNRPFQTGPP  386 (944)
T ss_pred             cchhheeeecccccccccchhhhhcCcc-cccccchhhhhcCCCcCCceEEEecCcchHHHHHhcCchhhhhcceeecCC
Confidence            4567888889999999999999999754 46666666666 444589999999999999999999999999999998766


Q ss_pred             cccCCCC--------C-CC----CCCCC-CC--ccCC-----CCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEE
Q 045516          492 RERGAYT--------P-YS----GGNES-NS--FQKG-----GRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEIT  550 (675)
Q Consensus       492 ~~~~~~~--------~-~~----~~~~~-~~--~~~~-----~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~  550 (675)
                      .......        . ..    .++.. ..  ....     ........|||..||..++...+.    .+|...-.|+
T Consensus       387 g~~~~~~a~~~~~~~~~~~~~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v----~~f~~~~~Ve  462 (944)
T KOG4307|consen  387 GNLGRNGAPPFQAGVPPPVIQNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPV----NKFMGAAAVE  462 (944)
T ss_pred             CccccccCccccccCCCCcccccCCCCCCCcccccCCCCCCCCCCCccceEEeccCCccccccchh----hhhhhhhhhh
Confidence            5432110        0 00    00000 00  0000     112347899999999999998844    4444445566


Q ss_pred             E-EEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEec
Q 045516          551 R-ISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVDE  597 (675)
Q Consensus       551 ~-v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~~  597 (675)
                      + |.|.+. -+++.++.|||.|...+.+..|+. .+-++++.|.|+|.-
T Consensus       463 d~I~lt~~-P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~s  510 (944)
T KOG4307|consen  463 DFIELTRL-PTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDS  510 (944)
T ss_pred             heeEeccC-CcccccchhhheeccccccchhhhcccccccCceEEEeec
Confidence            6 444443 468889999999999998888887 788888889998863

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

Probab=98.39  E-value=4.6e-07  Score=101.11  Aligned_cols=76  Identities=24%  Similarity=0.443  Sum_probs=70.1

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEE
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVV  595 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V  595 (675)
                      .++||||++|+.++++.+    |..+|+.||.|..|.|+..      ||+|||.+....+|.+||. |++..|.++.|+|
T Consensus       420 ~SrTLwvG~i~k~v~e~d----L~~~feefGeiqSi~li~~------R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki  489 (894)
T KOG0132|consen  420 CSRTLWVGGIPKNVTEQD----LANLFEEFGEIQSIILIPP------RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKI  489 (894)
T ss_pred             eeeeeeeccccchhhHHH----HHHHHHhcccceeEeeccC------CceeEEEEeehhHHHHHHHHHhcccccceeeEE
Confidence            589999999999999998    7788888999999999776      8999999999999999998 9999999999999


Q ss_pred             eccccCC
Q 045516          596 DEAKQRG  602 (675)
Q Consensus       596 ~~a~~r~  602 (675)
                      .|+...+
T Consensus       490 ~Wa~g~G  496 (894)
T KOG0132|consen  490 AWAVGKG  496 (894)
T ss_pred             eeeccCC
Confidence            9997543

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

Probab=98.38  E-value=3.8e-07  Score=100.68  Aligned_cols=79  Identities=24%  Similarity=0.421  Sum_probs=72.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCC----CCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEE
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD----GRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLD  489 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~----g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~  489 (675)
                      .++.|||+||++.++++.|...|..||+|..|+|+.-++    .+.+.|+||.|-+..++++||. |+|+.+.++.|++.
T Consensus       173 ~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K~g  252 (877)
T KOG0151|consen  173 QTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMKLG  252 (877)
T ss_pred             cccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeeeec
Confidence            467899999999999999999999999999999987662    5578899999999999999997 99999999999999


Q ss_pred             eccc
Q 045516          490 FARE  493 (675)
Q Consensus       490 ~a~~  493 (675)
                      |...
T Consensus       253 Wgk~  256 (877)
T KOG0151|consen  253 WGKA  256 (877)
T ss_pred             cccc
Confidence            8854

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

Probab=98.38  E-value=1e-06  Score=87.21  Aligned_cols=62  Identities=26%  Similarity=0.390  Sum_probs=52.9

Q ss_pred             HHHHHHhh-hCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecc
Q 045516          431 ADVQNFFS-EVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       431 ~~L~~~F~-~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~  492 (675)
                      ++|...|. +||+|..+.|..+..-+..|-+||.|...++|++|++ ||+.+|.|++|+..+..
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~p  146 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            34444445 8999999988877666779999999999999999998 99999999999998863

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

Probab=98.34  E-value=5.5e-06  Score=91.40  Aligned_cols=80  Identities=24%  Similarity=0.248  Sum_probs=70.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEE-EEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVD-VRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~-v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      ...+..|||..||+.+++..+..+|...-.|++ |.|.+.++++.++-|||.|.+++.+..|+. .+-++++.|.|+|+.
T Consensus       431 ~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~s  510 (944)
T KOG4307|consen  431 GGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLPTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDS  510 (944)
T ss_pred             CCccceEEeccCCccccccchhhhhhhhhhhhheeEeccCCcccccchhhheeccccccchhhhcccccccCceEEEeec
Confidence            356789999999999999999999998777777 888888899999999999999998888887 677788888899875


Q ss_pred             cc
Q 045516          491 AR  492 (675)
Q Consensus       491 a~  492 (675)
                      ..
T Consensus       511 i~  512 (944)
T KOG4307|consen  511 IA  512 (944)
T ss_pred             hh
Confidence            53

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

Probab=98.30  E-value=4.2e-06  Score=72.32  Aligned_cols=78  Identities=22%  Similarity=0.305  Sum_probs=67.0

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhh--CCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccC----CeeEEE
Q 045516          417 KTLFVGNLPFSVEQADVQNFFSE--VAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLG----NRAIRL  488 (675)
Q Consensus       417 ~tlfV~nLp~~~te~~L~~~F~~--~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~----gr~i~V  488 (675)
                      +||.|+|||...|.+.|.+++..  .|...-+.|+.|. ++.+.|||||-|.++..|..... ++|..+.    .+...|
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i   81 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEI   81 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEE
Confidence            69999999999999999998875  4778889999997 88899999999999999999997 9998885    455667


Q ss_pred             Eecccc
Q 045516          489 DFARER  494 (675)
Q Consensus       489 ~~a~~~  494 (675)
                      .+|+-.
T Consensus        82 ~yAriQ   87 (97)
T PF04059_consen   82 SYARIQ   87 (97)
T ss_pred             ehhHhh
Confidence            766543

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

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

Probab=98.28  E-value=1.1e-06  Score=94.40  Aligned_cols=82  Identities=17%  Similarity=0.379  Sum_probs=74.2

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      ...+.|||.+|...+...+    |+.||++||.|+-..|+++..+--.+.|+||++.+.+.|.+||+ ||...|.|+.|.
T Consensus       403 ~~gRNlWVSGLSstTRAtD----LKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmIS  478 (940)
T KOG4661|consen  403 TLGRNLWVSGLSSTTRATD----LKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMIS  478 (940)
T ss_pred             ccccceeeeccccchhhhH----HHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeee
Confidence            3478999999998887777    88999999999999999987777789999999999999999998 999999999999


Q ss_pred             EeccccC
Q 045516          595 VDEAKQR  601 (675)
Q Consensus       595 V~~a~~r  601 (675)
                      |..++.-
T Consensus       479 VEkaKNE  485 (940)
T KOG4661|consen  479 VEKAKNE  485 (940)
T ss_pred             eeecccC
Confidence            9988643

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

Probab=98.20  E-value=1.3e-06  Score=86.00  Aligned_cols=80  Identities=26%  Similarity=0.467  Sum_probs=73.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ....+||.+.|...++.+.|-..|.+|-.....+++++. +|+++||+||-|.+..++..||. |||.+++.|+|.+.-+
T Consensus       188 ~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS  267 (290)
T KOG0226|consen  188 EDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKS  267 (290)
T ss_pred             cccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhh
Confidence            456899999999999999999999999988889999997 99999999999999999999996 9999999999998665


Q ss_pred             cc
Q 045516          492 RE  493 (675)
Q Consensus       492 ~~  493 (675)
                      ..
T Consensus       268 ~w  269 (290)
T KOG0226|consen  268 EW  269 (290)
T ss_pred             hH
Confidence            43

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

Probab=98.19  E-value=1e-05  Score=69.89  Aligned_cols=81  Identities=19%  Similarity=0.343  Sum_probs=72.0

Q ss_pred             eEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeC----Ceee
Q 045516          519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIG----GYSL  593 (675)
Q Consensus       519 ~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~----Gr~l  593 (675)
                      +||.|+|||-..+...|.+.|...|.  |..-.+.|+.|..++...|||||.|.++..+..-.. ++|..+.    .+.+
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~--g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc   79 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFK--GKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVC   79 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhcc--CcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEE
Confidence            68999999999999999999998874  889999999999999999999999999999999988 9998885    4567


Q ss_pred             EEeccccC
Q 045516          594 VVDEAKQR  601 (675)
Q Consensus       594 ~V~~a~~r  601 (675)
                      .|.||+-.
T Consensus        80 ~i~yAriQ   87 (97)
T PF04059_consen   80 EISYARIQ   87 (97)
T ss_pred             EEehhHhh
Confidence            77877643

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

>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=98.16  E-value=9.4e-06  Score=66.93  Aligned_cols=74  Identities=18%  Similarity=0.402  Sum_probs=55.2

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccC-cEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEE
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCG-EITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVV  595 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G-~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V  595 (675)
                      ...|+|.|||.+.....|+.-|++++..|| .|..|.          .+.|+|.|.+.+.|.+|+. |+|..+.|+.|.|
T Consensus         2 ~s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~----------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v   71 (90)
T PF11608_consen    2 HSLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS----------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISV   71 (90)
T ss_dssp             SEEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EE
T ss_pred             ccEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe----------CCEEEEEeCCHHHHHHHHHhhcccccccceEEE
Confidence            367999999999999999999999999997 455551          3679999999999999998 9999999999999


Q ss_pred             eccccC
Q 045516          596 DEAKQR  601 (675)
Q Consensus       596 ~~a~~r  601 (675)
                      .|....
T Consensus        72 ~~~~~~   77 (90)
T PF11608_consen   72 SFSPKN   77 (90)
T ss_dssp             ESS--S
T ss_pred             EEcCCc
Confidence            998543

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

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

Probab=98.13  E-value=4.7e-06  Score=85.48  Aligned_cols=78  Identities=26%  Similarity=0.488  Sum_probs=70.1

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEE--------EEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCcee
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITR--------ISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEI  588 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~--------v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~  588 (675)
                      ...|||.|||.++|.++    |.++|.+||.|..        |.|.++.. |..+|-|+|.|--.+++..||. |++..|
T Consensus       134 Nt~VYVsgLP~DiT~dE----~~~~~sKcGiI~~d~~t~epk~KlYrd~~-G~lKGDaLc~y~K~ESVeLA~~ilDe~~~  208 (382)
T KOG1548|consen  134 NTSVYVSGLPLDITVDE----FAEVMSKCGIIMRDPQTGEPKVKLYRDNQ-GKLKGDALCCYIKRESVELAIKILDEDEL  208 (382)
T ss_pred             CceEEecCCCCcccHHH----HHHHHHhcceEeccCCCCCeeEEEEecCC-CCccCceEEEeecccHHHHHHHHhCcccc
Confidence            46699999999999998    8899999998854        67777755 9999999999999999999999 999999


Q ss_pred             CCeeeEEecccc
Q 045516          589 GGYSLVVDEAKQ  600 (675)
Q Consensus       589 ~Gr~l~V~~a~~  600 (675)
                      .|+.|+|..|+-
T Consensus       209 rg~~~rVerAkf  220 (382)
T KOG1548|consen  209 RGKKLRVERAKF  220 (382)
T ss_pred             cCcEEEEehhhh
Confidence            999999998853

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

Probab=98.12  E-value=1.7e-05  Score=81.05  Aligned_cols=82  Identities=21%  Similarity=0.365  Sum_probs=69.2

Q ss_pred             CCCCCCCCCceEEEcCCCCCCCHHHHHHHhhhCC--CeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCC
Q 045516          408 PFTPQSGGSKTLFVGNLPFSVEQADVQNFFSEVA--EVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGN  483 (675)
Q Consensus       408 ~~~~~~~~~~tlfV~nLp~~~te~~L~~~F~~~G--~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~g  483 (675)
                      +.+...+-..++||+||-|++|..+|.+.+...|  .|.+++|+.++ +|+++|||+|.+.+...+.+.|+ |-...|.|
T Consensus        72 ~~~s~~Grk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHG  151 (498)
T KOG4849|consen   72 PATSSEGRKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHG  151 (498)
T ss_pred             ccccccCceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecC
Confidence            3344456667899999999999999999988877  47888888888 89999999999999999999998 78888888


Q ss_pred             eeEEEE
Q 045516          484 RAIRLD  489 (675)
Q Consensus       484 r~i~V~  489 (675)
                      +.-.|.
T Consensus       152 Q~P~V~  157 (498)
T KOG4849|consen  152 QSPTVL  157 (498)
T ss_pred             CCCeee
Confidence            765553

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

Probab=98.02  E-value=2.4e-05  Score=75.72  Aligned_cols=83  Identities=18%  Similarity=0.259  Sum_probs=64.7

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEeccc-CCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeC---Cee
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKD-YDTGSVKGIAYLDFTDADSFNKALE-MSGTEIG---GYS  592 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d-~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~---Gr~  592 (675)
                      .+||||.+||.++...+    |+.+|..|-.-+.+.|... ....-++-+|||.|.+...|..|+. |||..|+   +..
T Consensus        34 VRTLFVSGLP~DvKpRE----iynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~st  109 (284)
T KOG1457|consen   34 VRTLFVSGLPNDVKPRE----IYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGST  109 (284)
T ss_pred             cceeeeccCCcccCHHH----HHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCce
Confidence            69999999999999998    5566666655555555433 2223456899999999999999998 9999996   789


Q ss_pred             eEEeccccCCCC
Q 045516          593 LVVDEAKQRGDF  604 (675)
Q Consensus       593 l~V~~a~~r~~~  604 (675)
                      |+|++++....+
T Consensus       110 LhiElAKSNtK~  121 (284)
T KOG1457|consen  110 LHIELAKSNTKR  121 (284)
T ss_pred             eEeeehhcCccc
Confidence            999999764443

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

Probab=97.98  E-value=7.3e-06  Score=80.68  Aligned_cols=72  Identities=24%  Similarity=0.503  Sum_probs=63.6

Q ss_pred             eEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEec
Q 045516          519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVDE  597 (675)
Q Consensus       519 ~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~~  597 (675)
                      ..|||++|++.+.+.+    |+.||..||.|..|.|..        ||+||+|.+.-+|.-|+. ||+..|+|-.|.|.|
T Consensus         2 ~rv~vg~~~~~~~~~d----~E~~f~~yg~~~d~~mk~--------gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~   69 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERD----VERFFKGYGKIPDADMKN--------GFGFVEFEDPRDADDAVHDLDGKELCGERLVVEH   69 (216)
T ss_pred             CceeecccCCccchhH----HHHHHhhccccccceeec--------ccceeccCchhhhhcccchhcCceecceeeeeec
Confidence            4689999999999998    778888899999987754        688999999999999998 999999998899998


Q ss_pred             cccCC
Q 045516          598 AKQRG  602 (675)
Q Consensus       598 a~~r~  602 (675)
                      ++...
T Consensus        70 ~r~~~   74 (216)
T KOG0106|consen   70 ARGKR   74 (216)
T ss_pred             ccccc
Confidence            87543

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

Probab=97.97  E-value=2.1e-05  Score=78.04  Aligned_cols=53  Identities=21%  Similarity=0.371  Sum_probs=46.8

Q ss_pred             ccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEecc
Q 045516          545 SCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVDEA  598 (675)
Q Consensus       545 ~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~~a  598 (675)
                      +||+|..+.|..+. .-..+|-+||.|...++|.+|++ ||+.+|+|++|++.+.
T Consensus        92 kygEiee~~Vc~Nl-~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~  145 (260)
T KOG2202|consen   92 KYGEIEELNVCDNL-GDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELS  145 (260)
T ss_pred             Hhhhhhhhhhhccc-chhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeec
Confidence            89999999776653 24568999999999999999998 9999999999999876

>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=97.94  E-value=3e-05  Score=64.03  Aligned_cols=69  Identities=22%  Similarity=0.393  Sum_probs=48.0

Q ss_pred             ceEEEcCCCCCCCHHH----HHHHhhhCC-CeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          417 KTLFVGNLPFSVEQAD----VQNFFSEVA-EVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       417 ~tlfV~nLp~~~te~~----L~~~F~~~G-~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      ..|||.|||.+..-..    |++|+..|| .|..|.         .+.|+|.|.+.+.|.+|+. |+|..+.|+.|.|.|
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~---------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~   73 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS---------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSF   73 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE-----------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEES
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe---------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEEE
Confidence            4699999999988766    456777786 576662         5899999999999999998 999999999999998


Q ss_pred             cccc
Q 045516          491 ARER  494 (675)
Q Consensus       491 a~~~  494 (675)
                      ....
T Consensus        74 ~~~~   77 (90)
T PF11608_consen   74 SPKN   77 (90)
T ss_dssp             S--S
T ss_pred             cCCc
Confidence            8543

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

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=97.92  E-value=8.6e-06  Score=84.79  Aligned_cols=82  Identities=33%  Similarity=0.590  Sum_probs=73.6

Q ss_pred             CCCceEE-EcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEec
Q 045516          414 GGSKTLF-VGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFA  491 (675)
Q Consensus       414 ~~~~tlf-V~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a  491 (675)
                      ....+|| |+||+++++.++|+.+|..+|.|+.|+++.+. ++..+||+||.|........+|..+...+.+++|.|.+.
T Consensus       182 ~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  261 (285)
T KOG4210|consen  182 GPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALNDQTRSIGGRPLRLEED  261 (285)
T ss_pred             CccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhcccCcccCcccccccC
Confidence            3456666 99999999999999999999999999999987 899999999999999999999877788899999999887


Q ss_pred             cccC
Q 045516          492 RERG  495 (675)
Q Consensus       492 ~~~~  495 (675)
                      ..+.
T Consensus       262 ~~~~  265 (285)
T KOG4210|consen  262 EPRP  265 (285)
T ss_pred             CCCc
Confidence            6653

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

Probab=97.90  E-value=7.8e-06  Score=88.89  Aligned_cols=69  Identities=29%  Similarity=0.505  Sum_probs=63.3

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      +.++|+|.|||..++.++    |.++|+.||+|+.|+..+.     .+|++||+|.+.-.|.+|+. |++..|.|++|.
T Consensus        74 ~~~~L~v~nl~~~Vsn~~----L~~~f~~yGeir~ir~t~~-----~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   74 NQGTLVVFNLPRSVSNDT----LLRIFGAYGEIREIRETPN-----KRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             ccceEEEEecCCcCCHHH----HHHHHHhhcchhhhhcccc-----cCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            478999999999999998    8899999999999877665     48999999999999999998 999999999988

>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]

Probab=97.87  E-value=3.1e-05  Score=79.30  Aligned_cols=10  Identities=10%  Similarity=0.225  Sum_probs=3.9

Q ss_pred             EcCCCCCCCH
Q 045516          421 VGNLPFSVEQ  430 (675)
Q Consensus       421 V~nLp~~~te  430 (675)
                      +.-.|-++++
T Consensus       154 ~~k~p~Nin~  163 (465)
T KOG3973|consen  154 FPKQPGNINE  163 (465)
T ss_pred             CCCCCCCchH
Confidence            3333344443

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

Probab=97.77  E-value=3.4e-05  Score=85.65  Aligned_cols=79  Identities=16%  Similarity=0.368  Sum_probs=71.0

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccC---CCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCee
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDY---DTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYS  592 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~---~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~  592 (675)
                      ..+.|||+||+..+++..    |-..|+.||.|..|.|+..+   +..+.+.++||.|.+..++.+|+. |+|..+.++.
T Consensus       173 ~TTNlyv~Nlnpsv~E~~----ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e  248 (877)
T KOG0151|consen  173 QTTNLYVGNLNPSVDENF----LLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYE  248 (877)
T ss_pred             cccceeeecCCccccHHH----HHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeee
Confidence            368899999999999987    77899999999999988754   346678899999999999999998 9999999999


Q ss_pred             eEEeccc
Q 045516          593 LVVDEAK  599 (675)
Q Consensus       593 l~V~~a~  599 (675)
                      |++-|++
T Consensus       249 ~K~gWgk  255 (877)
T KOG0151|consen  249 MKLGWGK  255 (877)
T ss_pred             eeecccc
Confidence            9999984

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

Probab=97.76  E-value=2.1e-06  Score=97.15  Aligned_cols=165  Identities=15%  Similarity=0.163  Sum_probs=127.0

Q ss_pred             CCCceEEEcCCCCCCCHH-HHHHHhhhCCCeEEEEEeeCCCCCc-ccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEec
Q 045516          414 GGSKTLFVGNLPFSVEQA-DVQNFFSEVAEVVDVRLSSDADGRF-KGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFA  491 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~-~L~~~F~~~G~I~~v~i~~~~~g~~-kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a  491 (675)
                      ...+.+++.|+-+..... .++..|..+|.|..|++.......+ ..+.|+.|.....++.|....+..+.++.+.|.++
T Consensus       569 ~~~~e~~s~~v~p~~~~ke~~~~~~k~~~~vekv~~p~~g~k~h~q~~~~~~~s~~~~~esat~pa~~~~a~~~~av~~a  648 (881)
T KOG0128|consen  569 LERREKESTNVYPEQQKKEIQRRQFKGEGNVEKVNGPKRGFKAHEQPQQQKVQSKHGSAESATVPAGGALANRSAAVGLA  648 (881)
T ss_pred             hhhhhhcccCCCcchhhHHhhHHHhhcccccccccCccccccccccchhhhhhccccchhhcccccccccCCccccCCCC
Confidence            456778899997777666 5788999999999999987443332 33899999999999999999999999999998887


Q ss_pred             cccCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEe
Q 045516          492 RERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDF  571 (675)
Q Consensus       492 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F  571 (675)
                      ..+.......        ..........++||+||+..+...+    |...|..||.|..|+|.....+++.||+|||.|
T Consensus       649 d~~~~~~~~k--------vs~n~~R~~~~~fvsnl~~~~~~~d----l~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F  716 (881)
T KOG0128|consen  649 DAEEKEENFK--------VSPNEIRDLIKIFVSNLSPKMSEED----LSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEF  716 (881)
T ss_pred             CchhhhhccC--------cCchHHHHHHHHHHhhcchhhcCch----hhhhcCccchhhhHHHHHHhhccccccceeeEe
Confidence            6543111100        0001112257899999999999988    778888889888888886677899999999999


Q ss_pred             CCHHHHHHHHHhCCceeCC
Q 045516          572 TDADSFNKALEMSGTEIGG  590 (675)
Q Consensus       572 ~~~e~A~~Al~lng~~~~G  590 (675)
                      ...+.+.+||.++...|.|
T Consensus       717 ~~~~~~~aaV~f~d~~~~g  735 (881)
T KOG0128|consen  717 LKPEHAGAAVAFRDSCFFG  735 (881)
T ss_pred             ecCCchhhhhhhhhhhhhh
Confidence            9999999999855444444

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

Probab=97.71  E-value=0.00011  Score=77.43  Aligned_cols=78  Identities=27%  Similarity=0.388  Sum_probs=60.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeC---C-C--CC--------cccEEEEEecCHHHHHHHHH-hCC
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD---A-D--GR--------FKGYGHVEFASVEDAHKAIE-LNG  478 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~---~-~--g~--------~kG~afV~F~~~e~A~~Al~-l~g  478 (675)
                      -.+++|.+-|||.+-.-+.|..||..||.|..|+|+.-   + +  +.        .+-+|||+|...+.|.+|.+ ||.
T Consensus       229 l~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~  308 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNP  308 (484)
T ss_pred             cccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhch
Confidence            46899999999999999999999999999999999865   2 1  22        25689999999999999999 444


Q ss_pred             cccCCeeEEEEec
Q 045516          479 QMLGNRAIRLDFA  491 (675)
Q Consensus       479 ~~~~gr~i~V~~a  491 (675)
                      ....-..|+|.+.
T Consensus       309 e~~wr~glkvkLl  321 (484)
T KOG1855|consen  309 EQNWRMGLKVKLL  321 (484)
T ss_pred             hhhhhhcchhhhh
Confidence            3333333444443

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.70  E-value=3.8e-05  Score=78.27  Aligned_cols=79  Identities=14%  Similarity=0.392  Sum_probs=62.8

Q ss_pred             CceEEEcCCCCCCCHHH----H--HHHhhhCCCeEEEEEeeCC--CCCcccE--EEEEecCHHHHHHHHH-hCCcccCCe
Q 045516          416 SKTLFVGNLPFSVEQAD----V--QNFFSEVAEVVDVRLSSDA--DGRFKGY--GHVEFASVEDAHKAIE-LNGQMLGNR  484 (675)
Q Consensus       416 ~~tlfV~nLp~~~te~~----L--~~~F~~~G~I~~v~i~~~~--~g~~kG~--afV~F~~~e~A~~Al~-l~g~~~~gr  484 (675)
                      -+-|||-+||..+-.++    |  .+||.+||.|..|.|-+..  ...-.+.  .||.|.+.++|.+||. .+|..++||
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr  193 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGR  193 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCc
Confidence            45789999998887776    2  5699999999998876543  1222232  3999999999999997 999999999


Q ss_pred             eEEEEecccc
Q 045516          485 AIRLDFARER  494 (675)
Q Consensus       485 ~i~V~~a~~~  494 (675)
                      .|+..|...+
T Consensus       194 ~lkatYGTTK  203 (480)
T COG5175         194 VLKATYGTTK  203 (480)
T ss_pred             eEeeecCchH
Confidence            9999887543

>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=97.63  E-value=0.00014  Score=64.20  Aligned_cols=68  Identities=28%  Similarity=0.363  Sum_probs=42.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-h--C---CcccCCeeEEEE
Q 045516          417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-L--N---GQMLGNRAIRLD  489 (675)
Q Consensus       417 ~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l--~---g~~~~gr~i~V~  489 (675)
                      +.|+|.||+..++.++|+++|..||.|..|.+...     ...|||.|.+.+.|+.|+. +  .   +..|.+..+.+.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G-----~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG-----DTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC-----CCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            57999999999999999999999999999988753     4589999999999999996 3  3   334455554443

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

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

Probab=97.62  E-value=2.3e-05  Score=75.69  Aligned_cols=76  Identities=22%  Similarity=0.330  Sum_probs=67.3

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~  596 (675)
                      .+||||.||-..++++-    |.++|-+.|.|..|.|+.+.+ +..+ ||||.|.+.....-|++ |||..|.++.|.|.
T Consensus         9 drtl~v~n~~~~v~eel----L~ElfiqaGPV~kv~ip~~~d-~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~   82 (267)
T KOG4454|consen    9 DRTLLVQNMYSGVSEEL----LSELFIQAGPVYKVGIPSGQD-QEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRT   82 (267)
T ss_pred             hhHHHHHhhhhhhhHHH----HHHHhhccCceEEEeCCCCcc-CCCc-eeeeecccccchhhhhhhcccchhccchhhcc
Confidence            68999999999999886    778888889999999998865 5555 99999999999999999 99999999988887


Q ss_pred             ccc
Q 045516          597 EAK  599 (675)
Q Consensus       597 ~a~  599 (675)
                      +..
T Consensus        83 ~r~   85 (267)
T KOG4454|consen   83 LRC   85 (267)
T ss_pred             ccc
Confidence            653

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=97.58  E-value=0.00029  Score=81.86  Aligned_cols=74  Identities=12%  Similarity=0.105  Sum_probs=45.1

Q ss_pred             eEEEEe-cCCCCcCHHHHHHHHHhhhcc-cCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEE
Q 045516          519 HTIFIK-GFDSSVGEDQVRASLEEHFGS-CGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVV  595 (675)
Q Consensus       519 ~~lfV~-nLp~~~te~~i~~~L~~~F~~-~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V  595 (675)
                      .++||. +--..+....|...|...-.- -..|-.|.|+.+        |.||+.... .+...+. |++..+.|+.|.|
T Consensus       487 ~~~~~~~g~~~~~~~~~~~~~i~~~~~~~~~~ig~i~i~~~--------~s~v~~~~~-~~~~~~~~~~~~~~~~~~~~~  557 (629)
T PRK11634        487 QLYRIEVGRDDGVEVRHIVGAIANEGDISSRYIGNIKLFAS--------HSTIELPKG-MPGEVLQHFTRTRILNKPMNM  557 (629)
T ss_pred             EEEEEecccccCCCHHHHHHHHHhhcCCChhhCCcEEEeCC--------ceEEEcChh-hHHHHHHHhccccccCCceEE
Confidence            345443 334567777765555544211 013455555543        678877544 3566666 9999999999999


Q ss_pred             eccccC
Q 045516          596 DEAKQR  601 (675)
Q Consensus       596 ~~a~~r  601 (675)
                      ..+...
T Consensus       558 ~~~~~~  563 (629)
T PRK11634        558 QLLGDA  563 (629)
T ss_pred             EECCCC
Confidence            987533

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

Probab=97.57  E-value=0.00018  Score=75.99  Aligned_cols=65  Identities=23%  Similarity=0.356  Sum_probs=52.6

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEeccc---CCC--CCe--------eeEEEEEeCCHHHHHHHHH
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKD---YDT--GSV--------KGIAYLDFTDADSFNKALE  582 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d---~~t--G~~--------rG~afV~F~~~e~A~~Al~  582 (675)
                      .++++|.+-|||.+-..+    .|..||+.||.|..|+|+..   ...  +.+        +-+|||+|...+.|.+|.+
T Consensus       229 l~srtivaenLP~Dh~~e----nl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e  304 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDHSYE----NLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARE  304 (484)
T ss_pred             cccceEEEecCCcchHHH----HHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHH
Confidence            358999999999877664    48999999999999999876   322  222        4579999999999999998


Q ss_pred             hC
Q 045516          583 MS  584 (675)
Q Consensus       583 ln  584 (675)
                      |.
T Consensus       305 ~~  306 (484)
T KOG1855|consen  305 LL  306 (484)
T ss_pred             hh
Confidence            43

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

Probab=97.48  E-value=0.0002  Score=73.51  Aligned_cols=77  Identities=14%  Similarity=0.209  Sum_probs=64.2

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~  596 (675)
                      ..++||+||-+.+++.+|...|+.+  ....|..+.++.++.+|.++|||+|...+.....+.|+ |-...|.|+.-.|.
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~--G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~  157 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQST--GLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVL  157 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhh--hHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeee
Confidence            4689999999999999988877765  11256777888888899999999999999999999998 88888988765553

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.31  E-value=0.00037  Score=71.28  Aligned_cols=83  Identities=19%  Similarity=0.429  Sum_probs=66.7

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHH--hhhcccCcEEEEEecccCCC---CCeeeEEEEEeCCHHHHHHHHH-hCCceeCCe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLE--EHFGSCGEITRISVPKDYDT---GSVKGIAYLDFTDADSFNKALE-MSGTEIGGY  591 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~--~~F~~~G~I~~v~i~~d~~t---G~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr  591 (675)
                      -+.+||-+|+..+..+++...|.  +||++||.|..|.|-+.-..   -...--.||.|.+.++|.+||. .+|..++||
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr  193 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGR  193 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCc
Confidence            46789999999998887666665  69999999999988764311   1111235999999999999998 999999999


Q ss_pred             eeEEecccc
Q 045516          592 SLVVDEAKQ  600 (675)
Q Consensus       592 ~l~V~~a~~  600 (675)
                      .|+..|...
T Consensus       194 ~lkatYGTT  202 (480)
T COG5175         194 VLKATYGTT  202 (480)
T ss_pred             eEeeecCch
Confidence            999998753

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

Probab=97.30  E-value=0.00028  Score=70.05  Aligned_cols=71  Identities=25%  Similarity=0.394  Sum_probs=60.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-C--------CCcccE----EEEEecCHHHHHHHHH-hCCcc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-D--------GRFKGY----GHVEFASVEDAHKAIE-LNGQM  480 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~--------g~~kG~----afV~F~~~e~A~~Al~-l~g~~  480 (675)
                      .+..|||+|||+.+.-..|++||..||.|-+|.|.... .        |.++++    |+|+|.+...|..+.. |||..
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~  152 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTP  152 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCc
Confidence            45799999999999999999999999999999997654 2        233332    6799999999999887 99999


Q ss_pred             cCCee
Q 045516          481 LGNRA  485 (675)
Q Consensus       481 ~~gr~  485 (675)
                      |+|+.
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99875

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

Probab=97.28  E-value=0.0013  Score=60.78  Aligned_cols=79  Identities=22%  Similarity=0.352  Sum_probs=58.2

Q ss_pred             CCCCceEEEEecCC-----CCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCcee
Q 045516          514 RGQAAHTIFIKGFD-----SSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEI  588 (675)
Q Consensus       514 ~~~~~~~lfV~nLp-----~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~  588 (675)
                      .+++..||.|.-+.     ...-.+.+...|-+.|..||.|.-||+..+        .-+|+|.+-..|.+|+.|+|..+
T Consensus        23 ~GPpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals~dg~~v   94 (146)
T PF08952_consen   23 QGPPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALSLDGIQV   94 (146)
T ss_dssp             ---TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHHGCCSEE
T ss_pred             cCCCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHccCCcEE
Confidence            34556777777665     233456677778888999999999988765        47999999999999999999999


Q ss_pred             CCeeeEEecccc
Q 045516          589 GGYSLVVDEAKQ  600 (675)
Q Consensus       589 ~Gr~l~V~~a~~  600 (675)
                      +|+.|+|..-.+
T Consensus        95 ~g~~l~i~LKtp  106 (146)
T PF08952_consen   95 NGRTLKIRLKTP  106 (146)
T ss_dssp             TTEEEEEEE---
T ss_pred             CCEEEEEEeCCc
Confidence            999999987654

; PDB: 1UFW_A 2DNR_A.

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

Probab=97.27  E-value=0.0008  Score=58.65  Aligned_cols=76  Identities=14%  Similarity=0.192  Sum_probs=54.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEE-EeeC-------CCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeE
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVR-LSSD-------ADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAI  486 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~-i~~~-------~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i  486 (675)
                      ..+.|.|=+.|.. ....|.++|++||.|++.. +.++       +.-...++..|.|.++.+|.+||..||..|.|..|
T Consensus         5 ~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~NG~i~~g~~m   83 (100)
T PF05172_consen    5 SETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQKNGTIFSGSLM   83 (100)
T ss_dssp             GCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTTTTEEETTCEE
T ss_pred             CCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHhCCeEEcCcEE
Confidence            3467889999988 6778999999999998885 1111       11124679999999999999999999999988655


Q ss_pred             -EEEec
Q 045516          487 -RLDFA  491 (675)
Q Consensus       487 -~V~~a  491 (675)
                       -|.++
T Consensus        84 vGV~~~   89 (100)
T PF05172_consen   84 VGVKPC   89 (100)
T ss_dssp             EEEEE-
T ss_pred             EEEEEc
Confidence             45555

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.

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

Probab=97.22  E-value=0.00072  Score=73.70  Aligned_cols=79  Identities=30%  Similarity=0.478  Sum_probs=64.7

Q ss_pred             CCCceEEEcCCCCCC--CHH----HHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccC-Cee
Q 045516          414 GGSKTLFVGNLPFSV--EQA----DVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLG-NRA  485 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~--te~----~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~-gr~  485 (675)
                      +-...|+|-|+|---  ..+    -|..+|++||.|+.+.++.+..|..+||.|++|.+..+|..|+. |||+.|+ ++.
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHt  135 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHT  135 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccce
Confidence            556799999998432  222    35679999999999999999877799999999999999999998 9999884 566


Q ss_pred             EEEEecc
Q 045516          486 IRLDFAR  492 (675)
Q Consensus       486 i~V~~a~  492 (675)
                      +.|..-.
T Consensus       136 f~v~~f~  142 (698)
T KOG2314|consen  136 FFVRLFK  142 (698)
T ss_pred             EEeehhh
Confidence            7776544

>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=97.19  E-value=0.0012  Score=58.37  Aligned_cols=69  Identities=19%  Similarity=0.431  Sum_probs=41.5

Q ss_pred             eEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-h--C---CceeCCee
Q 045516          519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-M--S---GTEIGGYS  592 (675)
Q Consensus       519 ~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-l--n---g~~~~Gr~  592 (675)
                      ..|+|.|++..++.++    |+.+|..||.|.+|.+.+.      ...|||.|.+.+.|..|+. +  .   +..|.+..
T Consensus         2 ~il~~~g~~~~~~re~----iK~~f~~~g~V~yVD~~~G------~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~   71 (105)
T PF08777_consen    2 CILKFSGLGEPTSRED----IKEAFSQFGEVAYVDFSRG------DTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKE   71 (105)
T ss_dssp             -EEEEEE--SS--HHH----HHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSS
T ss_pred             eEEEEecCCCCcCHHH----HHHHHHhcCCcceEEecCC------CCEEEEEECCcchHHHHHHHHHhccCCceEEcCce
Confidence            5789999999988666    8888999999999999876      3479999999999999986 3  3   44566666


Q ss_pred             eEEec
Q 045516          593 LVVDE  597 (675)
Q Consensus       593 l~V~~  597 (675)
                      +.+..
T Consensus        72 ~~~~v   76 (105)
T PF08777_consen   72 VTLEV   76 (105)
T ss_dssp             EEEE-
T ss_pred             EEEEE
Confidence            55543

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

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

Probab=97.18  E-value=0.00076  Score=51.77  Aligned_cols=52  Identities=23%  Similarity=0.403  Sum_probs=43.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHH
Q 045516          417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI  474 (675)
Q Consensus       417 ~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al  474 (675)
                      +.|-|.+.+.... +.|+.+|.+||+|..+.+..     ...+.||.|.+..+|++||
T Consensus         2 ~wI~V~Gf~~~~~-~~vl~~F~~fGeI~~~~~~~-----~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLA-EEVLEHFASFGEIVDIYVPE-----STNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHH-HHHHHHHHhcCCEEEEEcCC-----CCcEEEEEECCHHHHHhhC
Confidence            6788999987766 45566999999999998872     3679999999999999986

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

Probab=97.13  E-value=0.0012  Score=57.44  Aligned_cols=76  Identities=21%  Similarity=0.233  Sum_probs=51.4

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEec-ccC------CCCCeeeEEEEEeCCHHHHHHHHHhCCceeCC
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVP-KDY------DTGSVKGIAYLDFTDADSFNKALEMSGTEIGG  590 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~-~d~------~tG~~rG~afV~F~~~e~A~~Al~lng~~~~G  590 (675)
                      .+.|.|-|+|......     +-++|.+||.|....-. ++.      ..-....+..|+|.++.+|.+||..||..|+|
T Consensus         6 ~~wVtVFGfp~~~~~~-----Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~NG~i~~g   80 (100)
T PF05172_consen    6 ETWVTVFGFPPSASNQ-----VLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQKNGTIFSG   80 (100)
T ss_dssp             CCEEEEE---GGGHHH-----HHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTTTTEEETT
T ss_pred             CeEEEEEccCHHHHHH-----HHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHhCCeEEcC
Confidence            4678888998876554     66789999999887511 110      00123579999999999999999999999998


Q ss_pred             eee-EEecc
Q 045516          591 YSL-VVDEA  598 (675)
Q Consensus       591 r~l-~V~~a  598 (675)
                      ..| -|.+.
T Consensus        81 ~~mvGV~~~   89 (100)
T PF05172_consen   81 SLMVGVKPC   89 (100)
T ss_dssp             CEEEEEEE-
T ss_pred             cEEEEEEEc
Confidence            654 45554

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.

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

Probab=97.05  E-value=0.00047  Score=75.53  Aligned_cols=77  Identities=21%  Similarity=0.293  Sum_probs=65.7

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhh-hCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCccc---CCeeE
Q 045516          412 QSGGSKTLFVGNLPFSVEQADVQNFFS-EVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQML---GNRAI  486 (675)
Q Consensus       412 ~~~~~~tlfV~nLp~~~te~~L~~~F~-~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~---~gr~i  486 (675)
                      ....++.|||.||-.-+|.-+|+.|+. .+|.|...||-+     -+-.|||.|.+.+.|...+. |||..|   +++.|
T Consensus       440 R~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~WmDk-----IKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L  514 (718)
T KOG2416|consen  440 RKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWMDK-----IKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHL  514 (718)
T ss_pred             CCCccceEeeecccccchHHHHHHHHhhccCchHHHHHHH-----hhcceeEecccHHHHHHHHHHHhccccCCCCCcee
Confidence            456789999999999999999999999 677888886643     37789999999999999997 999887   57888


Q ss_pred             EEEeccc
Q 045516          487 RLDFARE  493 (675)
Q Consensus       487 ~V~~a~~  493 (675)
                      .|.|...
T Consensus       515 ~adf~~~  521 (718)
T KOG2416|consen  515 IADFVRA  521 (718)
T ss_pred             Eeeecch
Confidence            8888764

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

Probab=96.97  E-value=0.0021  Score=70.22  Aligned_cols=79  Identities=18%  Similarity=0.406  Sum_probs=66.8

Q ss_pred             ceEEEEecCCCC--cCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeC-Ceee
Q 045516          518 AHTIFIKGFDSS--VGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIG-GYSL  593 (675)
Q Consensus       518 ~~~lfV~nLp~~--~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~-Gr~l  593 (675)
                      ...|+|.|+|--  ..-.-|+..|..+|+++|.|..+.++.+..+| .+||.|++|.+..+|..|+. |||+.|+ .+.+
T Consensus        58 D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~gg-tkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf  136 (698)
T KOG2314|consen   58 DSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGG-TKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTF  136 (698)
T ss_pred             ceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCC-eeeEEEEEecChhhHHHHHHhcccceecccceE
Confidence            578889998853  33567888899999999999999999997766 99999999999999999998 9999986 5566


Q ss_pred             EEec
Q 045516          594 VVDE  597 (675)
Q Consensus       594 ~V~~  597 (675)
                      .|..
T Consensus       137 ~v~~  140 (698)
T KOG2314|consen  137 FVRL  140 (698)
T ss_pred             Eeeh
Confidence            6653

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

Probab=96.94  E-value=0.0022  Score=63.83  Aligned_cols=101  Identities=25%  Similarity=0.377  Sum_probs=80.4

Q ss_pred             HHHHHH-hCCcccCCeeEEEEeccccCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCc
Q 045516          470 AHKAIE-LNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGE  548 (675)
Q Consensus       470 A~~Al~-l~g~~~~gr~i~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~  548 (675)
                      |..|-. |++..+.|+.|+|.|+.                         ...|||.||...+..+.    |.+.|..||.
T Consensus         7 ae~ak~eLd~~~~~~~~lr~rfa~-------------------------~a~l~V~nl~~~~sndl----l~~~f~~fg~   57 (275)
T KOG0115|consen    7 AEIAKRELDGRFPKGRSLRVRFAM-------------------------HAELYVVNLMQGASNDL----LEQAFRRFGP   57 (275)
T ss_pred             HHHHHHhcCCCCCCCCceEEEeec-------------------------cceEEEEecchhhhhHH----HHHhhhhcCc
Confidence            455554 99999999999999985                         36799999999998876    7888999999


Q ss_pred             EEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hC-C---ceeCCeeeEEecccc
Q 045516          549 ITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MS-G---TEIGGYSLVVDEAKQ  600 (675)
Q Consensus       549 I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-ln-g---~~~~Gr~l~V~~a~~  600 (675)
                      |....++.|+ .+++.+-++|.|...-.+..|+. .+ +   ....++.+-|.....
T Consensus        58 ~e~av~~vD~-r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~VeP~eq  113 (275)
T KOG0115|consen   58 IERAVAKVDD-RGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGVEPMEQ  113 (275)
T ss_pred             cchheeeecc-cccccccchhhhhcchhHHHHHHHhccCccccCCCCCccCCChhhc
Confidence            9998888874 48899999999999999999986 32 2   233566666655443

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

Probab=96.89  E-value=0.0026  Score=58.79  Aligned_cols=71  Identities=23%  Similarity=0.260  Sum_probs=53.6

Q ss_pred             CceEEEcCCC-----CCCCH----HHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeE
Q 045516          416 SKTLFVGNLP-----FSVEQ----ADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAI  486 (675)
Q Consensus       416 ~~tlfV~nLp-----~~~te----~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i  486 (675)
                      ..||.|.=+.     ...-.    .+|.+.|..||.|+-||+.       .+.-+|+|.+-..|-+||.|+|..+.|+.|
T Consensus        27 DaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv-------~~~mwVTF~dg~sALaals~dg~~v~g~~l   99 (146)
T PF08952_consen   27 DATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFV-------GDTMWVTFRDGQSALAALSLDGIQVNGRTL   99 (146)
T ss_dssp             T-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEE-------TTCEEEEESSCHHHHHHHHGCCSEETTEEE
T ss_pred             CceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEe-------CCeEEEEECccHHHHHHHccCCcEECCEEE
Confidence            3566666555     11222    3678889999999999988       457899999999999999999999999999


Q ss_pred             EEEeccc
Q 045516          487 RLDFARE  493 (675)
Q Consensus       487 ~V~~a~~  493 (675)
                      +|.+..+
T Consensus       100 ~i~LKtp  106 (146)
T PF08952_consen  100 KIRLKTP  106 (146)
T ss_dssp             EEEE---
T ss_pred             EEEeCCc
Confidence            9988754

; PDB: 1UFW_A 2DNR_A.

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=96.86  E-value=0.011  Score=68.97  Aligned_cols=60  Identities=8%  Similarity=0.170  Sum_probs=45.8

Q ss_pred             CCCCCHHHHHHHhhhCCC-----eEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecc
Q 045516          425 PFSVEQADVQNFFSEVAE-----VVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       425 p~~~te~~L~~~F~~~G~-----I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~  492 (675)
                      -..++..+|..++..-+.     |-.|.|.       ..|.||+.... .+...|. |++..+.|+.|.|..+.
T Consensus       496 ~~~~~~~~~~~~i~~~~~~~~~~ig~i~i~-------~~~s~v~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~  561 (629)
T PRK11634        496 DDGVEVRHIVGAIANEGDISSRYIGNIKLF-------ASHSTIELPKG-MPGEVLQHFTRTRILNKPMNMQLLG  561 (629)
T ss_pred             ccCCCHHHHHHHHHhhcCCChhhCCcEEEe-------CCceEEEcChh-hHHHHHHHhccccccCCceEEEECC
Confidence            356888899888887654     4556666       56899998755 4667776 99999999999998763

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

Probab=96.78  E-value=0.004  Score=67.76  Aligned_cols=63  Identities=27%  Similarity=0.369  Sum_probs=59.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhh-hCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFS-EVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE  475 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~-~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~  475 (675)
                      ....+|||||+||--++.++|-.+|. .||.|..|-|-.|+ .+..+|-|-|.|.+...-.+||.
T Consensus       367 lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIs  431 (520)
T KOG0129|consen  367 IDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAIS  431 (520)
T ss_pred             cCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHh
Confidence            45679999999999999999999999 79999999999995 78899999999999999999996

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

Probab=96.63  E-value=0.0038  Score=47.86  Aligned_cols=52  Identities=37%  Similarity=0.602  Sum_probs=42.4

Q ss_pred             eEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHH
Q 045516          519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKAL  581 (675)
Q Consensus       519 ~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al  581 (675)
                      +.|.|.|++....+.     +..+|..||+|..+.+...      ..+.||.|.+..+|.+||
T Consensus         2 ~wI~V~Gf~~~~~~~-----vl~~F~~fGeI~~~~~~~~------~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-----VLEHFASFGEIVDIYVPES------TNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHH-----HHHHHHhcCCEEEEEcCCC------CcEEEEEECCHHHHHhhC
Confidence            578899988665544     5568889999999998733      568999999999999985

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

Probab=96.57  E-value=0.0041  Score=62.80  Aligned_cols=82  Identities=11%  Similarity=0.185  Sum_probs=61.6

Q ss_pred             ceEEEEecCC-CCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCe-eeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          518 AHTIFIKGFD-SSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSV-KGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       518 ~~~lfV~nLp-~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~-rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      .+.|.++|+- ..--.++|...+.+.+++||.|.+|.|+.....-.. ---.||+|...+.|.+|+- |||++|+||.++
T Consensus       281 tkvlllrnmVg~gevd~elede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~  360 (378)
T KOG1996|consen  281 TKVLLLRNMVGAGEVDEELEDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVS  360 (378)
T ss_pred             hHHHHhhhhcCcccccHHHHHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeee
Confidence            4445555543 333456777778899999999999988876432111 2247999999999999986 999999999998


Q ss_pred             Eeccc
Q 045516          595 VDEAK  599 (675)
Q Consensus       595 V~~a~  599 (675)
                      ..|..
T Consensus       361 A~Fyn  365 (378)
T KOG1996|consen  361 ACFYN  365 (378)
T ss_pred             heecc
Confidence            87764

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

Probab=96.42  E-value=0.0047  Score=64.75  Aligned_cols=77  Identities=22%  Similarity=0.357  Sum_probs=64.8

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCC---CCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeE
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDT---GSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLV  594 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~t---G~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~  594 (675)
                      ...|.|.||.++++.++    |+.||+..|.|..++|+.....   ......|||.|.+...+..|..|.++.|-++.|.
T Consensus         7 ~~vIqvanispsat~dq----m~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQhLtntvfvdrali   82 (479)
T KOG4676|consen    7 LGVIQVANISPSATKDQ----MQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQHLTNTVFVDRALI   82 (479)
T ss_pred             CceeeecccCchhhHHH----HHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhhhccceeeeeeEE
Confidence            35899999999999887    8889999999999999885432   3456789999999999999998999998888877


Q ss_pred             Eecc
Q 045516          595 VDEA  598 (675)
Q Consensus       595 V~~a  598 (675)
                      |..+
T Consensus        83 v~p~   86 (479)
T KOG4676|consen   83 VRPY   86 (479)
T ss_pred             EEec
Confidence            7644

>PF05918 API5: Apoptosis inhibitory protein 5 (API5); InterPro: IPR008383 This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organisms

Probab=96.28  E-value=0.0011  Score=74.62  Aligned_cols=7  Identities=0%  Similarity=0.079  Sum_probs=1.5

Q ss_pred             eEEeccc
Q 045516          593 LVVDEAK  599 (675)
Q Consensus       593 l~V~~a~  599 (675)
                      |.+.|-.
T Consensus       457 itlSWk~  463 (556)
T PF05918_consen  457 ITLSWKE  463 (556)
T ss_dssp             ---TTS-
T ss_pred             cceeeee
Confidence            4455443

Apoptosis or programmed cell death is a physiological form of cell death that occurs in embryonic development and organ formation. It is characterised by biochemical and morphological changes such as DNA fragmentation and cell volume shrinkage. API5 is an anti apoptosis gene located in Homo sapiens chromosome 11, whose expression prevents the programmed cell death that occurs upon the deprivation of growth factors [,].; PDB: 3U0R_A 3V6A_A.

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

Probab=96.19  E-value=0.0038  Score=68.69  Aligned_cols=77  Identities=14%  Similarity=0.289  Sum_probs=60.1

Q ss_pred             CCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCcee---C
Q 045516          514 RGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEI---G  589 (675)
Q Consensus       514 ~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~---~  589 (675)
                      +...++.|||.||-..+|.-+|+.+|..   .||.|....|-+      .+-.|||.|.+.+.|...+. |||..|   +
T Consensus       440 R~~~SnvlhI~nLvRPFTlgQLkelL~r---tgg~Vee~WmDk------IKShCyV~yss~eEA~atr~AlhnV~WP~sN  510 (718)
T KOG2416|consen  440 RKEPSNVLHIDNLVRPFTLGQLKELLGR---TGGNVEEFWMDK------IKSHCYVSYSSVEEAAATREALHNVQWPPSN  510 (718)
T ss_pred             CCCccceEeeecccccchHHHHHHHHhh---ccCchHHHHHHH------hhcceeEecccHHHHHHHHHHHhccccCCCC
Confidence            4456899999999999998885544443   467777664432      36789999999999999998 999887   6


Q ss_pred             CeeeEEeccc
Q 045516          590 GYSLVVDEAK  599 (675)
Q Consensus       590 Gr~l~V~~a~  599 (675)
                      ++.|.+.|..
T Consensus       511 PK~L~adf~~  520 (718)
T KOG2416|consen  511 PKHLIADFVR  520 (718)
T ss_pred             CceeEeeecc
Confidence            7889888885

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

Probab=96.19  E-value=0.012  Score=59.63  Aligned_cols=76  Identities=26%  Similarity=0.301  Sum_probs=58.1

Q ss_pred             ceEEEcCC--CCCCC---HHHHHHHhhhCCCeEEEEEeeCCCC--CcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEE
Q 045516          417 KTLFVGNL--PFSVE---QADVQNFFSEVAEVVDVRLSSDADG--RFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRL  488 (675)
Q Consensus       417 ~tlfV~nL--p~~~t---e~~L~~~F~~~G~I~~v~i~~~~~g--~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V  488 (675)
                      +.|.++|+  +-.+.   ++++.+-+.+||.|..|.|+..++.  .-.-.-||+|...+.|.+|+- |||.+|+||.+..
T Consensus       282 kvlllrnmVg~gevd~elede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A  361 (378)
T KOG1996|consen  282 KVLLLRNMVGAGEVDEELEDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSA  361 (378)
T ss_pred             HHHHhhhhcCcccccHHHHHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeh
Confidence            44666665  22333   4567888999999999999877521  123457999999999999995 9999999999988


Q ss_pred             Eecc
Q 045516          489 DFAR  492 (675)
Q Consensus       489 ~~a~  492 (675)
                      .|..
T Consensus       362 ~Fyn  365 (378)
T KOG1996|consen  362 CFYN  365 (378)
T ss_pred             eecc
Confidence            7753

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

Probab=96.14  E-value=0.0061  Score=70.18  Aligned_cols=79  Identities=23%  Similarity=0.304  Sum_probs=68.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCC--eeEEEE
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGN--RAIRLD  489 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~g--r~i~V~  489 (675)
                      ...++.|||++|..++....|...|..||.|..|.+..     ..-|+||.|.+...++.|+. |-|..|+|  ++|+|.
T Consensus       452 st~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~h-----gq~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvd  526 (975)
T KOG0112|consen  452 STPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRH-----GQPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVD  526 (975)
T ss_pred             cccceeeccCCCCCCChHHHHHHHhhccCcceeeeccc-----CCcceeeecccCccchhhHHHHhcCcCCCCCcccccc
Confidence            34678999999999999999999999999999987763     25799999999999999998 99999975  779999


Q ss_pred             eccccCC
Q 045516          490 FARERGA  496 (675)
Q Consensus       490 ~a~~~~~  496 (675)
                      |+...+.
T Consensus       527 la~~~~~  533 (975)
T KOG0112|consen  527 LASPPGA  533 (975)
T ss_pred             cccCCCC
Confidence            9876543

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

Probab=96.13  E-value=0.003  Score=62.90  Aligned_cols=71  Identities=18%  Similarity=0.382  Sum_probs=57.7

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCC--------CCee----eEEEEEeCCHHHHHHHHH-hC
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDT--------GSVK----GIAYLDFTDADSFNKALE-MS  584 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~t--------G~~r----G~afV~F~~~e~A~~Al~-ln  584 (675)
                      ...|||.+||+.+....    |++||+.||.|-+|.|.+...+        |..+    --|.|+|.+...|.++.. ||
T Consensus        74 ~GVvylS~IPp~m~~~r----lReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Ln  149 (278)
T KOG3152|consen   74 TGVVYLSNIPPYMDPVR----LREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLN  149 (278)
T ss_pred             ceEEEeccCCCccCHHH----HHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhC
Confidence            57899999999999988    6677778899999998876544        2222    237789999999999987 99


Q ss_pred             CceeCCee
Q 045516          585 GTEIGGYS  592 (675)
Q Consensus       585 g~~~~Gr~  592 (675)
                      |..|+|+.
T Consensus       150 n~~Iggkk  157 (278)
T KOG3152|consen  150 NTPIGGKK  157 (278)
T ss_pred             CCccCCCC
Confidence            99999864

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

Probab=95.24  E-value=0.013  Score=65.62  Aligned_cols=118  Identities=14%  Similarity=0.117  Sum_probs=79.3

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEE
Q 045516          411 PQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLD  489 (675)
Q Consensus       411 ~~~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~  489 (675)
                      .+.....+|||+||.+.+..+-++.++..||.|..+....        |||..|........|+. ++-..++|..|.+.
T Consensus        35 ~~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~--------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~  106 (668)
T KOG2253|consen   35 QPLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK--------FGFCEFLKHIGDLRASRLLTELNIDDQKLIEN  106 (668)
T ss_pred             cCCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh--------hcccchhhHHHHHHHHHHhcccCCCcchhhcc
Confidence            3356778999999999999999999999999998876653        99999999999999998 78888888888776


Q ss_pred             eccccCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHH
Q 045516          490 FARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVR  536 (675)
Q Consensus       490 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~  536 (675)
                      .-..........+...............-+.++|.|++..+....+.
T Consensus       107 ~d~q~~~n~~k~~~~~~~~~~~f~p~~srr~e~i~~k~~~l~~~~~~  153 (668)
T KOG2253|consen  107 VDEQTIENADKEKSIANKESHKFVPSSSRRQESIQNKPLSLDEQIHK  153 (668)
T ss_pred             chhhhhcCccccccchhhhhcccCCchhHHHHHhhccccchhHHHHH
Confidence            53221111111100001111111111114667778877776665533

>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]

Probab=95.09  E-value=0.1  Score=49.47  Aligned_cols=8  Identities=25%  Similarity=0.555  Sum_probs=3.9

Q ss_pred             CcEEEEEe
Q 045516          547 GEITRISV  554 (675)
Q Consensus       547 G~I~~v~i  554 (675)
                      |.|..+.+
T Consensus        99 G~i~d~~f  106 (215)
T KOG3262|consen   99 GPINDVHF  106 (215)
T ss_pred             ccccccEE
Confidence            55554443

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=94.94  E-value=0.23  Score=55.88  Aligned_cols=9  Identities=0%  Similarity=-0.020  Sum_probs=3.7

Q ss_pred             EEEEecCCC
Q 045516          520 TIFIKGFDS  528 (675)
Q Consensus       520 ~lfV~nLp~  528 (675)
                      .|+.-++|.
T Consensus       316 ~VI~~~~P~  324 (456)
T PRK10590        316 HVVNYELPN  324 (456)
T ss_pred             EEEEeCCCC
Confidence            344344443

>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=94.92  E-value=0.023  Score=55.20  Aligned_cols=68  Identities=10%  Similarity=0.117  Sum_probs=45.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhh-CCCe---EEEEEeeCC--C-CCcccEEEEEecCHHHHHHHHH-hCCcccC
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSE-VAEV---VDVRLSSDA--D-GRFKGYGHVEFASVEDAHKAIE-LNGQMLG  482 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~-~G~I---~~v~i~~~~--~-g~~kG~afV~F~~~e~A~~Al~-l~g~~~~  482 (675)
                      ....|.|++||+++|++++++.+.. ++..   ..+......  . -.....|||.|.+.+++...+. ++|+.|.
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~   81 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFV   81 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEE
Confidence            4569999999999999999998877 6665   333322332  1 1234579999999999999997 9998773

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.

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

Probab=94.90  E-value=0.027  Score=56.27  Aligned_cols=75  Identities=24%  Similarity=0.297  Sum_probs=62.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hC--C--cccCCeeEEEEec
Q 045516          417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LN--G--QMLGNRAIRLDFA  491 (675)
Q Consensus       417 ~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~--g--~~~~gr~i~V~~a  491 (675)
                      ..|||.||...+..+.|..-|..||.|....++.|..++..+-++|.|...-.+.+|+. ++  +  ....+++.-|...
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~VeP~  111 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGVEPM  111 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccccchhhhhcchhHHHHHHHhccCccccCCCCCccCCChh
Confidence            68999999999999999999999999999888888889999999999999999999996 32  2  2334555555444

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

Probab=94.65  E-value=0.047  Score=55.75  Aligned_cols=73  Identities=22%  Similarity=0.294  Sum_probs=56.5

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeE-EEEecccc
Q 045516          416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAI-RLDFARER  494 (675)
Q Consensus       416 ~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i-~V~~a~~~  494 (675)
                      ..-|-|-++|... -.-|..+|.+||.|+.+...     +.-.|-||.|.+.-+|++||..||++|+|..| =|..+..+
T Consensus       197 D~WVTVfGFppg~-~s~vL~~F~~cG~Vvkhv~~-----~ngNwMhirYssr~~A~KALskng~ii~g~vmiGVkpCtDk  270 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQ-VSIVLNLFSRCGEVVKHVTP-----SNGNWMHIRYSSRTHAQKALSKNGTIIDGDVMIGVKPCTDK  270 (350)
T ss_pred             cceEEEeccCccc-hhHHHHHHHhhCeeeeeecC-----CCCceEEEEecchhHHHHhhhhcCeeeccceEEeeeecCCH
Confidence            3567777777654 35688999999999888765     23569999999999999999999999988654 45555443

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=94.53  E-value=0.015  Score=60.49  Aligned_cols=79  Identities=16%  Similarity=0.369  Sum_probs=63.3

Q ss_pred             CceEEEcCCCCCCCHHHHH---HHhhhCCCeEEEEEeeCC--CCCc--ccEEEEEecCHHHHHHHHH-hCCcccCCeeEE
Q 045516          416 SKTLFVGNLPFSVEQADVQ---NFFSEVAEVVDVRLSSDA--DGRF--KGYGHVEFASVEDAHKAIE-LNGQMLGNRAIR  487 (675)
Q Consensus       416 ~~tlfV~nLp~~~te~~L~---~~F~~~G~I~~v~i~~~~--~g~~--kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~  487 (675)
                      .+-+||-+|+..+..+.+.   ++|.+||.|..|.+..+.  ....  ---+||+|...++|..||. .+|+.+.|+.|+
T Consensus        77 knlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lk  156 (327)
T KOG2068|consen   77 KNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALK  156 (327)
T ss_pred             hhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhH
Confidence            4678999999888776664   499999999999998865  2111  2237999999999999998 999999999988


Q ss_pred             EEecccc
Q 045516          488 LDFARER  494 (675)
Q Consensus       488 V~~a~~~  494 (675)
                      +.+....
T Consensus       157 a~~gttk  163 (327)
T KOG2068|consen  157 ASLGTTK  163 (327)
T ss_pred             HhhCCCc
Confidence            8776543

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

Probab=94.35  E-value=0.095  Score=53.58  Aligned_cols=72  Identities=21%  Similarity=0.335  Sum_probs=55.8

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeee-EEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSL-VVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l-~V~  596 (675)
                      ...|.|-+|+....-     +|-.+|.+||.|.......+      -.|-+|.|.+.-+|.+||..||..|+|..| -|.
T Consensus       197 D~WVTVfGFppg~~s-----~vL~~F~~cG~Vvkhv~~~n------gNwMhirYssr~~A~KALskng~ii~g~vmiGVk  265 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQVS-----IVLNLFSRCGEVVKHVTPSN------GNWMHIRYSSRTHAQKALSKNGTIIDGDVMIGVK  265 (350)
T ss_pred             cceEEEeccCccchh-----HHHHHHHhhCeeeeeecCCC------CceEEEEecchhHHHHhhhhcCeeeccceEEeee
Confidence            467778888776554     36678999999988766533      569999999999999999999999998653 444


Q ss_pred             cccc
Q 045516          597 EAKQ  600 (675)
Q Consensus       597 ~a~~  600 (675)
                      .+..
T Consensus       266 pCtD  269 (350)
T KOG4285|consen  266 PCTD  269 (350)
T ss_pred             ecCC
Confidence            4443

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

Probab=94.32  E-value=0.021  Score=61.53  Aligned_cols=77  Identities=22%  Similarity=0.336  Sum_probs=65.6

Q ss_pred             CCCceEEEcCCCCCC-CHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEecc
Q 045516          414 GGSKTLFVGNLPFSV-EQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~-te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a~  492 (675)
                      .+.+.|-+.-+|+.+ +..+|..+|.+||.|.+|.+-+.     .-.|.|+|.+...|..|...++..|++|.|+|.|..
T Consensus       370 ~dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~-----~~~a~vTF~t~aeag~a~~s~~avlnnr~iKl~whn  444 (526)
T KOG2135|consen  370 VDHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS-----SLHAVVTFKTRAEAGEAYASHGAVLNNRFIKLFWHN  444 (526)
T ss_pred             cccchhhhhccCCCCchHhhhhhhhhhcCccccccccCc-----hhhheeeeeccccccchhccccceecCceeEEEEec
Confidence            456777777777776 56789999999999999998764     456899999999999999999999999999999987


Q ss_pred             ccC
Q 045516          493 ERG  495 (675)
Q Consensus       493 ~~~  495 (675)
                      ...
T Consensus       445 ps~  447 (526)
T KOG2135|consen  445 PSP  447 (526)
T ss_pred             CCc
Confidence            643

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.28  E-value=0.26  Score=54.75  Aligned_cols=126  Identities=17%  Similarity=0.173  Sum_probs=74.7

Q ss_pred             CCCCceEEEcCCCCC-CCHHHHHHHhhhC----CCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEE
Q 045516          413 SGGSKTLFVGNLPFS-VEQADVQNFFSEV----AEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIR  487 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~-~te~~L~~~F~~~----G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~  487 (675)
                      ...+++|-|-||.|. +...+|.-+|..|    |.|+.|.|+...-|+.+                  |.--.+.|-++.
T Consensus       171 ~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeR------------------M~eEeV~GP~~e  232 (650)
T KOG2318|consen  171 GEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKER------------------MKEEEVHGPPKE  232 (650)
T ss_pred             ccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHH------------------hhhhcccCChhh
Confidence            457899999999987 6888999999876    47999998865422211                  222334444333


Q ss_pred             EEeccccCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEE
Q 045516          488 LDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIA  567 (675)
Q Consensus       488 V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~a  567 (675)
                      +.-......   .                 ..      ......+..++..|++|-  ++.+             ..-||
T Consensus       233 l~~~~e~~~---~-----------------s~------sD~ee~~~~~~~kLR~Yq--~~rL-------------kYYyA  271 (650)
T KOG2318|consen  233 LFKPVEEYK---E-----------------SE------SDDEEEEDVDREKLRQYQ--LNRL-------------KYYYA  271 (650)
T ss_pred             hccccccCc---c-----------------cc------cchhhhhhHHHHHHHHHH--hhhh-------------eeEEE
Confidence            321110000   0                 00      111222233455566551  1111             13489


Q ss_pred             EEEeCCHHHHHHHHH-hCCceeCCeeeEEec
Q 045516          568 YLDFTDADSFNKALE-MSGTEIGGYSLVVDE  597 (675)
Q Consensus       568 fV~F~~~e~A~~Al~-lng~~~~Gr~l~V~~  597 (675)
                      .|+|.+...|..... .+|..|....+.+.+
T Consensus       272 VvecDsi~tA~~vYe~CDG~EfEsS~~~~DL  302 (650)
T KOG2318|consen  272 VVECDSIETAKAVYEECDGIEFESSANKLDL  302 (650)
T ss_pred             EEEecCchHHHHHHHhcCcceeccccceeee
Confidence            999999999999998 999999765544443

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

Probab=94.03  E-value=0.19  Score=41.98  Aligned_cols=53  Identities=13%  Similarity=0.278  Sum_probs=41.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hC
Q 045516          417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LN  477 (675)
Q Consensus       417 ~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~  477 (675)
                      +..||. +|......+|.+||+.||.|.--+|-       -.-|||.+.+.+.|..++. ++
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspfG~I~VsWi~-------dTSAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPFGQIYVSWIN-------DTSAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCCCCEEEEEEC-------TTEEEEEECCCHHHHHHHHHHT
T ss_pred             eEEEEe-CchHhhhhhHHHHhccCCcEEEEEEc-------CCcEEEEeecHHHHHHHHHHhc
Confidence            456666 99999999999999999999877764       4589999999999999987 54

; 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.

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=93.48  E-value=0.37  Score=44.23  Aligned_cols=79  Identities=15%  Similarity=0.183  Sum_probs=60.1

Q ss_pred             CCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCe
Q 045516          513 GRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGY  591 (675)
Q Consensus       513 ~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr  591 (675)
                      ...++..+|.|+=|..++...+-...+....+.||.|..|.+..       +-.|.|.|.+..+|.+|+. ++. ...|.
T Consensus        81 ~kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG-------rqsavVvF~d~~SAC~Av~Af~s-~~pgt  152 (166)
T PF15023_consen   81 TKEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG-------RQSAVVVFKDITSACKAVSAFQS-RAPGT  152 (166)
T ss_pred             CCCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC-------CceEEEEehhhHHHHHHHHhhcC-CCCCc
Confidence            34567899999988888765433334455568899999998865       4569999999999999998 544 66778


Q ss_pred             eeEEeccc
Q 045516          592 SLVVDEAK  599 (675)
Q Consensus       592 ~l~V~~a~  599 (675)
                      .+++.|..
T Consensus       153 m~qCsWqq  160 (166)
T PF15023_consen  153 MFQCSWQQ  160 (166)
T ss_pred             eEEeeccc
Confidence            88887754

>PRK06958 single-stranded DNA-binding protein; Provisional

Probab=93.45  E-value=0.22  Score=48.36  Aligned_cols=8  Identities=63%  Similarity=1.074  Sum_probs=4.4

Q ss_pred             ceEEEcCC
Q 045516          417 KTLFVGNL  424 (675)
Q Consensus       417 ~tlfV~nL  424 (675)
                      +.++|+||
T Consensus         6 ~V~LiGrL   13 (182)
T PRK06958          6 KVILVGNL   13 (182)
T ss_pred             EEEEEEEe
Confidence            44556665

>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=93.02  E-value=0.69  Score=41.16  Aligned_cols=68  Identities=16%  Similarity=0.195  Sum_probs=51.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCC-CeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccC
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVA-EVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLG  482 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G-~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~  482 (675)
                      ..+..+.+...|+.++.+.|..|...+- .|..++|+++.. .++=.+.|.|.+...|...+. +||+.|.
T Consensus        11 ~~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~-pnrymVLikF~~~~~Ad~Fy~~fNGk~Fn   80 (110)
T PF07576_consen   11 RRSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGT-PNRYMVLIKFRDQESADEFYEEFNGKPFN   80 (110)
T ss_pred             CCceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCC-CceEEEEEEECCHHHHHHHHHHhCCCccC
Confidence            3445566666677777777877766654 477888988743 256679999999999999997 9999885

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

>KOG2295 consensus C2H2 Zn-finger protein [General function prediction only]

Probab=92.91  E-value=0.14  Score=56.33  Aligned_cols=70  Identities=21%  Similarity=0.261  Sum_probs=57.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCe
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNR  484 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr  484 (675)
                      -.|+|||+|++++++-.+|..++..+-.+..+-+.... ...+..+++|+|.---.+.-|+. ||++.+.-.
T Consensus       230 ke~sll~rni~Pnis~aeIe~~ck~i~~~lrfals~~~aek~~~r~lwv~fk~~~ni~~a~~aLn~irl~s~  301 (648)
T KOG2295|consen  230 KECSLLVRNILPNISVAEIENLCKGIPGFLRFALSTINAEKNFERRLWVTFKRGTNIKEACWALNGIRLRSN  301 (648)
T ss_pred             HHHHHHHhccCCcccHHHHHHHhccCchheeeeccCchHHHHHHHHhhHhhccccchHHHHHHhhhcccccc
Confidence            35899999999999999999999998777777766554 56678889999998888888886 888777543

>PF05918 API5: Apoptosis inhibitory protein 5 (API5); InterPro: IPR008383 This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organisms

Probab=92.83  E-value=0.031  Score=63.14  Aligned_cols=9  Identities=33%  Similarity=0.010  Sum_probs=3.3

Q ss_pred             cCHHHHHHH
Q 045516          465 ASVEDAHKA  473 (675)
Q Consensus       465 ~~~e~A~~A  473 (675)
                      ...|..-.+
T Consensus       331 s~vEcLL~a  339 (556)
T PF05918_consen  331 SYVECLLYA  339 (556)
T ss_dssp             HHHHHHHHH
T ss_pred             hHhhHHHHH
Confidence            333333333

Apoptosis or programmed cell death is a physiological form of cell death that occurs in embryonic development and organ formation. It is characterised by biochemical and morphological changes such as DNA fragmentation and cell volume shrinkage. API5 is an anti apoptosis gene located in Homo sapiens chromosome 11, whose expression prevents the programmed cell death that occurs upon the deprivation of growth factors [,].; PDB: 3U0R_A 3V6A_A.

>PF10567 Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IPR018885 This conserved domain is found in fungal proteins and appears to be involved in RNA-processing

Probab=92.82  E-value=2.6  Score=43.41  Aligned_cols=166  Identities=16%  Similarity=0.148  Sum_probs=102.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC--------CCCcccEEEEEecCHHHHHHHHH-----hC--Cc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA--------DGRFKGYGHVEFASVEDAHKAIE-----LN--GQ  479 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~--------~g~~kG~afV~F~~~e~A~~Al~-----l~--g~  479 (675)
                      -+|.|.+.||...++--.+...|-+||+|..|+|+.+.        .-.....+.+-|-+.+.+-..+.     |+  .+
T Consensus        14 rTRSLLfeNv~~sidLh~Fl~~fv~~~pIESiYL~~~~~~~~d~~~~d~~~~SilLSFlsr~~CLdFYNnvLQrLsEfK~   93 (309)
T PF10567_consen   14 RTRSLLFENVNNSIDLHSFLTKFVKFGPIESIYLIKSNDKPSDDYNDDKNNQSILLSFLSREICLDFYNNVLQRLSEFKT   93 (309)
T ss_pred             eeHHHHHhhccccccHHHHHHHhhccCceeEEEEecCCCcccccccccccceEEEEeeechHHHHHHHHHHHHHHHHHHH
Confidence            46899999999999999999999999999999999775        22345678899999988765542     21  23


Q ss_pred             ccCCeeEEEEeccccCCCCC--CCCCCCC-----CCcc-CCCCCCCceEEEEecCCCCc-CHHHHHHHHHhhhcccC---
Q 045516          480 MLGNRAIRLDFARERGAYTP--YSGGNES-----NSFQ-KGGRGQAAHTIFIKGFDSSV-GEDQVRASLEEHFGSCG---  547 (675)
Q Consensus       480 ~~~gr~i~V~~a~~~~~~~~--~~~~~~~-----~~~~-~~~~~~~~~~lfV~nLp~~~-te~~i~~~L~~~F~~~G---  547 (675)
                      .|.-..|.|.|..-.-....  .....+.     ..++ ........+.|.|.= ...+ ..+-++..| .+...-+   
T Consensus        94 ~L~S~~L~lsFV~l~y~~~~~~~~~~~~~~~~~~~~L~~~i~~~gATRSl~IeF-~~~~~~~dl~~~kL-~fL~~~~n~R  171 (309)
T PF10567_consen   94 KLKSESLTLSFVSLNYQKKTDPNDEEADFSDYLVASLQYNIINRGATRSLAIEF-KDPVDKDDLIEKKL-PFLKNSNNKR  171 (309)
T ss_pred             hcCCcceeEEEEEEeccccccccccccchhhHHhhhhhheeecCCcceEEEEEe-cCccchhHHHHHhh-hhhccCCCce
Confidence            45556666666542111100  0000000     0111 111122356666653 3444 444444444 3333334   


Q ss_pred             -cEEEEEecccC--CCCCeeeEEEEEeCCHHHHHHHHH
Q 045516          548 -EITRISVPKDY--DTGSVKGIAYLDFTDADSFNKALE  582 (675)
Q Consensus       548 -~I~~v~i~~d~--~tG~~rG~afV~F~~~e~A~~Al~  582 (675)
                       .|+.|.|+...  ....+..||.++|-+...|...+.
T Consensus       172 YVlEsIDlVna~~~~~~Fp~~YaILtFlnIsMAiEV~d  209 (309)
T PF10567_consen  172 YVLESIDLVNADEPSKHFPKNYAILTFLNISMAIEVLD  209 (309)
T ss_pred             EEEEEEEEeccCcccccCCcceEEEeehhHHhHHHHHH
Confidence             35666666542  335578899999999999999887

It binds to poly-adenylated RNA, interacts genetically with mRNA 3'-end processing factors, co-purifies with the nuclear cap-binding protein Cbp20p, and is found in complexes containing other translation factors, such as EIF4G as in P39935 from SWISSPROT and P39936 from SWISSPROT.

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

Probab=92.82  E-value=0.51  Score=37.33  Aligned_cols=52  Identities=19%  Similarity=0.337  Sum_probs=42.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhC---CCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH
Q 045516          417 KTLFVGNLPFSVEQADVQNFFSEV---AEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE  475 (675)
Q Consensus       417 ~tlfV~nLp~~~te~~L~~~F~~~---G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~  475 (675)
                      ..|+|+||. +++.++|+.||..|   .....|..+.|      --|=|.|.+...|.+||.
T Consensus         6 eavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdD------tScNvvf~d~~~A~~AL~   60 (62)
T PF10309_consen    6 EAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDD------TSCNVVFKDEETAARALV   60 (62)
T ss_pred             ceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecC------CcEEEEECCHHHHHHHHH
Confidence            479999995 68999999999998   23556777765      358899999999999995

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

Probab=92.57  E-value=0.082  Score=57.18  Aligned_cols=75  Identities=17%  Similarity=0.162  Sum_probs=60.6

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEec
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDE  597 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~~  597 (675)
                      .+.|-+.-.++.++.-   ..|..+|.+||.|..|.|-..      --.|.|+|.+...|..|...++..|++|.|.|.|
T Consensus       372 hs~l~lek~~~glnt~---a~ln~hfA~fG~i~n~qv~~~------~~~a~vTF~t~aeag~a~~s~~avlnnr~iKl~w  442 (526)
T KOG2135|consen  372 HSPLALEKSPFGLNTI---ADLNPHFAQFGEIENIQVDYS------SLHAVVTFKTRAEAGEAYASHGAVLNNRFIKLFW  442 (526)
T ss_pred             cchhhhhccCCCCchH---hhhhhhhhhcCccccccccCc------hhhheeeeeccccccchhccccceecCceeEEEE
Confidence            3455555566665532   358999999999999988554      3458999999999999999999999999999999


Q ss_pred             cccC
Q 045516          598 AKQR  601 (675)
Q Consensus       598 a~~r  601 (675)
                      -.+.
T Consensus       443 hnps  446 (526)
T KOG2135|consen  443 HNPS  446 (526)
T ss_pred             ecCC
Confidence            8773

>PF07292 NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909 This entry represents a domain of approximately 90 residues that is tandemly repeated within interferon-induced 35 kDa protein (IFP 35) and the homologous N-myc-interactor (Nmi)

Probab=92.42  E-value=0.081  Score=44.92  Aligned_cols=76  Identities=20%  Similarity=0.302  Sum_probs=51.0

Q ss_pred             EEEEecCHHHHHHHHH--hCCcccCCeeEEEEeccccCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHH
Q 045516          460 GHVEFASVEDAHKAIE--LNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRA  537 (675)
Q Consensus       460 afV~F~~~e~A~~Al~--l~g~~~~gr~i~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~  537 (675)
                      |+|+|....-|++.+.  .+...+.+..+.|....-....        ...++ .......++|.|.|||..+.++.+++
T Consensus         1 AlITF~e~~VA~~i~~~~~~~v~l~~~~~~V~v~P~~~~~--------~~k~q-v~~~vs~rtVlvsgip~~l~ee~l~D   71 (88)
T PF07292_consen    1 ALITFEEEGVAQRILKKKKHPVPLEDCCVRVKVSPVTLGH--------LQKFQ-VFSGVSKRTVLVSGIPDVLDEEELRD   71 (88)
T ss_pred             CEEEeCcHHHHHHHHhCCEEEEEECCEEEEEEEEeEecCC--------ceEEE-EEEcccCCEEEEeCCCCCCChhhhee
Confidence            6899999999999997  4566677777777554211100        00111 01123478999999999999999777


Q ss_pred             HHHhhhc
Q 045516          538 SLEEHFG  544 (675)
Q Consensus       538 ~L~~~F~  544 (675)
                      .|.-+|+
T Consensus        72 ~LeIhFq   78 (88)
T PF07292_consen   72 KLEIHFQ   78 (88)
T ss_pred             eEEEEEe
Confidence            6666665

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=92.22  E-value=0.51  Score=43.31  Aligned_cols=72  Identities=17%  Similarity=0.150  Sum_probs=55.7

Q ss_pred             CCceEEEcCCCCCCC----HHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEe
Q 045516          415 GSKTLFVGNLPFSVE----QADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDF  490 (675)
Q Consensus       415 ~~~tlfV~nLp~~~t----e~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~  490 (675)
                      ...||.|+=|..++.    ...|...++.||+|..|.+.-      +-.|.|.|.+...|-+|+..-.....|..+++.|
T Consensus        85 PMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG------rqsavVvF~d~~SAC~Av~Af~s~~pgtm~qCsW  158 (166)
T PF15023_consen   85 PMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG------RQSAVVVFKDITSACKAVSAFQSRAPGTMFQCSW  158 (166)
T ss_pred             CceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC------CceEEEEehhhHHHHHHHHhhcCCCCCceEEeec
Confidence            456899987766653    334566778899999998873      6689999999999999998334477788888877


Q ss_pred             cc
Q 045516          491 AR  492 (675)
Q Consensus       491 a~  492 (675)
                      -.
T Consensus       159 qq  160 (166)
T PF15023_consen  159 QQ  160 (166)
T ss_pred             cc
Confidence            54

>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=92.08  E-value=0.42  Score=46.42  Aligned_cols=79  Identities=13%  Similarity=0.183  Sum_probs=44.6

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcE---EEEEeccc--CCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCC-
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEI---TRISVPKD--YDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGG-  590 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I---~~v~i~~d--~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~G-  590 (675)
                      ...|.|++||+++++++++..|..+   ++..   .++.....  ...-....-|||.|.+.+++..-+. ++|+.|.+ 
T Consensus         7 ~~KvVIR~LPP~LteeeF~~~i~~~---l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~   83 (176)
T PF03467_consen    7 GTKVVIRRLPPNLTEEEFWEQISPW---LPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDS   83 (176)
T ss_dssp             --EEEEEEE-TTS-HHHHCCCCSS-----SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-T
T ss_pred             CceEEEeCCCCCCCHHHHHHHhhhh---cccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECC
Confidence            4689999999999999954422221   3433   33331111  1111234569999999999888887 99988743 


Q ss_pred             ----eeeEEeccc
Q 045516          591 ----YSLVVDEAK  599 (675)
Q Consensus       591 ----r~l~V~~a~  599 (675)
                          ....|.++.
T Consensus        84 kg~~~~~~VE~Ap   96 (176)
T PF03467_consen   84 KGNEYPAVVEFAP   96 (176)
T ss_dssp             TS-EEEEEEEE-S
T ss_pred             CCCCcceeEEEcc
Confidence                234555553

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=91.93  E-value=0.33  Score=47.36  Aligned_cols=60  Identities=23%  Similarity=0.305  Sum_probs=45.2

Q ss_pred             CHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hC--CcccCCeeEEEEeccc
Q 045516          429 EQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LN--GQMLGNRAIRLDFARE  493 (675)
Q Consensus       429 te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~--g~~~~gr~i~V~~a~~  493 (675)
                      ....|+.||..|+.+..+.+++     +-+-..|.|.+.+.|..|.. |+  +..|.|..|+|.|+..
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~-----sFrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~   70 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLK-----SFRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQP   70 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEET-----TTTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----
T ss_pred             hHHHHHHHHHhcCCceEEEEcC-----CCCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccc
Confidence            4578999999999988887774     36778999999999999998 88  9999999999999843

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

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

Probab=90.95  E-value=0.41  Score=52.86  Aligned_cols=73  Identities=15%  Similarity=0.237  Sum_probs=58.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhh--CCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-h--CCcccCCeeEE
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSE--VAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-L--NGQMLGNRAIR  487 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~--~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l--~g~~~~gr~i~  487 (675)
                      +...|.|+|+-||.++-.++|+.||..  |-.+++|.|..+      .-.||+|.+..+|+.|+. |  --..|.|++|.
T Consensus       172 ~~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N------~nWyITfesd~DAQqAykylreevk~fqgKpIm  245 (684)
T KOG2591|consen  172 NHKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHN------DNWYITFESDTDAQQAYKYLREEVKTFQGKPIM  245 (684)
T ss_pred             CcceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeec------CceEEEeecchhHHHHHHHHHHHHHhhcCcchh
Confidence            345688999999999999999999985  888999998764      357999999999999986 3  33567777775


Q ss_pred             EEec
Q 045516          488 LDFA  491 (675)
Q Consensus       488 V~~a  491 (675)
                      .++.
T Consensus       246 ARIK  249 (684)
T KOG2591|consen  246 ARIK  249 (684)
T ss_pred             hhhh
Confidence            5443

>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]

Probab=90.59  E-value=0.63  Score=44.33  Aligned_cols=13  Identities=15%  Similarity=0.158  Sum_probs=5.6

Q ss_pred             EEEecCHHHHHHH
Q 045516          461 HVEFASVEDAHKA  473 (675)
Q Consensus       461 fV~F~~~e~A~~A  473 (675)
                      =|.+++.+.+-+.
T Consensus        82 PIylenk~qIGKV   94 (215)
T KOG3262|consen   82 PIYLENKEQIGKV   94 (215)
T ss_pred             ceeecchhhhcch
Confidence            3444444444333

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=90.28  E-value=0.12  Score=54.06  Aligned_cols=82  Identities=17%  Similarity=0.370  Sum_probs=61.2

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCC--CC-CeeeEEEEEeCCHHHHHHHHH-hCCceeCCeee
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYD--TG-SVKGIAYLDFTDADSFNKALE-MSGTEIGGYSL  593 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~--tG-~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l  593 (675)
                      .+-+||-+|+..+..+.+.+ =..+|++||.|..|.+..+.-  .+ ...--+||+|...++|..||. .+|..+.|+.|
T Consensus        77 knlvyvvgl~~~~ade~~l~-~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~l  155 (327)
T KOG2068|consen   77 KNLVYVVGLPLDLADESVLE-RTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRAL  155 (327)
T ss_pred             hhhhhhhCCCccccchhhhh-CcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhh
Confidence            35678888888876554221 236899999999999988762  11 112238999999999999998 99999999987


Q ss_pred             EEecccc
Q 045516          594 VVDEAKQ  600 (675)
Q Consensus       594 ~V~~a~~  600 (675)
                      .+.+...
T Consensus       156 ka~~gtt  162 (327)
T KOG2068|consen  156 KASLGTT  162 (327)
T ss_pred             HHhhCCC
Confidence            7776643

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=90.18  E-value=0.74  Score=51.73  Aligned_cols=8  Identities=25%  Similarity=0.019  Sum_probs=3.4

Q ss_pred             eeEEEEEe
Q 045516          564 KGIAYLDF  571 (675)
Q Consensus       564 rG~afV~F  571 (675)
                      .|.|++-+
T Consensus       342 ~G~ai~l~  349 (456)
T PRK10590        342 TGEALSLV  349 (456)
T ss_pred             CeeEEEEe
Confidence            34454433

>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=89.82  E-value=0.65  Score=45.34  Aligned_cols=63  Identities=24%  Similarity=0.260  Sum_probs=44.5

Q ss_pred             HHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hC--CceeCCeeeEEeccccC
Q 045516          533 DQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MS--GTEIGGYSLVVDEAKQR  601 (675)
Q Consensus       533 ~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-ln--g~~~~Gr~l~V~~a~~r  601 (675)
                      .++...|+.+|..|+.+..+.+++.+      +-..|.|.+.+.|..|+. |+  +..|.|..|+|.|+..-
T Consensus         6 ~~~~~~l~~l~~~~~~~~~~~~L~sF------rRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~   71 (184)
T PF04847_consen    6 PDNLAELEELFSTYDPPVQFSPLKSF------RRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPT   71 (184)
T ss_dssp             ---HHHHHHHHHTT-SS-EEEEETTT------TEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----S
T ss_pred             hhhHHHHHHHHHhcCCceEEEEcCCC------CEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcccc
Confidence            34556799999999988888777654      347899999999999998 89  99999999999998543

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

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

Probab=89.56  E-value=0.81  Score=49.53  Aligned_cols=67  Identities=21%  Similarity=0.321  Sum_probs=57.8

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhhCC-CeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCC
Q 045516          416 SKTLFVGNLPFSVEQADVQNFFSEVA-EVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGN  483 (675)
Q Consensus       416 ~~tlfV~nLp~~~te~~L~~~F~~~G-~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~g  483 (675)
                      ++.|+|-.+|-.++--+|..|+..|- .|.+|+|+++... ++=..+|.|.+..+|...++ +||..|.-
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~p-nrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMP-NRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCC-ceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            78999999999999999999998754 5999999996422 34568999999999999997 99999964

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

Probab=87.89  E-value=0.56  Score=54.34  Aligned_cols=79  Identities=23%  Similarity=0.312  Sum_probs=66.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCccc--CCeeEEEEeccc
Q 045516          417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQML--GNRAIRLDFARE  493 (675)
Q Consensus       417 ~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~--~gr~i~V~~a~~  493 (675)
                      .+.++.|++-+.+-.-|..+|..||.|.++|+.++     -..|.|.|...+.|..|+. |+|+.+  -|-+.+|.++..
T Consensus       299 p~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~-----~N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~  373 (1007)
T KOG4574|consen  299 PKQSLENNAVNLTSSSLATLCSDYGSVASAWTLRD-----LNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKT  373 (1007)
T ss_pred             chhhhhcccccchHHHHHHHHHhhcchhhheeccc-----ccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccc
Confidence            35566677778888999999999999999999876     5789999999999999998 999876  688899999987


Q ss_pred             cCCCCCC
Q 045516          494 RGAYTPY  500 (675)
Q Consensus       494 ~~~~~~~  500 (675)
                      -..+.+.
T Consensus       374 ~~~~ep~  380 (1007)
T KOG4574|consen  374 LPMYEPP  380 (1007)
T ss_pred             cccccCC
Confidence            6555443

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

Probab=85.68  E-value=4.5  Score=32.04  Aligned_cols=56  Identities=27%  Similarity=0.418  Sum_probs=42.2

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE  582 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~  582 (675)
                      ...|+|+|+. +++.++|..+|..||..-+ ..+|..+-|-       -|-|.|.+...|.+||.
T Consensus         5 peavhirGvd-~lsT~dI~~y~~~y~~~~~-~~~IEWIdDt-------ScNvvf~d~~~A~~AL~   60 (62)
T PF10309_consen    5 PEAVHIRGVD-ELSTDDIKAYFSEYFDEEG-PFRIEWIDDT-------SCNVVFKDEETAARALV   60 (62)
T ss_pred             eceEEEEcCC-CCCHHHHHHHHHHhcccCC-CceEEEecCC-------cEEEEECCHHHHHHHHH
Confidence            4689999986 5777888888888865433 4455555552       48899999999999986

>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=84.41  E-value=4.1  Score=33.38  Aligned_cols=58  Identities=21%  Similarity=0.330  Sum_probs=36.1

Q ss_pred             CCCCHHHHHHHhhhCCC-----eEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          426 FSVEQADVQNFFSEVAE-----VVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       426 ~~~te~~L~~~F~~~G~-----I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ..++..+|..+|...+.     |-.|.|.       ..|+||+.... .+..+|. |++..+.|+.|.|..+
T Consensus        11 dg~~~~~iv~~i~~~~gi~~~~IG~I~I~-------~~~S~vev~~~-~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   11 DGLTPRDIVGAICNEAGIPGRDIGRIDIF-------DNFSFVEVPEE-VAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE--------SS-EEEEE-TT--HHHHHHHHTT--SSS----EEE-
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEe-------eeEEEEEECHH-HHHHHHHHhcCCCCCCeeEEEEEC
Confidence            45788899999887653     6788887       46999998766 6778887 9999999999999864

; PDB: 2G0C_A 3MOJ_B.

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

Probab=84.34  E-value=0.56  Score=50.11  Aligned_cols=75  Identities=20%  Similarity=0.297  Sum_probs=52.9

Q ss_pred             eEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCc-eeCCeeeEEe
Q 045516          519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGT-EIGGYSLVVD  596 (675)
Q Consensus       519 ~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~-~~~Gr~l~V~  596 (675)
                      +.||++||...++..++...|.+.-..+    .-.++      .-.||+||.+.+...+.+|++ ++|. .+.|.++.|.
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~----~g~fl------~k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~   71 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPG----SGQFL------VKSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVE   71 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCC----Cccee------eecceeeccCCchhhhhhhHHhhchhhhhcCceeecc
Confidence            4689999999999999544433331110    00111      126899999999999999999 7774 5889999988


Q ss_pred             ccccCCC
Q 045516          597 EAKQRGD  603 (675)
Q Consensus       597 ~a~~r~~  603 (675)
                      ..-+...
T Consensus        72 ~sv~kkq   78 (584)
T KOG2193|consen   72 HSVPKKQ   78 (584)
T ss_pred             chhhHHH
Confidence            7765443

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

Probab=84.18  E-value=0.73  Score=52.17  Aligned_cols=69  Identities=13%  Similarity=0.198  Sum_probs=56.5

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      ++..++||+|+-+.+...-    +..+...||.|..+....         |||+.|..+....+|+. ++-..++|..|.
T Consensus        38 ~~~~~vfv~~~~~~~s~~~----~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~  104 (668)
T KOG2253|consen   38 PPRDTVFVGNISYLVSQEF----WKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELNIDDQKLI  104 (668)
T ss_pred             CCCceeEecchhhhhhHHH----HHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhcccCCCcchhh
Confidence            4478999999999888875    667777889887775543         89999999999999998 888888887776


Q ss_pred             Eec
Q 045516          595 VDE  597 (675)
Q Consensus       595 V~~  597 (675)
                      +..
T Consensus       105 ~~~  107 (668)
T KOG2253|consen  105 ENV  107 (668)
T ss_pred             ccc
Confidence            654

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

Probab=82.94  E-value=2.7  Score=46.72  Aligned_cols=65  Identities=9%  Similarity=0.262  Sum_probs=47.8

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhc--ccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCC--ceeCCee
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFG--SCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSG--TEIGGYS  592 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~--~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng--~~~~Gr~  592 (675)
                      .++|+|+-|+.++..++    ++-||.  .|-.++.|.+..+.       -=||+|.+..+|..|+. |..  ..|.|..
T Consensus       175 RcIvilREIpettp~e~----Vk~lf~~encPk~iscefa~N~-------nWyITfesd~DAQqAykylreevk~fqgKp  243 (684)
T KOG2591|consen  175 RCIVILREIPETTPIEV----VKALFKGENCPKVISCEFAHND-------NWYITFESDTDAQQAYKYLREEVKTFQGKP  243 (684)
T ss_pred             eeEEEEeecCCCChHHH----HHHHhccCCCCCceeeeeeecC-------ceEEEeecchhHHHHHHHHHHHHHhhcCcc
Confidence            48889999999999988    455664  47788888887653       25999999999999975 322  3455554


Q ss_pred             e
Q 045516          593 L  593 (675)
Q Consensus       593 l  593 (675)
                      |
T Consensus       244 I  244 (684)
T KOG2591|consen  244 I  244 (684)
T ss_pred             h
Confidence            4

>PHA00370 III attachment protein

Probab=82.89  E-value=5.9  Score=39.89  Aligned_cols=7  Identities=14%  Similarity=-0.112  Sum_probs=2.5

Q ss_pred             CeeeEEe
Q 045516          590 GYSLVVD  596 (675)
Q Consensus       590 Gr~l~V~  596 (675)
                      +..+-|.
T Consensus        72 ~~W~P~g   78 (297)
T PHA00370         72 GSWKPTG   78 (297)
T ss_pred             cceeecc
Confidence            3333333

>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=82.14  E-value=4.5  Score=32.48  Aligned_cols=54  Identities=15%  Similarity=0.252  Sum_probs=42.5

Q ss_pred             CCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEE
Q 045516          427 SVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRL  488 (675)
Q Consensus       427 ~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V  488 (675)
                      .++-++|+..|..|+-.   +|+.+.    .| -||.|.+..+|++++. .|+..|.+..|.+
T Consensus        11 ~~~v~d~K~~Lr~y~~~---~I~~d~----tG-fYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRWD---RIRDDR----TG-FYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCcc---eEEecC----CE-EEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            46788999999999632   333444    33 4899999999999998 8999998888765

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

>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=81.58  E-value=7.9  Score=34.48  Aligned_cols=67  Identities=13%  Similarity=0.124  Sum_probs=45.7

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhccc-CcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCC
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSC-GEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGG  590 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~-G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~G  590 (675)
                      ...+.+...|+-++-+.|    ..+...+ ..|..++|+++.  ...+-+++|.|.+...|..-.. +||..|+.
T Consensus        13 ~~~~~l~vp~~~~~~d~l----~~f~~~~~~~i~~~riird~--~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   13 STLCCLAVPPYMTPSDFL----LFFGAPFREDIEHIRIIRDG--TPNRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             ceEEEEEeCcccccHHHH----HHhhhcccccEEEEEEeeCC--CCceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            344455555555555553    2222222 467888998873  2357789999999999999987 99999875

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

>PF14111 DUF4283: Domain of unknown function (DUF4283)

Probab=80.99  E-value=1.3  Score=41.54  Aligned_cols=121  Identities=11%  Similarity=0.014  Sum_probs=75.4

Q ss_pred             eEEEcCC-C-CCCCHHHHHHHhhh-CCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEecccc
Q 045516          418 TLFVGNL-P-FSVEQADVQNFFSE-VAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARER  494 (675)
Q Consensus       418 tlfV~nL-p-~~~te~~L~~~F~~-~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a~~~  494 (675)
                      ...|+.+ . ..++-..|...+.. ++....+.+..-    ..++..+.|.+.+++.+++......|.|..|.+..-.+.
T Consensus        17 ~~lVg~~l~~~~~~~~~l~~~l~~~W~~~~~~~i~~l----~~~~fl~~F~~~~d~~~vl~~~p~~~~~~~~~l~~W~~~   92 (153)
T PF14111_consen   17 LCLVGRVLSPKPISLSALEQELAKIWKLKGGVKIRDL----GDNLFLFQFESEEDRQRVLKGGPWNFNGHFLILQRWSPD   92 (153)
T ss_pred             eEEEEEECCCCCCCHHHHHHHHHHHhCCCCcEEEEEe----CCCeEEEEEEeccceeEEEecccccccccchhhhhhccc
Confidence            3444444 2 34566667666654 232223333221    268999999999999999998888888888887665432


Q ss_pred             CCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEeccc
Q 045516          495 GAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKD  557 (675)
Q Consensus       495 ~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d  557 (675)
                      .......            ......-|.|.|||..+-..+   .|..+.+.+|.+..+.....
T Consensus        93 ~~~~~~~------------~~~~~vWVri~glP~~~~~~~---~~~~i~~~iG~~i~vD~~t~  140 (153)
T PF14111_consen   93 FNPSEVK------------FEHIPVWVRIYGLPLHLWSEE---ILKAIGSKIGEPIEVDENTL  140 (153)
T ss_pred             ccccccc------------eeccchhhhhccCCHHHhhhH---HHHHHHHhcCCeEEEEcCCC
Confidence            1111000            011135577889997755443   36777788899999877654

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	675
2yh0_A	198	Solution Structure Of The Closed Conformation Of Hu		2e-10
2dng_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		2e-10
3vaf_A	174	Structure Of U2af65 Variant With Bru3 Dna Length =		5e-10
2g4b_A	172	Structure Of U2af65 Variant With Polyuridine Tract		6e-10
2krr_A	180	Solution Structure Of The Rbd1,2 Domains From Human		3e-09
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		2e-08
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		2e-07
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		3e-07
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		3e-07
1fje_B	175	Solution Structure Of Nucleolin Rbd12 In Complex Wi		3e-07
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		3e-07
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		5e-07
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		6e-07
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		6e-07
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		7e-07
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		7e-07
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		7e-07
2fc9_A	101	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		1e-06
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		1e-06
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		5e-06
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		7e-06
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		7e-06
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		8e-06
2jwn_A	124	Solution Nmr Structure Of The Protease-Resistent Do		1e-05
4f25_A	115	Crystal Structure Of The Second Rrm Domain Of Human		1e-05
1wi8_A	104	Solution Structure Of The Rna Binding Domain Of Euk		2e-05
2cq4_A	114	Solution Structure Of Rna Binding Domain In Rna Bin		2e-05
2x1a_A	97	Structure Of Rna15 Rrm With Rna Bound (G) Length =		2e-05
1x5t_A	96	Solution Structure Of The Second Rrm Domain In Spli		3e-05
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		3e-05
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		6e-05
2x1f_A	96	Structure Of Rna15 Rrm With Bound Rna (Gu) Length =		6e-05
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		7e-05
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		8e-05
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		2e-04
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		9e-05
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		9e-05
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		4e-04
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		9e-05
2km8_B	84	Interdomain Rrm Packing Contributes To Rna Recognit		1e-04
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		1e-04
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		1e-04
2hgn_A	139	Nmr Structure Of The Third Qrrm Domain Of Human Hnr		2e-04
2j76_E	100	Solution Structure And Rna Interactions Of The Rna		2e-04
1hd0_A	75	Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D		2e-04
2j0s_D	89	The Crystal Structure Of The Exon Junction Complex		2e-04
1p27_B	106	Crystal Structure Of The Human Y14MAGOH COMPLEX Len		3e-04
2xb2_D	90	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		3e-04
3md1_A	83	Crystal Structure Of The Second Rrm Domain Of Yeast		4e-04
2hyi_B	91	Structure Of The Human Exon Junction Complex With A		4e-04
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		4e-04
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		4e-04
2xsf_A	89	Crystal Structure Of The Rrm Domain Of Mouse Delete		4e-04
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		4e-04
2k8g_A	95	Solution Structure Of Rrm2 Domain Of Pabp1 Length =		4e-04
2xs5_A	87	Crystal Structure Of The Rrm Domain Of Mouse Delete		5e-04
2cph_A	107	Solution Structure Of The C-Terminal Rna Recognitio		5e-04
1x5o_A	114	Solution Structure Of Rrm Domain In Rna Binding Mot		6e-04
1h6k_Z	98	Nuclear Cap Binding Complex Length = 98		6e-04
3ex7_B	126	The Crystal Structure Of Ejc In Its Transition Stat		6e-04
2xs2_A	102	Crystal Structure Of The Rrm Domain Of Mouse Delete		6e-04
2dh9_A	89	Solution Structure Of The C-Terminal Rna Binding Do		7e-04
2do0_A	114	Solution Structure Of The Rna Binding Domain Of Het		8e-04
3b4d_A	96	Crystal Structure Of Human Pabpn1 Rrm Length = 96		9e-04
1fjc_A	96	Solution Structure Of Nucleolin Rbd2 Length = 96		9e-04

>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human U2af65 Tandem Rrm1 And Rrm2 Domains Length = 198

Iteration: 1
 Score = 64.7 bits (156), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 50/200 (25%), Positives = 99/200 (49%), Gaps = 29/200 (14%)
Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAE-----------VVDVRLSSDADGRFKGYGHVEF 464
           ++ L+VGN+PF + +  + +FF+               V+ V+++ D     K +  +EF
Sbjct: 4   ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-----KNFAFLEF 58
Query: 465 ASVEDAHKAIELNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQ-----AAH 519
            SV++  +A+  +G +   +++++   R    Y P  G +E+ S    G        +AH
Sbjct: 59  RSVDETTQAMAFDGIIFQGQSLKI---RRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAH 115
Query: 520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNK 579
            +FI G  + + +DQV+    E   S G +   ++ KD  TG  KG A+ ++ D +  ++
Sbjct: 116 KLFIGGLPNYLNDDQVK----ELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQ 171
Query: 580 ALE-MSGTEIGGYSLVVDEA 598
           A+  ++G ++G   L+V  A
Sbjct: 172 AIAGLNGMQLGDKKLLVQRA 191

>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 4h Length = 103

Iteration: 1
 Score = 64.7 bits (156), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 31/78 (39%), Positives = 50/78 (64%), Gaps = 2/78 (2%)
Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAIEL 476
           T +VGNLPF+  Q D+   F +++ +  VRL  D D  +FKG+ +VEF  V+   +A+  
Sbjct: 17  TAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTY 75
Query: 477 NGQMLGNRAIRLDFARER 494
           +G +LG+R++R+D A  R
Sbjct: 76  DGALLGDRSLRVDIAEGR 93

>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna Length = 174

Iteration: 1
 Score = 63.2 bits (152), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 48/197 (24%), Positives = 94/197 (47%), Gaps = 39/197 (19%)
Query: 414 GGSKTLFVGNLPFSVEQADVQNFFSEVAE-----------VVDVRLSSDADGRFKGYGHV 462
           G ++ L+VGN+PF + +  + +FF+               V+ V+++ D     K +  +
Sbjct: 4   GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-----KNFAFL 58
Query: 463 EFASVEDAHKAIELNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIF 522
           EF SV++  +A+  +G +   +++++   R    Y P  G               AH +F
Sbjct: 59  EFRSVDETTQAMAFDGIIFQGQSLKI---RRPHDYQPLPG---------------AHKLF 100
Query: 523 IKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE 582
           I G  + + +DQV+    E   S G +   ++ KD  TG  KG A+ ++ D +  ++A+ 
Sbjct: 101 IGGLPNYLNDDQVK----ELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 156
Query: 583 -MSGTEIGGYSLVVDEA 598
            ++G ++G   L+V  A
Sbjct: 157 GLNGMQLGDKKLLVQRA 173

>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract Length = 172

Iteration: 1
 Score = 62.8 bits (151), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 48/197 (24%), Positives = 94/197 (47%), Gaps = 39/197 (19%)
Query: 414 GGSKTLFVGNLPFSVEQADVQNFFSEVAE-----------VVDVRLSSDADGRFKGYGHV 462
           G ++ L+VGN+PF + +  + +FF+               V+ V+++ D     K +  +
Sbjct: 2   GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-----KNFAFL 56
Query: 463 EFASVEDAHKAIELNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIF 522
           EF SV++  +A+  +G +   +++++   R    Y P  G               AH +F
Sbjct: 57  EFRSVDETTQAMAFDGIIFQGQSLKI---RRPHDYQPLPG---------------AHKLF 98
Query: 523 IKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE 582
           I G  + + +DQV+    E   S G +   ++ KD  TG  KG A+ ++ D +  ++A+ 
Sbjct: 99  IGGLPNYLNDDQVK----ELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 154
Query: 583 -MSGTEIGGYSLVVDEA 598
            ++G ++G   L+V  A
Sbjct: 155 GLNGMQLGDKKLLVQRA 171

>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human Nucleoli Length = 180

Iteration: 1
 Score = 60.5 bits (145), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 60/181 (33%), Positives = 88/181 (48%), Gaps = 36/181 (19%)
Query: 419 LFVGNLPFSVEQADVQNFFSEV-----AEVVDVRLSSDADGRFKGYGHVEFASVEDAHKA 473
           LFVGNL F+    +++   S+V       VVDVR+     G  + +G+V+F S ED  KA
Sbjct: 10  LFVGNLNFNKSAPELKTGISDVFAKNDLAVVDVRI-----GMTRKFGYVDFESAEDLEKA 64
Query: 474 IELNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGED 533
           +EL G  +    I+L+  +          G +S       + + A T+  K     V +D
Sbjct: 65  LELTGLKVFGNEIKLEKPK----------GKDSK------KERDARTLLAKNLPYKVTQD 108
Query: 534 QVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDF-TDADSFNKALEMSGTEIGGYS 592
           +    L+E F    EI  +S  KD   G  KGIAY++F T+AD+     E  GTEI G S
Sbjct: 109 E----LKEVFEDAAEIRLVS--KD---GKSKGIAYIEFKTEADAEKTFEEKQGTEIDGRS 159
Query: 593 L 593
           +
Sbjct: 160 I 160

>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage Stimulation Factor 64 Kda Subunit Length = 104

Iteration: 1
 Score = 57.4 bits (137), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 30/75 (40%), Positives = 46/75 (61%), Gaps = 2/75 (2%)
Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAIE 475
           +++FVGN+P+   +  +++ FSEV  VV  RL  D + G+ KGYG  E+   E A  A+ 
Sbjct: 9   RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68
Query: 476 -LNGQMLGNRAIRLD 489
            LNG+    RA+R+D
Sbjct: 69  NLNGREFSGRALRVD 83

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 54.7 bits (130), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 35/94 (37%), Positives = 53/94 (56%), Gaps = 4/94 (4%)
Query: 413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAH 471
           S GS  L+VG+L F++ +  ++  F    ++ ++ L  D+D GR KGYG + F+  E A 
Sbjct: 2   SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECAR 61
Query: 472 KAIE-LNGQMLGNRAIRLDFARER--GAYTPYSG 502
           +A+E LNG  L  R +R+    ER  G   P SG
Sbjct: 62  RALEQLNGFELAGRPMRVGHVTERLDGGSGPSSG 95

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

Iteration: 1
 Score = 53.9 bits (128), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 44/159 (27%), Positives = 72/159 (45%), Gaps = 24/159 (15%)
Query: 415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKA 473
           G   L V  LP ++ Q ++++ FS + EV   +L  D   G   GYG V + + +DA +A
Sbjct: 1   GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 474 IE-LNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGE 532
           I  LNG  L ++ I++ +AR             S+   K         ++I G   ++ +
Sbjct: 61  INTLNGLRLQSKTIKVSYAR------------PSSEVIKDA------NLYISGLPRTMTQ 102
Query: 533 DQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDF 571
             V    E+ F   G I    V  D  TG  +G+A++ F
Sbjct: 103 KDV----EDMFSRFGRIINSRVLVDQTTGLSRGVAFIRF 137

>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 = 53.9 bits (128), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 29/78 (37%), Positives = 44/78 (56%), Gaps = 2/78 (2%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAI-EL 476
           +FVG+L   +   D++  F+    + D R+  D A G+ KGYG V F +  DA  AI ++
Sbjct: 18  VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 477 NGQMLGNRAIRLDFARER 494
            GQ LG R IR ++A  +
Sbjct: 78  GGQWLGGRQIRTNWATRK 95

>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre Rna Length = 175

Iteration: 1
 Score = 53.5 bits (127), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 57/193 (29%), Positives = 89/193 (46%), Gaps = 44/193 (22%)
Query: 407 TPFTPQSGGSKTLFVGNLPFSVEQADVQNFFSEV-----AEVVDVRLSSDADGRFKGYGH 461
           TPF         LF+GNL  +   A+++   SE+       VVDVR  ++     + +G+
Sbjct: 12  TPFN--------LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTN-----RKFGY 58
Query: 462 VEFASVEDAHKAIELNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTI 521
           V+F S ED  KA+EL G  +    I+L+  + R +                 + +AA T+
Sbjct: 59  VDFESAEDLEKALELTGLKVFGNEIKLEKPKGRDS----------------KKVRAARTL 102
Query: 522 FIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDF-TDADSFNKA 580
             K    ++ ED+    L+E F    EI  +S       G  KGIAY++F ++AD+    
Sbjct: 103 LAKNLSFNITEDE----LKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNL 153
Query: 581 LEMSGTEIGGYSL 593
            E  G EI G S+
Sbjct: 154 EEKQGAEIDGRSV 166

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

Iteration: 1
 Score = 53.5 bits (127), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 44/159 (27%), Positives = 72/159 (45%), Gaps = 24/159 (15%)
Query: 415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKA 473
           G   L V  LP ++ Q ++++ FS + EV   +L  D   G   GYG V + + +DA +A
Sbjct: 1   GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 474 IE-LNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGE 532
           I  LNG  L ++ I++ +AR             S+   K         ++I G   ++ +
Sbjct: 61  INTLNGLRLQSKTIKVSYAR------------PSSEVIKDA------NLYISGLPRTMTQ 102
Query: 533 DQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDF 571
             V    E+ F   G I    V  D  TG  +G+A++ F
Sbjct: 103 KDV----EDMFSRFGRIINSRVLVDQTTGLSRGVAFIRF 137

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 53.1 bits (126), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 29/78 (37%), Positives = 45/78 (57%), Gaps = 2/78 (2%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAI-EL 476
           +FVG+L   +   D+++ F+   ++ D R+  D A G+ KGYG V F +  DA  AI  +
Sbjct: 18  VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 477 NGQMLGNRAIRLDFARER 494
            GQ LG R IR ++A  +
Sbjct: 78  GGQWLGGRQIRTNWATRK 95

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 52.8 bits (125), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 43/183 (23%), Positives = 79/183 (43%), Gaps = 17/183 (9%)
Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADG-RFKGYGHVEFASVEDAHKAIE 475
           + LF+G L F      +++ F +   + D  +  D +  R +G+G V +A+VE+   A+ 
Sbjct: 12  RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 71
Query: 476 LNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQV 535
                +  R +            P    +  +S Q+ G       IF+ G    + ED  
Sbjct: 72  ARPHKVDGRVVE-----------PKRAVSREDS-QRPGAHLTVKKIFVGG----IKEDTE 115
Query: 536 RASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVV 595
              L ++F   G+I  I +  D  +G  +G A++ F D DS +K +      + G++  V
Sbjct: 116 EHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEV 175
Query: 596 DEA 598
            +A
Sbjct: 176 RKA 178

>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi) G); A Human Telomeric Repeat Containing 6-Methyl-8-(2- Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi) Length = 195

Iteration: 1
 Score = 52.8 bits (125), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 43/183 (23%), Positives = 79/183 (43%), Gaps = 17/183 (9%)
Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADG-RFKGYGHVEFASVEDAHKAIE 475
           + LF+G L F      +++ F +   + D  +  D +  R +G+G V +A+VE+   A+ 
Sbjct: 13  RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 72
Query: 476 LNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQV 535
                +  R +            P    +  +S Q+ G       IF+ G    + ED  
Sbjct: 73  ARPHKVDGRVVE-----------PKRAVSREDS-QRPGAHLTVKKIFVGG----IKEDTE 116
Query: 536 RASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVV 595
              L ++F   G+I  I +  D  +G  +G A++ F D DS +K +      + G++  V
Sbjct: 117 EHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEV 176
Query: 596 DEA 598
            +A
Sbjct: 177 RKA 179

>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1 (up1) Using Segmental Isotope Labeling Length = 197

Iteration: 1
 Score = 52.8 bits (125), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 43/183 (23%), Positives = 78/183 (42%), Gaps = 17/183 (9%)
Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADG-RFKGYGHVEFASVEDAHKAIE 475
           + LF+G L F      +++ F +   + D  +  D +  R +G+G V +A+VE+   A+ 
Sbjct: 15  RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 74
Query: 476 LNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQV 535
                +  R +            P    +  +S + G     AH    K F   + ED  
Sbjct: 75  ARPHKVDGRVVE-----------PKRAVSREDSQRPG-----AHLTVKKIFVGGIKEDTE 118
Query: 536 RASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVV 595
              L ++F   G+I  I +  D  +G  +G A++ F D DS +K +      + G++  V
Sbjct: 119 EHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEV 178
Query: 596 DEA 598
            +A
Sbjct: 179 RKA 181

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 52.8 bits (125), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 43/183 (23%), Positives = 78/183 (42%), Gaps = 17/183 (9%)
Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADG-RFKGYGHVEFASVEDAHKAIE 475
           + LF+G L F      +++ F +   + D  +  D +  R +G+G V +A+VE+   A+ 
Sbjct: 14  RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 476 LNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQV 535
                +  R +            P    +  +S + G     AH    K F   + ED  
Sbjct: 74  ARPHKVDGRVVE-----------PKRAVSREDSQRPG-----AHLTVKKIFVGGIKEDTE 117
Query: 536 RASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVV 595
              L ++F   G+I  I +  D  +G  +G A++ F D DS +K +      + G++  V
Sbjct: 118 EHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEV 177
Query: 596 DEA 598
            +A
Sbjct: 178 RKA 180

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 52.4 bits (124), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 43/183 (23%), Positives = 79/183 (43%), Gaps = 17/183 (9%)
Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADG-RFKGYGHVEFASVEDAHKAIE 475
           + LF+G L F      +++ F +   + D  +  D +  R +G+G V +A+VE+   A+ 
Sbjct: 14  RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 476 LNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQV 535
                +  R +            P    +  +S Q+ G       IF+ G    + ED  
Sbjct: 74  ARPHKVDGRVVE-----------PKRAVSREDS-QRPGAHLTVKKIFVGG----IKEDTE 117
Query: 536 RASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVV 595
              L ++F   G+I  I +  D  +G  +G A++ F D DS +K +      + G++  V
Sbjct: 118 EHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEV 177
Query: 596 DEA 598
            +A
Sbjct: 178 RKA 180

>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 101

Iteration: 1
 Score = 52.0 bits (123), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 32/88 (36%), Positives = 50/88 (56%), Gaps = 6/88 (6%)
Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE 475
           SKTL + NL +S  +  +Q  F +      +++  + +G+ KGY  +EFAS EDA +A+ 
Sbjct: 15  SKTLVLSNLSYSATEETLQEVFEKA---TFIKVPQNQNGKSKGYAFIEFASFEDAKEALN 71
Query: 476 -LNGQMLGNRAIRLDFARERGAYTPYSG 502
             N + +  RAIRL+    RG  +P SG
Sbjct: 72  SCNKREIEGRAIRLELQGPRG--SPNSG 97

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 52.0 bits (123), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 43/183 (23%), Positives = 79/183 (43%), Gaps = 17/183 (9%)
Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADG-RFKGYGHVEFASVEDAHKAIE 475
           + LF+G L F      +++ F +   + D  +  D +  R +G+G V +A+VE+   A+ 
Sbjct: 7   RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66
Query: 476 LNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQV 535
                +  R +            P    +  +S Q+ G       IF+ G    + ED  
Sbjct: 67  ARPHKVDGRVVE-----------PKRAVSREDS-QRPGAHLTVKKIFVGG----IKEDTE 110
Query: 536 RASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVV 595
              L ++F   G+I  I +  D  +G  +G A++ F D DS +K +      + G++  V
Sbjct: 111 EHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEV 170
Query: 596 DEA 598
            +A
Sbjct: 171 RKA 173

>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition Motif (Rrm1) Of The Au-Rich Element (Are) Binding Protein Hur At 2.0 Angstrom Resolution Length = 84

Iteration: 1
 Score = 50.1 bits (118), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 28/80 (35%), Positives = 45/80 (56%), Gaps = 2/80 (2%)
Query: 415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKA 473
           G   L V  LP ++ Q ++++ FS + EV   +L  D   G   GYG V + + +DA +A
Sbjct: 3   GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 62
Query: 474 IE-LNGQMLGNRAIRLDFAR 492
           I  LNG  L ++ I++ +AR
Sbjct: 63  INTLNGLRLQSKTIKVSYAR 82

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 49.3 bits (116), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 40/186 (21%), Positives = 89/186 (47%), Gaps = 22/186 (11%)
Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE- 475
           + L+VGNL  ++ +  ++ +F     + ++++  D + +   Y  VE+    DA+ A++ 
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQT 60
Query: 476 LNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQV 535
           LNG+ + N  +++++A +           +S+S            +F+   + +V ++ +
Sbjct: 61  LNGKQIENNIVKINWAFQ---------SQQSSS-------DDTFNLFVGDLNVNVDDETL 104
Query: 536 RASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV 594
           R + ++ F S        V  D  TGS +G  ++ FT  D    A++ M G ++ G  L 
Sbjct: 105 RNAFKD-FPS---YLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLR 160
Query: 595 VDEAKQ 600
           ++ A +
Sbjct: 161 INWAAK 166

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 49.3 bits (116), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 42/159 (26%), Positives = 72/159 (45%), Gaps = 25/159 (15%)
Query: 416 SKT-LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKA 473
           SKT L V  LP ++ Q + ++ F  + E+   +L  D   G+  GYG V +   +DA KA
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 474 IE-LNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGE 532
           I  LNG  L  + I++ +AR   A        ++N             +++ G   ++ +
Sbjct: 61  INTLNGLRLQTKTIKVSYARPSSASI-----RDAN-------------LYVSGLPKTMTQ 102
Query: 533 DQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDF 571
            +    LE+ F   G I    +  D  TG  +G+ ++ F
Sbjct: 103 KE----LEQLFSQYGRIITSRILVDQVTGVSRGVGFIRF 137

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 49.3 bits (116), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 29/84 (34%), Positives = 47/84 (55%), Gaps = 2/84 (2%)
Query: 413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAH 471
           S G   L+VG+L F++ +  ++  F     +  ++L  D++ GR KGYG + F+  E A 
Sbjct: 23  SAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAK 82
Query: 472 KAIE-LNGQMLGNRAIRLDFARER 494
           KA+E LNG  L  R +++    ER
Sbjct: 83  KALEQLNGFELAGRPMKVGHVTER 106

>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of Xenopus Laevis Epabp2 Length = 124

Iteration: 1
 Score = 48.5 bits (114), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 23/57 (40%), Positives = 34/57 (59%)
Query: 539 LEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVV 595
           LE HF SCG I RI++  D  +G  KG AY++F + +S + A+ M  T   G ++ V
Sbjct: 53  LEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMDETVFRGRTIKV 109

>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1 At Ph 6.0 Length = 115

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 34/116 (29%), Positives = 56/116 (48%), Gaps = 18/116 (15%)
Query: 415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI 474
           GS  +F+ NL  S++   + + FS    ++  ++  D +G  KGYG V F + E A +AI
Sbjct: 4   GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS-KGYGFVHFETQEAAERAI 62
Query: 475 E-LNGQMLGNRAI---RLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGF 526
           E +NG +L +R +   R    +ER A             + G R +    ++IK F
Sbjct: 63  EKMNGMLLNDRKVFVGRFKSRKEREA-------------ELGARAKEFTNVYIKNF 105

>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of Eukaryotic Initiation Factor 4b Length = 104

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 28/76 (36%), Positives = 44/76 (57%), Gaps = 3/76 (3%)
Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADG--RFKGYGHVEFASVEDAHKAIE 475
           T F+GNLP+ V +  ++ FF  +  +  VRL  +     R KG+G+ EF  ++    A+ 
Sbjct: 17  TAFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 75
Query: 476 LNGQMLGNRAIRLDFA 491
           LN + LGN+ IR+D A
Sbjct: 76  LNEESLGNKRIRVDVA 91

>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding Motif Protein 23 Length = 114

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 1/74 (1%)
Query: 409 FTPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADG-RFKGYGHVEFASV 467
            +P+   ++T+F   L   +   D+++FFS V +V DVR+ SD +  R KG  +VEF  +
Sbjct: 18  LSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEI 77
Query: 468 EDAHKAIELNGQML 481
           +    AI L GQ L
Sbjct: 78  QSVPLAIGLTGQRL 91

>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G) Length = 97

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 23/80 (28%), Positives = 47/80 (58%), Gaps = 2/80 (2%)
Query: 414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHK 472
           G S+ +++G++P+   +  + +  S V  V+++++  D   GR KGY  +EF  +E +  
Sbjct: 1   GPSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSAS 60
Query: 473 AIE-LNGQMLGNRAIRLDFA 491
           A+  LNG  LG+R ++  ++
Sbjct: 61  AVRNLNGYQLGSRFLKCGYS 80

>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing Factor 3b Length = 96

Iteration: 1
 Score = 47.4 bits (111), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 29/85 (34%), Positives = 48/85 (56%), Gaps = 3/85 (3%)
Query: 413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDV-RLSSDAD-GRFKGYGHVEFASVEDA 470
           S GS  +F+GNL   +++  + + FS    ++   ++  D D G  KGY  + FAS + +
Sbjct: 2   SSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDAS 61
Query: 471 HKAIE-LNGQMLGNRAIRLDFARER 494
             AIE +NGQ L NR I + +A ++
Sbjct: 62  DAAIEAMNGQYLCNRPITVSYAFKK 86

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 40/159 (25%), Positives = 72/159 (45%), Gaps = 25/159 (15%)
Query: 416 SKT-LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKA 473
           SKT L V  LP ++ Q + ++ F  + ++   +L  D   G+  GYG V ++   DA KA
Sbjct: 3   SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 474 IE-LNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGE 532
           I  LNG  L  + I++ +AR   A        ++N             +++ G   ++ +
Sbjct: 63  INTLNGLKLQTKTIKVSYARPSSASI-----RDAN-------------LYVSGLPKTMSQ 104
Query: 533 DQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDF 571
            +    +E+ F   G I    +  D  TG  +G+ ++ F
Sbjct: 105 KE----MEQLFSQYGRIITSRILLDQATGVSRGVGFIRF 139

>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From Homo Sapiens At 1.90 A Resolution Length = 99

Iteration: 1
 Score = 46.2 bits (108), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 27/76 (35%), Positives = 43/76 (56%), Gaps = 2/76 (2%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAIE-L 476
           L V  LP +  Q ++++ FS + EV   +L  D   G   GYG V + + +DA +AI  L
Sbjct: 22  LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 81
Query: 477 NGQMLGNRAIRLDFAR 492
           NG  L ++ I++ +AR
Sbjct: 82  NGLRLQSKTIKVSYAR 97

>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu) Length = 96

Iteration: 1
 Score = 46.2 bits (108), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 22/78 (28%), Positives = 46/78 (58%), Gaps = 2/78 (2%)
Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAI 474
           S+ +++G++P+   +  + +  S V  V+++++  D   GR KGY  +EF  +E +  A+
Sbjct: 2   SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61
Query: 475 E-LNGQMLGNRAIRLDFA 491
             LNG  LG+R ++  ++
Sbjct: 62  RNLNGYQLGSRFLKCGYS 79

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 45.8 bits (107), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 42/183 (22%), Positives = 86/183 (46%), Gaps = 14/183 (7%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-L 476
           ++VG++ + + +  ++  F+    +  + +S D+   + KG+  VE+   E A  A+E +
Sbjct: 16  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 477 NGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVR 536
           N  MLG R I++      G   P          Q     +A + I++      + +D ++
Sbjct: 76  NSVMLGGRNIKVGRPSNIGQAQPIID-------QLAEEARAFNRIYVASVHQDLSDDDIK 128
Query: 537 ASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKAL-EMSGTEIGGYSLVV 595
           +  E    + G+I   ++ +D  TG  KG  ++++  A S   A+  M+  ++GG  L V
Sbjct: 129 SVFE----AFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 184
Query: 596 DEA 598
            +A
Sbjct: 185 GKA 187

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 45.8 bits (107), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 24/73 (32%), Positives = 41/73 (56%), Gaps = 2/73 (2%)
Query: 415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI 474
           G   +F+ NL  S++   + + FS    ++  ++  D +G  KGYG V F + E A +AI
Sbjct: 102 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS-KGYGFVHFETQEAAERAI 160
Query: 475 E-LNGQMLGNRAI 486
           E +NG +L +R +
Sbjct: 161 EKMNGMLLNDRKV 173

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 45/174 (25%), Positives = 81/174 (46%), Gaps = 25/174 (14%)
Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFK-GYGHVEFASVEDAHKAIE- 475
           +L+VG+L   V +A +   FS    ++ +R+  D   R   GY +V F    DA +A++ 
Sbjct: 17  SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 76
Query: 476 LNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQV 535
           +N  ++  + +R+ +++               S +K G G     IFIK  D S+     
Sbjct: 77  MNFDVIKGKPVRIMWSQ------------RDPSLRKSGVGN----IFIKNLDKSIDN--- 117
Query: 536 RASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEI 588
             +L + F + G I    V  D + GS KG  ++ F   ++  +A+E M+G  +
Sbjct: 118 -KALYDTFSAFGNILSCKVVCD-ENGS-KGYGFVHFETQEAAERAIEKMNGMLL 168

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 45.4 bits (106), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 36/155 (23%), Positives = 67/155 (43%), Gaps = 24/155 (15%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-L 476
           L V  LP      ++   F  +  +   R+  D   G   GY  V+F S  D+ +AI+ L
Sbjct: 17  LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 477 NGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVR 536
           NG  + N+ +++ +AR                   GG       +++     ++ +DQ  
Sbjct: 77  NGITVRNKRLKVSYAR------------------PGGESIKDTNLYVTNLPRTITDDQ-- 116
Query: 537 ASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDF 571
             L+  FG  G I + ++ +D  TG  +G+A++ +
Sbjct: 117 --LDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRY 149

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score = 45.4 bits (106), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 24/73 (32%), Positives = 41/73 (56%), Gaps = 2/73 (2%)
Query: 415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI 474
           G   +F+ NL  S++   + + FS    ++  ++  D +G  KGYG V F + E A +AI
Sbjct: 97  GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS-KGYGFVHFETQEAAERAI 155
Query: 475 E-LNGQMLGNRAI 486
           E +NG +L +R +
Sbjct: 156 EKMNGMLLNDRKV 168

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score = 43.5 bits (101), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 47/185 (25%), Positives = 84/185 (45%), Gaps = 25/185 (13%)
Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFK-GYGHVEFASVEDAHKAIE- 475
           +L+VG+L   V +A +   FS    ++ +R+  D   R   GY +V F    DA +A++ 
Sbjct: 12  SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 71
Query: 476 LNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQV 535
           +N  ++  + +R+ +++               S +K G G     IFIK  D S+     
Sbjct: 72  MNFDVIKGKPVRIMWSQ------------RDPSLRKSGVG----NIFIKNLDKSIDN--- 112
Query: 536 RASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV 594
             +L + F + G I    V  D + GS KG  ++ F   ++  +A+E M+G  +    + 
Sbjct: 113 -KALYDTFSAFGNILSCKVVCD-ENGS-KGYGFVHFETQEAAERAIEKMNGMLLNDRKVF 169
Query: 595 VDEAK 599
           V   K
Sbjct: 170 VGRFK 174

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 45.4 bits (106), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 37/165 (22%), Positives = 72/165 (43%), Gaps = 24/165 (14%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAIE-L 476
           L V  LP  +   ++   F  +  +   R+  D   G   GY  V+F S  D+ +AI+ L
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 477 NGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVR 536
           NG  + N+ +++ +AR                   GG       +++     ++ +DQ  
Sbjct: 66  NGITVRNKRLKVSYAR------------------PGGESIKDTNLYVTNLPRTITDDQ-- 105
Query: 537 ASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKAL 581
             L+  FG  G I + ++ +D  TG  +G+A++ +   +   +A+
Sbjct: 106 --LDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 148

>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary Complex Length = 84

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 22/78 (28%), Positives = 46/78 (58%), Gaps = 2/78 (2%)
Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAI 474
           S+ +++G++P+   +  + +  S V  V+++++  D   GR KGY  +EF  +E +  A+
Sbjct: 4   SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 63
Query: 475 E-LNGQMLGNRAIRLDFA 491
             LNG  LG+R ++  ++
Sbjct: 64  RNLNGYQLGSRFLKCGYS 81

>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To Ssdna From A Portion Of Fuse Length = 216

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 42/183 (22%), Positives = 86/183 (46%), Gaps = 14/183 (7%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-L 476
           ++VG++ + + +  ++  F+    +  + +S D+   + KG+  VE+   E A  A+E +
Sbjct: 31  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 477 NGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVR 536
           N  MLG R I++      G   P          Q     +A + I++      + +D ++
Sbjct: 91  NSVMLGGRNIKVGRPSNIGQAQPIID-------QLAEEARAFNRIYVASVHQDLSDDDIK 143
Query: 537 ASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKAL-EMSGTEIGGYSLVV 595
           +  E    + G+I   ++ +D  TG  KG  ++++  A S   A+  M+  ++GG  L V
Sbjct: 144 SVFE----AFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 199
Query: 596 DEA 598
            +A
Sbjct: 200 GKA 202

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/73 (32%), Positives = 43/73 (58%), Gaps = 2/73 (2%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADG-RFKGYGHVEFASVEDAHKA-IEL 476
           LFVG L F   +  ++  FS+  ++ +V +  D +  R +G+G V F +++DA  A + +
Sbjct: 15  LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 477 NGQMLGNRAIRLD 489
           NG+ +  R IR+D
Sbjct: 75  NGKSVDGRQIRVD 87

>pdb|2HGN|A Chain A, Nmr Structure Of The Third Qrrm Domain Of Human Hnrnp F Length = 139

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 34/114 (29%), Positives = 53/114 (46%), Gaps = 5/114 (4%)
Query: 399 ESGKKAAQTPFTPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKG 458
           + G+ +  + FT QS     + +  LP+   + D+ NFFS +   V V +    DGR  G
Sbjct: 29  QMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPL-NPVRVHIEIGPDGRVTG 87
Query: 459 YGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKG 512
              VEFA+ E+A  A+  +   + +R I L      GA    S G  S+   +G
Sbjct: 88  EADVEFATHEEAVAAMSKDRANMQHRYIELFLNSTTGA----SNGAYSSQVMQG 137

>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna Recognition Motif From Eukaryotic Translation Initiation Factor 4b Length = 100

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 29/78 (37%), Positives = 45/78 (57%), Gaps = 3/78 (3%)
Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADG--RFKGYGHVEFASVEDAHKAIE 475
           T F+GNLP+ V +  ++ FF  +  +  VRL  +     R KG+G+ EF  ++    A+ 
Sbjct: 21  TAFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 79
Query: 476 LNGQMLGNRAIRLDFARE 493
           LN + LGNR IR+D A +
Sbjct: 80  LNEESLGNRRIRVDVADQ 97

>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0 Rbd1), Nmr Length = 75

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/69 (33%), Positives = 39/69 (56%), Gaps = 6/69 (8%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAIE-- 475
           +F+G L +   + D++++FS+  EVVD  L  D   GR +G+G V F   E   K ++  
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 476 ---LNGQML 481
              LNG+++
Sbjct: 62  EHKLNGKVI 70

>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2 A Resolution Length = 89

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 27/79 (34%), Positives = 44/79 (55%), Gaps = 2/79 (2%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAIE-L 476
           LFV  +     + D+ + F+E  E+ ++ L+ D   G  KGY  VE+ + ++A  A+E L
Sbjct: 10  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 477 NGQMLGNRAIRLDFARERG 495
           NGQ L  + I +D+   RG
Sbjct: 70  NGQDLMGQPISVDWCFVRG 88

>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX Length = 106

Iteration: 1
 Score = 43.9 bits (102), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 31/101 (30%), Positives = 52/101 (51%), Gaps = 2/101 (1%)
Query: 397 DAESGKKAAQTPFTPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGR 455
           D +S ++    P   +S     LFV  +     + D+ + F+E  E+ ++ L+ D   G 
Sbjct: 4   DYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGY 63
Query: 456 FKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARERG 495
            KGY  VE+ + ++A  A+E LNGQ L  + I +D+   RG
Sbjct: 64  LKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRG 104

>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd Machinery Length = 90

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 27/79 (34%), Positives = 44/79 (55%), Gaps = 2/79 (2%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAIE-L 476
           LFV  +     + D+ + F+E  E+ ++ L+ D   G  KGY  VE+ + ++A  A+E L
Sbjct: 10  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 477 NGQMLGNRAIRLDFARERG 495
           NGQ L  + I +D+   RG
Sbjct: 70  NGQDLMGQPISVDWCFVRG 88

>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast Poly(U)-Binding Protein (Pub1) Length = 83

Iteration: 1
 Score = 43.5 bits (101), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 25/75 (33%), Positives = 42/75 (56%), Gaps = 2/75 (2%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAIE-L 476
           LFVG+L  +V+   ++N F +    +   +  D   G  +GYG V F S +DA  A++ +
Sbjct: 4   LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 477 NGQMLGNRAIRLDFA 491
            GQ L  R +R+++A
Sbjct: 64  QGQDLNGRPLRINWA 78

>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A Trapped Dead-Box Helicase Bound To Rna Length = 91

Iteration: 1
 Score = 43.5 bits (101), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 27/79 (34%), Positives = 44/79 (55%), Gaps = 2/79 (2%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAIE-L 476
           LFV  +     + D+ + F+E  E+ ++ L+ D   G  KGY  VE+ + ++A  A+E L
Sbjct: 12  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 477 NGQMLGNRAIRLDFARERG 495
           NGQ L  + I +D+   RG
Sbjct: 72  NGQDLMGQPISVDWCFVRG 90

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 43.5 bits (101), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 31/104 (29%), Positives = 50/104 (48%), Gaps = 10/104 (9%)
Query: 396 VDAESGKKAAQTPFTPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGR 455
           +D +S  K  +  +T +      LFVGNLP  + + D +  F    E  +V ++ D    
Sbjct: 6   IDIKSFLKPGEKTYTQRC----RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD---- 57
Query: 456 FKGYGHVEFASVEDAHKA-IELNGQMLGNRAIRLDFARERGAYT 498
            +G+G +   S   A  A  EL+G +L +R +R+ FA    A T
Sbjct: 58  -RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATHGAALT 100

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 43.5 bits (101), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 28/80 (35%), Positives = 44/80 (55%), Gaps = 3/80 (3%)
Query: 416 SKT-LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKA 473
           SKT L V  LP ++ Q + ++ F  + ++   +L  D   G+  GYG V ++   DA KA
Sbjct: 3   SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 474 IE-LNGQMLGNRAIRLDFAR 492
           I  LNG  L  + I++ +AR
Sbjct: 63  INTLNGLKLQTKTIKVSYAR 82

>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like Length = 89

Iteration: 1
 Score = 43.5 bits (101), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 19/58 (32%), Positives = 35/58 (60%)
Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE 475
           T+FVG +   +++ ++++FF+    V +V++ +D  G  KGYG V F +  D  K +E
Sbjct: 12  TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE 69

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 43.5 bits (101), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 41/173 (23%), Positives = 75/173 (43%), Gaps = 34/173 (19%)
Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEF---ASVEDAH 471
           S  +F+G L +   + +++ +F +   V D+++  D A GR +G+G + F   +SV++  
Sbjct: 3   SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVV 62
Query: 472 KAIE-LNGQMLG-NRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSS 529
           K    L+G+++   RAI  D   + G                         IF+ G    
Sbjct: 63  KTQHILDGKVIDPKRAIPRDEQDKTGK------------------------IFVGG---- 94
Query: 530 VGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE 582
           +G D      EE F   G I    +  D DTG  +G  ++ +  AD+ ++  +
Sbjct: 95  IGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ 147

>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1 Length = 95

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 28/89 (31%), Positives = 47/89 (52%), Gaps = 5/89 (5%)
Query: 412 QSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAH 471
           +  G   +F+ NL  S++   + + FS    ++  ++  D +G  KGYG V F + E A 
Sbjct: 7   RKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS-KGYGFVHFETQEAAE 65
Query: 472 KAIE-LNGQMLGNRAI---RLDFARERGA 496
           +AIE +NG +L +R +   R    +ER A
Sbjct: 66  RAIEKMNGMLLNDRKVFVGRFKSRKEREA 94

>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Mvh Rna, Uguuc Length = 87

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 19/58 (32%), Positives = 35/58 (60%)
Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE 475
           T+FVG +   +++ ++++FF+    V +V++ +D  G  KGYG V F +  D  K +E
Sbjct: 11  TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE 68

>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif Of Hypothetical Rna-Binding Protein Rbm19 Length = 107

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 4/77 (5%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRL--SSDADGRFKGYGHVEFASVEDAHKAIE- 475
           + V N+PF   Q +++  FS   E+  VRL       G  +G+G V+F + +DA KA   
Sbjct: 18  ILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNA 77
Query: 476 -LNGQMLGNRAIRLDFA 491
             +   L  R + L++A
Sbjct: 78  LCHSTHLYGRRLVLEWA 94

>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif, Single-Stranded Interacting Protein 1 Length = 114

Iteration: 1
 Score = 42.7 bits (99), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 22/87 (25%), Positives = 39/87 (44%), Gaps = 9/87 (10%)
Query: 396 VDAESGKKAAQTPFTPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGR 455
           V A+  K+  Q P          L++ NLP S+++ +++N      +V+  R+  D+ G 
Sbjct: 13  VQAQMAKQQEQDP--------TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGT 64
Query: 456 FKGYGHVEFASVEDAHKAI-ELNGQML 481
            +G G     S E     I   NG+ +
Sbjct: 65  SRGVGFARMESTEKCEAVIGHFNGKFI 91

>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex Length = 98

Iteration: 1
 Score = 42.7 bits (99), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 25/76 (32%), Positives = 39/76 (51%), Gaps = 1/76 (1%)
Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE 475
           S TL+VGNL F   +  +   FS+  ++  + +  D      G+  VE+ S  DA  A+ 
Sbjct: 18  SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMR 77
Query: 476 -LNGQMLGNRAIRLDF 490
            +NG  L +R IR D+
Sbjct: 78  YINGTRLDDRIIRTDW 93

>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State Length = 126

Iteration: 1
 Score = 42.7 bits (99), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 29/96 (30%), Positives = 50/96 (52%), Gaps = 2/96 (2%)
Query: 397 DAESGKKAAQTPFTPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGR 455
           D +S ++    P   +S     LFV  +     + D+ + F+E  E+ ++ L+ D   G 
Sbjct: 3   DYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGY 62
Query: 456 FKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF 490
            KGY  VE+ + ++A  A+E LNGQ L  + I +D+
Sbjct: 63  LKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 98

>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Rna, Uuguucuu Length = 102

Iteration: 1
 Score = 42.7 bits (99), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 19/58 (32%), Positives = 35/58 (60%)
Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE 475
           T+FVG +   +++ ++++FF+    V +V++ +D  G  KGYG V F +  D  K +E
Sbjct: 11  TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE 68

>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein M Length = 89

Iteration: 1
 Score = 42.7 bits (99), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 34/93 (36%), Positives = 49/93 (52%), Gaps = 8/93 (8%)
Query: 413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVV--DVRLSSDADGRFKGYGHVEFASVEDA 470
           S GS  +FV NLPF      +++ F+E   V+  D+++    +G+ KG G V+F S E A
Sbjct: 2   SSGSSGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME---NGKSKGCGVVKFESPEVA 58
Query: 471 HKAIE-LNGQMLGNRAIRLDFARERGAYTPYSG 502
            +A   +NG  L  R I  D   +R A  P SG
Sbjct: 59  ERACRMMNGMKLSGREI--DVRIDRNASGPSSG 89

>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of Heterogeneous Nuclear Ribonucleoprotein M Length = 114

Iteration: 1
 Score = 42.4 bits (98), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 25/72 (34%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIEL- 476
           T+FV NL + V    ++  FS    VV   +  D DG+ +G G V F    +A +AI + 
Sbjct: 17  TVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMF 76
Query: 477 NGQMLGNRAIRL 488
           NGQ+L +R + +
Sbjct: 77  NGQLLFDRPMHV 88

>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm Length = 96

Iteration: 1
 Score = 42.4 bits (98), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 22/78 (28%), Positives = 40/78 (51%), Gaps = 4/78 (5%)
Query: 518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSF 577
           A +I++   D     ++    LE HF  CG + R+++  D  +G  KG AY++F+D +S 
Sbjct: 5   ARSIYVGNVDYGATAEE----LEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESV 60
Query: 578 NKALEMSGTEIGGYSLVV 595
             +L +  +   G  + V
Sbjct: 61  RTSLALDESLFRGRQIKV 78

>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2 Length = 96

Iteration: 1
 Score = 42.4 bits (98), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 26/81 (32%), Positives = 45/81 (55%), Gaps = 5/81 (6%)
Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE 475
           ++TL   NL F++ + +++  F +  E+   RL S  DG+ KG  ++EF S  DA K +E
Sbjct: 16  ARTLLAKNLSFNITEDELKEVFEDALEI---RLVSQ-DGKSKGIAYIEFKSEADAEKNLE 71
Query: 476 L-NGQMLGNRAIRLDFARERG 495
              G  +  R++ L +  E+G
Sbjct: 72  EKQGAEIDGRSVSLYYTGEKG 92

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	675
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	100.0
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	100.0
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	100.0
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.97
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.97
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.97
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.97
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.97
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.96
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.96
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.96
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.96
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.96
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.96
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.96
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.95
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.95
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.95
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.95
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.95
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.84
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.83
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.83
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.79
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.78
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.78
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.77
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.75
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.75
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.74
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.74
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.74
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.74
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.73
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.73
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.73
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.73
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.73
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.73
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.72
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.72
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.72
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.72
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.72
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.72
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.72
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.72
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.72
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.72
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.72
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.71
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.71
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.71
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.71
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.71
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.71
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.71
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.71
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.71
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.71
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.71
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.71
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.71
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.7
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.7
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.7
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.7
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.7
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.7
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.7
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.7
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.7
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.7
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.7
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.7
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.7
2div_A	99	TRNA selenocysteine associated protein; structural	99.7
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.69
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.69
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.69
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.69
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.69
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.69
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.69
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.69
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.69
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.69
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.69
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.69
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.69
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.69
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.69
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.68
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.68
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.68
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.68
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.68
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.68
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.68
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.68
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.68
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.68
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.68
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.68
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.68
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.68
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.68
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.67
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.67
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.67
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.67
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.67
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.67
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.67
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.67
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.67
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.67
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.67
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.67
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.66
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.66
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.66
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.66
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.66
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.66
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.66
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.66
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.66
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.65
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.65
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.65
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.65
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.65
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.65
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.65
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.65
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.65
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.65
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.65
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.65
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.65
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.65
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.65
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.64
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.64
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.64
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.64
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.64
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.64
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.64
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.64
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.64
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.64
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.63
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.63
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.63
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.63
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.63
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.63
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.63
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.63
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.63
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.63
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.63
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.63
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.63
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.63
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.62
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.62
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.62
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.62
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.62
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.62
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.62
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.62
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.62
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.62
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.62
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.62
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.62
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.62
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.62
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.62
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.62
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.61
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.61
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.61
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.61
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.61
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.61
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.61
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.61
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.61
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.61
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.6
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.6
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.6
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.6
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.6
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.6
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.6
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.59
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.59
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.59
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.59
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.59
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.59
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.59
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.59
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.58
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.58
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.37
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.58
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.58
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.58
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.58
1x5p_A	97	Negative elongation factor E; structure genomics,	99.58
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.58
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.58
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.58
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.58
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.58
2div_A	99	TRNA selenocysteine associated protein; structural	99.57
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.57
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.57
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.57
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.57
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.57
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.57
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.57
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.35
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.57
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.56
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.56
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.56
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.56
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.56
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.56
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.56
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.56
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.55
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.55
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.55
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.55
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.55
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.55
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.55
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.55
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.55
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.55
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.55
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.54
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.54
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.54
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.54
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.54
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.54
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.54
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.54
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.54
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.54
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.54
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.54
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.54
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.53
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.53
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.53
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.53
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.53
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.52
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.52
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.52
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.52
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.52
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.52
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.52
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.52
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.52
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.51
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.51
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.51
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.51
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.51
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.51
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.5
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.5
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.5
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.5
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.5
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.5
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.5
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.5
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.5
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.49
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.49
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.49
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.49
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.49
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.49
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.49
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.49
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.48
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.48
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.48
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.48
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.48
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.48
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.48
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.48
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.47
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.47
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.46
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.46
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.46
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.46
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.46
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.46
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.46
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.45
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.45
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.45
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.45
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.45
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.44
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.43
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.43
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.43
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.43
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.42
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.42
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.42
1x5p_A	97	Negative elongation factor E; structure genomics,	99.42
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.42
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.42
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.42
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.41
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.41
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.41
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.4
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.4
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.39
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.38
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.38
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.36
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.36
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.36
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.35
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.35
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.34
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.33
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.33
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.32
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.32
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.32
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.32
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.31
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.31
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.31
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.3
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.3
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.3
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.3
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.29
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.27
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.25
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.22
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.2
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.19
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.16
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.14
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.05
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.04
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.91
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.89
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.84
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	98.81
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.72
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.61
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.58
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.56
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.19
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.12
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	97.89
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.49
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.38
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.28
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.2
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.06
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	96.88
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	96.51
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.44
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.14
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	95.88
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	95.62
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	95.54
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.25
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	92.87
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	92.67
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	92.47
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	86.32
2pk2_A	358	Cyclin-T1, protein TAT; TAR, twinning, transcripti	80.35

>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=100.00  E-value=5e-33  Score=272.72  Aligned_cols=178  Identities=24%  Similarity=0.425  Sum_probs=152.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a  491 (675)
                      ....++|||+|||+++++++|++||+.||.|..|+|+++. +|+++|||||+|.+.++|.+||.+++..|.|+.|.|.++
T Consensus        10 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~l~v~~~   89 (196)
T 1l3k_A           10 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRA   89 (196)
T ss_dssp             CGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhcCCCEECCEEeeeecc
Confidence            4567999999999999999999999999999999999997 799999999999999999999999999999999999998


Q ss_pred             cccCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEe
Q 045516          492 RERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDF  571 (675)
Q Consensus       492 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F  571 (675)
                      ........            .......++|||+|||+.+++++    |+++|..||.|..|+|+++..+|.++|||||+|
T Consensus        90 ~~~~~~~~------------~~~~~~~~~l~V~nLp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F  153 (196)
T 1l3k_A           90 VSREDSQR------------PGAHLTVKKIFVGGIKEDTEEHH----LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF  153 (196)
T ss_dssp             CC-----------------------CCSEEEEECCTTTCCHHH----HHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEE
T ss_pred             cCcccccc------------cccCCCcceEEEeCCCCCCCHHH----HHHHHhcCCCeEEEEEeecCCCCCccceEEEEE
Confidence            65432111            11123468999999999999998    778999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHhCCceeCCeeeEEeccccCCCCCC
Q 045516          572 TDADSFNKALEMSGTEIGGYSLVVDEAKQRGDFGS  606 (675)
Q Consensus       572 ~~~e~A~~Al~lng~~~~Gr~l~V~~a~~r~~~~~  606 (675)
                      .+.++|.+||.+++..|+|+.|.|.++.++.....
T Consensus       154 ~~~~~A~~A~~~~~~~~~G~~i~v~~a~~k~~~~~  188 (196)
T 1l3k_A          154 DDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMAS  188 (196)
T ss_dssp             SSHHHHHHHHHCSCCEETTEECEEEECC-------
T ss_pred             CCHHHHHHHHHhCCcEECCEEEEEEecCChhHhcc
Confidence            99999999999889999999999999998877643

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=100.00  E-value=7.2e-33  Score=276.49  Aligned_cols=168  Identities=25%  Similarity=0.436  Sum_probs=150.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ...+||||+|||+++|+++|++||++||.|.+|+|+++. +++++|||||+|.+.++|.+||. ||+..+.|+.|+|.++
T Consensus        13 ~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~   92 (213)
T 4f02_A           13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWS   92 (213)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccccc
Confidence            356899999999999999999999999999999999997 89999999999999999999997 9999999999999987


Q ss_pred             cccCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEe
Q 045516          492 RERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDF  571 (675)
Q Consensus       492 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F  571 (675)
                      ........                ...++|||+||++.+++++    |+++|..||.|..|+|+++.  +.++|||||+|
T Consensus        93 ~~~~~~~~----------------~~~~~l~v~nl~~~~t~~~----l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f  150 (213)
T 4f02_A           93 QRDPSLRK----------------SGVGNIFIKNLDKSIDNKA----LYDTFSAFGNILSCKVVCDE--NGSKGYGFVHF  150 (213)
T ss_dssp             CCCTHHHH----------------HCTTEEEEESCCTTCCHHH----HHHHHGGGSCEEEEEEEEET--TEEEEEEEEEE
T ss_pred             cccccccc----------------cccccceECCcccccHHHH----HHHHHhhcCCeEEEEeeccC--CCCceEEEEEe
Confidence            64322111                1157899999999999998    77899999999999999874  55899999999


Q ss_pred             CCHHHHHHHHH-hCCceeCCeeeEEeccccCCC
Q 045516          572 TDADSFNKALE-MSGTEIGGYSLVVDEAKQRGD  603 (675)
Q Consensus       572 ~~~e~A~~Al~-lng~~~~Gr~l~V~~a~~r~~  603 (675)
                      .+.++|.+||. |||..|+|+.|+|.++.++..
T Consensus       151 ~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~~~~  183 (213)
T 4f02_A          151 ETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKE  183 (213)
T ss_dssp             SSHHHHHHHHHHHTTCEETTEECEEEECCCHHH
T ss_pred             CCHHHHHHHHHHhCCCEECCEEEEEEEcCCCcc
Confidence            99999999998 999999999999999987644

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=100.00  E-value=7.6e-32  Score=256.49  Aligned_cols=164  Identities=23%  Similarity=0.464  Sum_probs=151.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEeccccC
Q 045516          417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARERG  495 (675)
Q Consensus       417 ~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~~~  495 (675)
                      |+|||+|||+++++++|+++|+.||.|..|+|+++.+++++|||||+|.+.++|.+||. |||..|.|+.|.|.++....
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~~   80 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQ   80 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCCCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCCC
Confidence            69999999999999999999999999999999999988999999999999999999996 99999999999999986543


Q ss_pred             CCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHH
Q 045516          496 AYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDAD  575 (675)
Q Consensus       496 ~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e  575 (675)
                      ..                .....++|||+|||..+++++    |+++|..||.|..|.|+++..+|.++|||||+|.+.+
T Consensus        81 ~~----------------~~~~~~~l~v~nl~~~~t~~~----l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~  140 (166)
T 3md3_A           81 QS----------------SSDDTFNLFVGDLNVNVDDET----LRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQD  140 (166)
T ss_dssp             CC----------------CCTTCEEEEEESCCTTCCHHH----HHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHH
T ss_pred             CC----------------CCCCCceEEECCCCCCCCHHH----HHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHH
Confidence            21                123378999999999999998    7788999999999999999999999999999999999


Q ss_pred             HHHHHHH-hCCceeCCeeeEEecccc
Q 045516          576 SFNKALE-MSGTEIGGYSLVVDEAKQ  600 (675)
Q Consensus       576 ~A~~Al~-lng~~~~Gr~l~V~~a~~  600 (675)
                      +|.+||. |||..|+|+.|+|.|+++
T Consensus       141 ~A~~A~~~l~g~~~~g~~i~v~~a~~  166 (166)
T 3md3_A          141 DAQNAMDSMQGQDLNGRPLRINWAAK  166 (166)
T ss_dssp             HHHHHHHHHTTCEETTEECEEEESCC
T ss_pred             HHHHHHHHhCCCccCCcEEEEEecCC
Confidence            9999998 999999999999999863

>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=99.97  E-value=1.1e-30  Score=249.27  Aligned_cols=162  Identities=25%  Similarity=0.490  Sum_probs=150.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~  492 (675)
                      ..++|||+|||+++++++|+++|+.||.|..|+|+++. +|+++|||||+|.+.++|.+||. ||+..|.|+.|.|.++.
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   81 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR   81 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecC
Confidence            46899999999999999999999999999999999987 89999999999999999999997 99999999999999986


Q ss_pred             ccCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeC
Q 045516          493 ERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFT  572 (675)
Q Consensus       493 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~  572 (675)
                      ....                  ....++|||+|||..+++++    |+++|..||.|..|.|+++..+|.++|||||+|.
T Consensus        82 ~~~~------------------~~~~~~l~v~nl~~~~t~~~----l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~  139 (168)
T 1b7f_A           82 PGGE------------------SIKDTNLYVTNLPRTITDDQ----LDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYN  139 (168)
T ss_dssp             CCSS------------------TTTTCEEEEESCCTTCCHHH----HHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEES
T ss_pred             CCcc------------------cCCCCCEEEeCCCCCCCHHH----HHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEEC
Confidence            5432                  12368999999999999988    7889999999999999999889999999999999


Q ss_pred             CHHHHHHHHH-hCCceeCC--eeeEEecc
Q 045516          573 DADSFNKALE-MSGTEIGG--YSLVVDEA  598 (675)
Q Consensus       573 ~~e~A~~Al~-lng~~~~G--r~l~V~~a  598 (675)
                      +.++|.+|+. |||..|.|  +.|+|.|+
T Consensus       140 ~~~~A~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          140 KREEAQEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             SHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CHHHHHHHHHHhcCCEecCCCeEEEEEeC
Confidence            9999999998 99999988  99999885

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.97  E-value=1.3e-30  Score=259.39  Aligned_cols=180  Identities=23%  Similarity=0.403  Sum_probs=153.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~  492 (675)
                      ..++|||+|||+++++++|++||..||.|..|+|+++. +|+++|||||+|.+.++|.+||. ||+..|.|+.|.|.++.
T Consensus        27 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~  106 (216)
T 2qfj_A           27 IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPS  106 (216)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCS
T ss_pred             cCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCC
Confidence            35899999999999999999999999999999999987 89999999999999999999998 99999999999998875


Q ss_pred             ccCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeC
Q 045516          493 ERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFT  572 (675)
Q Consensus       493 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~  572 (675)
                      ......+..       ..........++|||+|||..+++++    |+++|..||.|..|+|+++..+|.++|||||+|.
T Consensus       107 ~~~~~~~~~-------~~~~~~~~~~~~l~v~nlp~~~t~~~----l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~  175 (216)
T 2qfj_A          107 NIGQAQPII-------DQLAEEARAFNRIYVASVHQDLSDDD----IKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYE  175 (216)
T ss_dssp             CCGGGHHHH-------HHHHHHHTTSCEEEEECCCTTCCHHH----HHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEES
T ss_pred             Cccccchhh-------hhhhcccCCCcEEEEeCCCCcCCHHH----HHHHHhccCCeeEEEEEecCCCCCcCceEEEEec
Confidence            432111000       00000112368999999999999998    7789999999999999999999999999999999


Q ss_pred             CHHHHHHHHH-hCCceeCCeeeEEeccccCCCCC
Q 045516          573 DADSFNKALE-MSGTEIGGYSLVVDEAKQRGDFG  605 (675)
Q Consensus       573 ~~e~A~~Al~-lng~~~~Gr~l~V~~a~~r~~~~  605 (675)
                      +.++|.+||. |||..|+|+.|+|.|+.++....
T Consensus       176 ~~~~A~~A~~~l~g~~~~g~~i~V~~a~~~~~~~  209 (216)
T 2qfj_A          176 KAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPL  209 (216)
T ss_dssp             SHHHHHHHHHHHTTCBCSSSBCEEEECSSCSSTT
T ss_pred             CHHHHHHHHHHccCCEeCCcEEEEEEecCCCCCC
Confidence            9999999998 99999999999999998875443

>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=99.97  E-value=2.2e-30  Score=246.58  Aligned_cols=161  Identities=27%  Similarity=0.517  Sum_probs=148.4

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEeccc
Q 045516          416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       416 ~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~  493 (675)
                      .++|||+|||+++++++|+++|..||.|..|+|+++. +|+++|||||+|.+.++|.+||. |||..|.|+.|.|.++..
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   81 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCC
Confidence            5899999999999999999999999999999999998 89999999999999999999998 999999999999999865


Q ss_pred             cCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCC
Q 045516          494 RGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTD  573 (675)
Q Consensus       494 ~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~  573 (675)
                      ...                  ....++|||+|||..+++++    |+++|..||.|..|+|+++..+|.++|||||+|.+
T Consensus        82 ~~~------------------~~~~~~l~v~nl~~~~t~~~----l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~  139 (167)
T 1fxl_A           82 SSA------------------SIRDANLYVSGLPKTMTQKE----LEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDK  139 (167)
T ss_dssp             CCG------------------GGTTCEEEEESCCTTCCHHH----HHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESS
T ss_pred             Ccc------------------cCCCCcEEECCCCCcCCHHH----HHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCC
Confidence            421                  11258899999999999988    77899999999999999998899999999999999


Q ss_pred             HHHHHHHHH-hCCceeCCee--eEEecc
Q 045516          574 ADSFNKALE-MSGTEIGGYS--LVVDEA  598 (675)
Q Consensus       574 ~e~A~~Al~-lng~~~~Gr~--l~V~~a  598 (675)
                      .++|.+|+. |||..|+|+.  |+|.||
T Consensus       140 ~~~A~~A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          140 RIEAEEAIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             HHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHHHHHHHHhcCCccCCCccceEEEeC
Confidence            999999998 9999999975  888775

>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=99.97  E-value=1.7e-31  Score=254.86  Aligned_cols=164  Identities=21%  Similarity=0.462  Sum_probs=150.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEeccc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a~~  493 (675)
                      ++++|||+|||+++++++|+++|+.||.|..|+|+++. +|+++|||||+|.+.++|.+||. ++..|.|+.|.|.++..
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~g~~i~v~~~~~   80 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK-TQHILDGKVIDPKRAIP   80 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHH-SCCEETTEECCCEECCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHh-cccccCCeEcccccccc
Confidence            46899999999999999999999999999999999997 89999999999999999999998 35789999999988764


Q ss_pred             cCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCC
Q 045516          494 RGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTD  573 (675)
Q Consensus       494 ~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~  573 (675)
                      ....                  ...++|||+|||..+++++    |+++|+.||.|..|+|+++..+|.++|||||+|.+
T Consensus        81 ~~~~------------------~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~  138 (167)
T 2cjk_A           81 RDEQ------------------DKTGKIFVGGIGPDVRPKE----FEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDS  138 (167)
T ss_dssp             HHHH------------------HHCEEEEEEEECTTCCHHH----HHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESS
T ss_pred             hhhc------------------cCCCeEEECCCCCCCCHHH----HHHHHHhCccEEEEEEEEcCCCCccceEEEEEECC
Confidence            3211                  1257999999999999998    77889999999999999999899999999999999


Q ss_pred             HHHHHHHHHhCCceeCCeeeEEeccccC
Q 045516          574 ADSFNKALEMSGTEIGGYSLVVDEAKQR  601 (675)
Q Consensus       574 ~e~A~~Al~lng~~~~Gr~l~V~~a~~r  601 (675)
                      .++|.+||++|+..|+|+.|+|.|+.+|
T Consensus       139 ~~~a~~A~~~~~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A          139 ADAVDRVCQNKFIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             HHHHHHHHHCSEECSSSSCEEEEECCCC
T ss_pred             HHHHHHHHhCCCEEeCCeEEEEeecCCC
Confidence            9999999999999999999999999876

>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=99.97  E-value=1.9e-29  Score=242.21  Aligned_cols=162  Identities=21%  Similarity=0.335  Sum_probs=143.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCC-C--CcccEEEEEecCHHHHHHHHH-hCCcccC---CeeEE
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-G--RFKGYGHVEFASVEDAHKAIE-LNGQMLG---NRAIR  487 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~-g--~~kG~afV~F~~~e~A~~Al~-l~g~~~~---gr~i~  487 (675)
                      +.++|||+|||+++++++|+++|..||.|..|+|+++.. +  +++|||||+|.+.++|.+||. ||+..+.   ++.|.
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~   81 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQ   81 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceE
Confidence            578999999999999999999999999999999999984 4  899999999999999999997 9998876   67788


Q ss_pred             EEeccccCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEE
Q 045516          488 LDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIA  567 (675)
Q Consensus       488 V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~a  567 (675)
                      +.++......                 ....++|||+|||..+++++    |+++|..||.|..|+|+++. +|.++|||
T Consensus        82 ~~~~~~~~~~-----------------~~~~~~l~v~nl~~~~t~~~----l~~~F~~~G~i~~v~~~~~~-~g~~~g~a  139 (175)
T 3nmr_A           82 MKPADSEKNN-----------------AVEDRKLFIGMISKKCTEND----IRVMFSSFGQIEECRILRGP-DGLSRGCA  139 (175)
T ss_dssp             EEECGGGCCS-----------------CGGGSEEEEESCCTTCCHHH----HHHHHGGGSCEEEEEEEECT-TSCEEEEE
T ss_pred             Eccccccccc-----------------cCCCCeEEEcCCCCcCCHHH----HHHHHHhCCCEEEEEEEECC-CCCEEEEE
Confidence            8777644321                 12368999999999999998    77889999999999999985 59999999


Q ss_pred             EEEeCCHHHHHHHHH-hCCceeC---CeeeEEecc
Q 045516          568 YLDFTDADSFNKALE-MSGTEIG---GYSLVVDEA  598 (675)
Q Consensus       568 fV~F~~~e~A~~Al~-lng~~~~---Gr~l~V~~a  598 (675)
                      ||+|.+.++|.+||. |||..|.   |+.|+|.|+
T Consensus       140 fV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~~a  174 (175)
T 3nmr_A          140 FVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA  174 (175)
T ss_dssp             EEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEEEC
T ss_pred             EEEECCHHHHHHHHHHhcCCcccCCCCCCeEEEec
Confidence            999999999999998 9998776   499999987

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.96  E-value=5.5e-29  Score=244.27  Aligned_cols=180  Identities=23%  Similarity=0.471  Sum_probs=149.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhC----C-------CeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCC
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEV----A-------EVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGN  483 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~----G-------~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~g  483 (675)
                      ..++|||+|||+.+++++|++||..|    |       .|..+++.     +++|||||+|.+.++|.+||.|||..|.|
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~-----~~~g~afV~F~~~~~A~~Al~l~g~~~~g   77 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN-----QDKNFAFLEFRSVDETTQAMAFDGIIFQG   77 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEE-----TTTTEEEEEESCSHHHHHHGGGTTEEETT
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEec-----CCCCEEEEEeCCHHHHHHHHHhcCCEEcC
Confidence            46899999999999999999999999    5       66777664     45899999999999999999999999999


Q ss_pred             eeEEEEeccccCCCCCCCCCC--CCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCC
Q 045516          484 RAIRLDFARERGAYTPYSGGN--ESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTG  561 (675)
Q Consensus       484 r~i~V~~a~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG  561 (675)
                      +.|.|.++.............  ..............++|||+|||..+++++    |+++|..||.|..|+|+++..+|
T Consensus        78 ~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~----l~~~f~~~G~v~~~~~~~~~~~~  153 (198)
T 2yh0_A           78 QSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQ----VKELLTSFGPLKAFNLVKDSATG  153 (198)
T ss_dssp             EEEEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHH----HHHHHHTBSCEEEEEEEECTTTC
T ss_pred             ceEEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHH----HHHHHHHcCCccEEEEeecCCCC
Confidence            999999987653221111000  000111112234579999999999999998    77889999999999999998899


Q ss_pred             CeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEeccccCCC
Q 045516          562 SVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVDEAKQRGD  603 (675)
Q Consensus       562 ~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~~a~~r~~  603 (675)
                      .++|||||+|.+.++|.+||. |||..|+|+.|+|.++.++..
T Consensus       154 ~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  196 (198)
T 2yh0_A          154 LSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK  196 (198)
T ss_dssp             SEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             CcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            999999999999999999998 999999999999999987654

>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=99.96  E-value=4.1e-30  Score=247.56  Aligned_cols=164  Identities=31%  Similarity=0.442  Sum_probs=144.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEecc
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a~  492 (675)
                      ....++|||+|||+++++++|+++|..||.|..+.|....+++++|||||+|.+.++|.+||+|||..|.|+.|.|.++.
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~v~~~~   89 (175)
T 1fje_B           10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPK   89 (175)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEECCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHHhcCCCEeCCeEEEEecCC
Confidence            45689999999999999999999999999877644444447889999999999999999999999999999999999987


Q ss_pred             ccCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeC
Q 045516          493 ERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFT  572 (675)
Q Consensus       493 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~  572 (675)
                      ......                ....++|||+|||..+++++    |+++|..||.|..+     ..+|.++|||||+|.
T Consensus        90 ~~~~~~----------------~~~~~~l~v~nlp~~~t~~~----l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~  144 (175)
T 1fje_B           90 GRDSKK----------------VRAARTLLAKNLSFNITEDE----LKEVFEDALEIRLV-----SQDGKSKGIAYIEFK  144 (175)
T ss_dssp             CSSCST----------------TGGGGEEEEESCCSSCCHHH----HHHHCTTCSEEEEE-----CSSSSCCSEEEEECS
T ss_pred             Cccccc----------------cccCCEEEEeCCCCCCCHHH----HHHHHHhcCeEEEe-----cCCCCCceEEEEEEC
Confidence            543211                12378999999999999998    77899999998877     466899999999999


Q ss_pred             CHHHHHHHHH-hCCceeCCeeeEEeccccC
Q 045516          573 DADSFNKALE-MSGTEIGGYSLVVDEAKQR  601 (675)
Q Consensus       573 ~~e~A~~Al~-lng~~~~Gr~l~V~~a~~r  601 (675)
                      +.++|.+||. |||..|+|+.|+|.|+.++
T Consensus       145 ~~~~A~~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          145 SEADAEKNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             SHHHHHHHHHHHTEEEETTEEEEEEECSSC
T ss_pred             CHHHHHHHHHHhCCCEECCeEEEEEecCCC
Confidence            9999999998 9999999999999999876

>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=99.96  E-value=6.2e-29  Score=238.30  Aligned_cols=157  Identities=26%  Similarity=0.566  Sum_probs=142.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhC----C-------CeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCC
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEV----A-------EVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGN  483 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~----G-------~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~g  483 (675)
                      +.++|||+|||+.+++++|+++|+.|    |       .|..+++.+     ++|||||+|.+.++|.+||.||+..|.|
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~-----~~g~afV~f~~~~~A~~A~~~~~~~~~g   77 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ-----DKNFAFLEFRSVDETTQAMAFDGIIFQG   77 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEET-----TTTEEEEEESSHHHHHHHGGGTTCEETT
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecC-----CCCEEEEEeCCHHHHHHHHHhCCcEecC
Confidence            46899999999999999999999999    7       788887764     4899999999999999999999999999


Q ss_pred             eeEEEEeccccCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCe
Q 045516          484 RAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSV  563 (675)
Q Consensus       484 r~i~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~  563 (675)
                      +.|.|.++.....                  ....++|||+|||..+++++    |+++|..||.|..|+|+++..+|.+
T Consensus        78 ~~i~v~~~~~~~~------------------~~~~~~l~v~nlp~~~t~~~----l~~~f~~~G~v~~v~i~~~~~~g~~  135 (172)
T 2g4b_A           78 QSLKIRRPHDYQP------------------LPGAHKLFIGGLPNYLNDDQ----VKELLTSFGPLKAFNLVKDSATGLS  135 (172)
T ss_dssp             EECEEECCSSCCC------------------CTTTTCEEEECCCTTCCHHH----HHHHHHTTSCEEEEEEEECTTTCSE
T ss_pred             ceeeecCCcccCC------------------CCCCCEEEEEcCCCcCCHHH----HHHHHHhcCCceEEEEEecCCCCCc
Confidence            9999988654321                  11268999999999999988    7788999999999999999889999


Q ss_pred             eeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEecc
Q 045516          564 KGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVDEA  598 (675)
Q Consensus       564 rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~~a  598 (675)
                      +|||||+|.+.++|.+|+. |||..|+|+.|.|.|+
T Consensus       136 ~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A          136 KGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             EEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             ceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            9999999999999999998 9999999999999987

>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=99.96  E-value=3.8e-28  Score=240.74  Aligned_cols=174  Identities=16%  Similarity=0.177  Sum_probs=140.7

Q ss_pred             CCceEEEcCCC-CCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecc
Q 045516          415 GSKTLFVGNLP-FSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       415 ~~~tlfV~nLp-~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~  492 (675)
                      ++++|||+||| +.+++++|+++|+.||.|.+|+|+++    .+|||||+|.+.++|.+||. |||..|.|+.|+|.++.
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~----~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~   78 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS----KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSK   78 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT----STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcc
Confidence            56899999999 89999999999999999999999875    38999999999999999998 99999999999999986


Q ss_pred             ccCCCCCC-----CCC--------CCCCCccC------CCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcE--EE
Q 045516          493 ERGAYTPY-----SGG--------NESNSFQK------GGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEI--TR  551 (675)
Q Consensus       493 ~~~~~~~~-----~~~--------~~~~~~~~------~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I--~~  551 (675)
                      ........     .+.        .....+..      .....+.++|||+|||+.+++++    |+++|..||.|  ..
T Consensus        79 ~~~~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~----L~~~F~~~G~v~~~~  154 (205)
T 3tyt_A           79 QPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEEN----FFEICDELGVKRPTS  154 (205)
T ss_dssp             CSCCCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHH----HHHHHHHHTCCCCSE
T ss_pred             CCccCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHH----HHHHHHhcCCcceEE
Confidence            54321100     000        00000100      01234578999999999999998    77889999999  89


Q ss_pred             EEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCe----eeEEecc
Q 045516          552 ISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGY----SLVVDEA  598 (675)
Q Consensus       552 v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr----~l~V~~a  598 (675)
                      |+|+.+.  +..+|||||+|.+.++|..||. |||..|.|+    ++.|.++
T Consensus       155 v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          155 VKVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             EEECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEEE
T ss_pred             EEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEec
Confidence            9998875  5567999999999999999998 999999887    5666654

>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=99.96  E-value=2.4e-28  Score=255.16  Aligned_cols=172  Identities=22%  Similarity=0.358  Sum_probs=145.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCC-CeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVA-EVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G-~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~  492 (675)
                      ..++|||+|||+.+++++|+++|..|| .|..|+|+++..|.++|||||+|.+.++|.+||. |||..|.|+.|.|.++.
T Consensus       116 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  195 (292)
T 2ghp_A          116 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSN  195 (292)
T ss_dssp             CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECC
Confidence            578999999999999999999999999 9999999998888999999999999999999998 99999999999999987


Q ss_pred             ccCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCC-cCHHHHHHHHHhhhcccCcEEEEEecccCC-CCCeeeEEEEE
Q 045516          493 ERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSS-VGEDQVRASLEEHFGSCGEITRISVPKDYD-TGSVKGIAYLD  570 (675)
Q Consensus       493 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~-~te~~i~~~L~~~F~~~G~I~~v~i~~d~~-tG~~rG~afV~  570 (675)
                      +.......           .......++|||+|||.. +++++    |+++|..||.|..|+|+++.. ||.++|||||+
T Consensus       196 ~~~~~~~~-----------~~~~~~~~~l~v~nlp~~~~t~~~----l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~  260 (292)
T 2ghp_A          196 PLEKSKRT-----------DSATLEGREIMIRNLSTELLDENL----LRESFEGFGSIEKINIPAGQKEHSFNNCCAFMV  260 (292)
T ss_dssp             CC--------------------CCTTTEEEEEEECTTTCCHHH----HHHHHGGGSCEEEEECCSCCC---CCCEEEEEE
T ss_pred             CCcccccc-----------cccCCCCceEEEECCCcccCCHHH----HHHHHhccCCeeEEEEEecCCcCCCCceEEEEE
Confidence            54322111           112334789999999999 99988    778999999999999999876 69999999999


Q ss_pred             eCCHHHHHHHHHhCCceeCCeeeEEeccccC
Q 045516          571 FTDADSFNKALEMSGTEIGGYSLVVDEAKQR  601 (675)
Q Consensus       571 F~~~e~A~~Al~lng~~~~Gr~l~V~~a~~r  601 (675)
                      |.+.++|.+||.|||..|+|+.|+|.|+.++
T Consensus       261 F~~~~~A~~A~~l~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          261 FENKDSAERALQMNRSLLGNREISVSLADKK  291 (292)
T ss_dssp             ESSHHHHHHHGGGTTEEETTEEEEEEECCCC
T ss_pred             eCCHHHHHHHHHhcCCEECCcEEEEEEecCC
Confidence            9999999999999999999999999999876

>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=99.96  E-value=6.4e-28  Score=250.67  Aligned_cols=177  Identities=18%  Similarity=0.339  Sum_probs=145.7

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHH----HHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeE
Q 045516          412 QSGGSKTLFVGNLPFSVEQADVQ----NFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAI  486 (675)
Q Consensus       412 ~~~~~~tlfV~nLp~~~te~~L~----~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i  486 (675)
                      .....++|||+|||+++++++|+    ++|..||.|..|+|++  +++++|||||+|.+.++|.+||. |||..|.|+.|
T Consensus         5 ~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~--~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   82 (282)
T 3pgw_A            5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   82 (282)
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC--CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEE
Confidence            34568999999999999999966    8999999999999986  78899999999999999999996 99999999999


Q ss_pred             EEEeccccCCCCCCCCCCC-------------------------------------------------------------
Q 045516          487 RLDFARERGAYTPYSGGNE-------------------------------------------------------------  505 (675)
Q Consensus       487 ~V~~a~~~~~~~~~~~~~~-------------------------------------------------------------  505 (675)
                      +|.++...........+..                                                             
T Consensus        83 ~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~  162 (282)
T 3pgw_A           83 RIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPP  162 (282)
T ss_pred             EEEEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCCCC
Confidence            9999865432100000000                                                             


Q ss_pred             --------------CC------------------CccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEE
Q 045516          506 --------------SN------------------SFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRIS  553 (675)
Q Consensus       506 --------------~~------------------~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~  553 (675)
                                    ..                  .........+.++|||+||+..+++++    |+++|..||.|..|+
T Consensus       163 ~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~----l~~~F~~~G~i~~v~  238 (282)
T 3pgw_A          163 YMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELM----LSMLFNQFPGFKEVR  238 (282)
T ss_pred             CCCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHH----HHHHHHhcCCeEEEE
Confidence                          00                  000001233568999999999999998    778899999999999


Q ss_pred             ecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeC-CeeeEEeccc
Q 045516          554 VPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIG-GYSLVVDEAK  599 (675)
Q Consensus       554 i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~-Gr~l~V~~a~  599 (675)
                      |+.+.     +|||||+|.+.++|.+||. |||..|+ |+.|+|.|++
T Consensus       239 ~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          239 LVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             EecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            99763     5899999999999999998 9999999 9999999986

>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=99.96  E-value=9.6e-28  Score=249.60  Aligned_cols=169  Identities=21%  Similarity=0.298  Sum_probs=153.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~  492 (675)
                      ..++|||+|||+.+++++|+++|..||.|..|+|+++. +|.++|||||+|.+.++|.+||. |||..|.|+.|.|.++.
T Consensus        94 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~  173 (284)
T 3smz_A           94 TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTD  173 (284)
T ss_dssp             CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECC
Confidence            45799999999999999999999999999999999987 89999999999999999999996 99999999999999987


Q ss_pred             ccCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCc-CHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEe
Q 045516          493 ERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSV-GEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDF  571 (675)
Q Consensus       493 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~-te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F  571 (675)
                      ......               .....++|||+|||..+ ++++    |+++|..||.|..|.|+++. +|.++|||||+|
T Consensus       174 ~~~~~~---------------~~~~~~~l~v~nlp~~~~~~~~----l~~~f~~~G~i~~v~i~~~~-~g~~~g~afV~f  233 (284)
T 3smz_A          174 AGQLTP---------------ALLHSRCLCVDRLPPGFNDVDA----LCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEY  233 (284)
T ss_dssp             GGGCCT---------------TTTSCSEEEEECCCTTCCCHHH----HHHHTCSSSCCSEEEEEECS-SCCEEEEEEEEC
T ss_pred             CCCCCc---------------ccCCccEEEEecCCcccCCHHH----HHHHhhCCCCeEEEEEEECC-CCCcccEEEEEe
Confidence            653211               12337899999999996 8887    88999999999999999986 799999999999


Q ss_pred             CCHHHHHHHHH-hCCceeCCeeeEEeccccCCC
Q 045516          572 TDADSFNKALE-MSGTEIGGYSLVVDEAKQRGD  603 (675)
Q Consensus       572 ~~~e~A~~Al~-lng~~~~Gr~l~V~~a~~r~~  603 (675)
                      .+.++|.+||. |||..|+|+.|+|.|+.++..
T Consensus       234 ~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~  266 (284)
T 3smz_A          234 ETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPP  266 (284)
T ss_dssp             SSHHHHHHHHHHHTTCEETTEECEEEECCSSSC
T ss_pred             CCHHHHHHHHHHhCCCccCCeEEEEEEecCCCc
Confidence            99999999998 999999999999999987655

>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=99.95  E-value=1.7e-27  Score=240.21  Aligned_cols=176  Identities=22%  Similarity=0.323  Sum_probs=146.5

Q ss_pred             CCCCceEEEcCCCC-CCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          413 SGGSKTLFVGNLPF-SVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       413 ~~~~~tlfV~nLp~-~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      ...+++|||+|||+ ++++++|++||+.||.|..|+|+++.    +|||||+|.+.++|.+||. |||..|.|+.|.|.+
T Consensus        31 ~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~  106 (229)
T 2adc_A           31 GAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITL  106 (229)
T ss_dssp             CCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEEC
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            45679999999999 99999999999999999999999875    8999999999999999997 999999999999999


Q ss_pred             ccccCCCCCCCCCCC-----------CCCcc------CCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccC-cEEEE
Q 045516          491 ARERGAYTPYSGGNE-----------SNSFQ------KGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCG-EITRI  552 (675)
Q Consensus       491 a~~~~~~~~~~~~~~-----------~~~~~------~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G-~I~~v  552 (675)
                      +.......+......           ...+.      ......+.++|||+|||..+++++    |+++|..|| .|..|
T Consensus       107 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~----l~~~f~~~G~~i~~v  182 (229)
T 2adc_A          107 SKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEED----LKVLFSSNGGVVKGF  182 (229)
T ss_dssp             CSCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHH----HHHHHHTTSCCEEEE
T ss_pred             ecCccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHH----HHHHHHHcCCCeeEE
Confidence            976532221111000           00000      011234579999999999999988    778899999 99999


Q ss_pred             EecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeC-CeeeEEeccccC
Q 045516          553 SVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIG-GYSLVVDEAKQR  601 (675)
Q Consensus       553 ~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~-Gr~l~V~~a~~r  601 (675)
                      +|+..     .+|||||+|.+.++|.+||. |||..|+ |+.|+|.|++++
T Consensus       183 ~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          183 KFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             EECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             EEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence            99763     27899999999999999998 9999999 999999999864

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.95  E-value=1.3e-27  Score=235.02  Aligned_cols=174  Identities=22%  Similarity=0.329  Sum_probs=144.8

Q ss_pred             CCceEEEcCCCC-CCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecc
Q 045516          415 GSKTLFVGNLPF-SVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       415 ~~~tlfV~nLp~-~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~  492 (675)
                      .+++|||+|||+ .+++++|+++|+.||.|..|+|+++.    +|||||+|.+.++|.+||. |||..|.|+.|.|.++.
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~   77 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   77 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEec
Confidence            358999999999 99999999999999999999999865    7899999999999999998 99999999999999997


Q ss_pred             ccCCCCCCCCCCCC-----------CCcc------CCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccC-cEEEEEe
Q 045516          493 ERGAYTPYSGGNES-----------NSFQ------KGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCG-EITRISV  554 (675)
Q Consensus       493 ~~~~~~~~~~~~~~-----------~~~~------~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G-~I~~v~i  554 (675)
                      ......+.......           ..+.      ......+.++|||+|||..+++++    |+++|..|| .|..|+|
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~----l~~~f~~~G~~v~~v~i  153 (198)
T 1qm9_A           78 HQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEED----LKVLFSSNGGVVKGFKF  153 (198)
T ss_dssp             CCSCCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHH----HHHHHHHTTSCCCEEEE
T ss_pred             CCCcCCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHH----HHHHHHHcCCCceEEEE
Confidence            65322221110000           0000      011234589999999999999988    778888999 9999999


Q ss_pred             cccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeC-CeeeEEeccccC
Q 045516          555 PKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIG-GYSLVVDEAKQR  601 (675)
Q Consensus       555 ~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~-Gr~l~V~~a~~r  601 (675)
                      +.+.     +|||||+|.+.++|.+||. |||..|+ |+.|+|.|++++
T Consensus       154 ~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          154 FQKD-----RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             SSTT-----SSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             EeCC-----CcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence            7752     7999999999999999998 9999999 999999998764

>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=99.95  E-value=2.1e-27  Score=248.06  Aligned_cols=161  Identities=21%  Similarity=0.349  Sum_probs=139.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEecc
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a~  492 (675)
                      ....++|||+|||+.+++++|++||..||.|..|+|+++..+ ++|||||+|.+.++|.+||.||+..|.|+.|.|.++.
T Consensus        38 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~-~~g~afV~f~~~~~A~~A~~~~~~~~~g~~i~v~~~~  116 (292)
T 2ghp_A           38 NRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK-NFRFARIEFARYDGALAAITKTHKVVGQNEIIVSHLT  116 (292)
T ss_dssp             ----CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS-SSEEEEEEESSHHHHHHHHTTTTCEETTEECEEEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCC-CcEEEEEEECCHHHHHHHHHhCCcEeCCcEEEEEECC
Confidence            456799999999999999999999999999999999998755 4899999999999999999999999999999998752


Q ss_pred             ccCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccC-cEEEEEecccCCCCCeeeEEEEEe
Q 045516          493 ERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCG-EITRISVPKDYDTGSVKGIAYLDF  571 (675)
Q Consensus       493 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G-~I~~v~i~~d~~tG~~rG~afV~F  571 (675)
                                               .++|||+|||+.+++++    |+++|..|| .|..|+|+++.. |.++|||||+|
T Consensus       117 -------------------------~~~l~v~nlp~~~t~~~----l~~~f~~~G~~i~~v~i~~~~~-~~~~g~afV~f  166 (292)
T 2ghp_A          117 -------------------------ECTLWMTNFPPSYTQRN----IRDLLQDINVVALSIRLPSLRF-NTSRRFAYIDV  166 (292)
T ss_dssp             -------------------------SCEEEEECCCTTCCHHH----HHHHHHHTTCCCCEEECC--------CCEEEEEC
T ss_pred             -------------------------CCEEEEECCCCCCCHHH----HHHHHHHhCCCeEEEEEEeCCC-CCcceEEEEEE
Confidence                                     68999999999999998    778888999 999999999866 88999999999


Q ss_pred             CCHHHHHHHHH-hCCceeCCeeeEEeccccCCCC
Q 045516          572 TDADSFNKALE-MSGTEIGGYSLVVDEAKQRGDF  604 (675)
Q Consensus       572 ~~~e~A~~Al~-lng~~~~Gr~l~V~~a~~r~~~  604 (675)
                      .+.+.|..||. |||..|+|+.|.|.++.+....
T Consensus       167 ~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~  200 (292)
T 2ghp_A          167 TSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKS  200 (292)
T ss_dssp             SSHHHHHHHHHHHTTCEETTEECEEEECCCC---
T ss_pred             CCHHHHHHHHHHhCCCEeCCcEEEEEECCCCccc
Confidence            99999999999 9999999999999999876543

>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=99.95  E-value=5.6e-27  Score=241.20  Aligned_cols=158  Identities=27%  Similarity=0.457  Sum_probs=143.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ....++|||+|||+++|+++|++||..||.|..|+|.+     ++|||||+|.+.++|.+||. |||..|.|+.|.|.++
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~-----~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a   93 (261)
T 3sde_A           19 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINR-----DRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFA   93 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEET-----TTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeC-----CCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeec
Confidence            45678999999999999999999999999999999975     38999999999999999997 9999999999999997


Q ss_pred             cccCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEe
Q 045516          492 RERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDF  571 (675)
Q Consensus       492 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F  571 (675)
                      ..                        ..+|||+|||+.+++++    |+.+|..||.|..|.|+++ .+|.++|||||+|
T Consensus        94 ~~------------------------~~~l~v~nl~~~~t~~~----l~~~F~~~G~i~~v~i~~~-~~g~~~g~afV~f  144 (261)
T 3sde_A           94 TH------------------------GAALTVKNLSPVVSNEL----LEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEF  144 (261)
T ss_dssp             CC------------------------SSEEEEESCCTTCCHHH----HHHHHGGGSCEEEEEEEEE-TTSCEEEEEEEEE
T ss_pred             cc------------------------CCcccccCCCCCCCHHH----HHHHHHhcCCeEEEEeeeC-CCCCcCcEEEEEe
Confidence            42                        47899999999999988    7788999999999999999 6899999999999


Q ss_pred             CCHHHHHHHHH-h-CCceeC---CeeeEEeccccCCCC
Q 045516          572 TDADSFNKALE-M-SGTEIG---GYSLVVDEAKQRGDF  604 (675)
Q Consensus       572 ~~~e~A~~Al~-l-ng~~~~---Gr~l~V~~a~~r~~~  604 (675)
                      .+.++|.+||. | ++..+.   ++.|.|.++.+....
T Consensus       145 ~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~~~~~~~~~  182 (261)
T 3sde_A          145 AAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDDE  182 (261)
T ss_dssp             SSHHHHHHHHHHHHHSCEESSSSCCBCEEEECCCEESS
T ss_pred             CCHHHHHHHHHHhcCCeEEecCCCceEEEeeccccCcc
Confidence            99999999998 7 555555   999999999876543

>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=99.95  E-value=8.8e-27  Score=242.32  Aligned_cols=155  Identities=20%  Similarity=0.335  Sum_probs=143.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEeccc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~  493 (675)
                      ..++|||+|||+.+++++|++||+.|| |..|.|     ++++|||||+|.+.++|.+||. |||..|.|+.|.|.+.. 
T Consensus        21 ~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~-----~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~~~-   93 (284)
T 3smz_A           21 NRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV-----DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQP-   93 (284)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEE-----ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC-
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEE-----ecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEecC-
Confidence            458999999999999999999999999 999988     4668999999999999999997 99999999999998742 


Q ss_pred             cCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCC
Q 045516          494 RGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTD  573 (675)
Q Consensus       494 ~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~  573 (675)
                                             ..++|||+|||+.+++++    |+++|..||.|..|.|+++..+|.++|||||+|.+
T Consensus        94 -----------------------~~~~l~v~nlp~~~t~~~----l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~  146 (284)
T 3smz_A           94 -----------------------TDALLCVANLPPSLTQQQ----FEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMK  146 (284)
T ss_dssp             -----------------------CSCEEEEESCCTTCCHHH----HHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESS
T ss_pred             -----------------------CCCEEEEcCCCCcCCHHH----HHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECC
Confidence                                   157999999999999998    77889999999999999999999999999999999


Q ss_pred             HHHHHHHHH-hCCceeCCeeeEEeccccCCC
Q 045516          574 ADSFNKALE-MSGTEIGGYSLVVDEAKQRGD  603 (675)
Q Consensus       574 ~e~A~~Al~-lng~~~~Gr~l~V~~a~~r~~  603 (675)
                      .++|..|+. |||..|+|+.|.|.++.+...
T Consensus       147 ~~~a~~A~~~l~~~~~~g~~i~v~~a~~~~~  177 (284)
T 3smz_A          147 KDSAARAKSDLLGKPLGPRTLYVHWTDAGQL  177 (284)
T ss_dssp             HHHHHHHHHHHTTCEETTEECEEEECCGGGC
T ss_pred             HHHHHHHHHHhCCCEeCCcEEEEEECCCCCC
Confidence            999999997 999999999999999987543

>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=99.84  E-value=2.8e-20  Score=176.14  Aligned_cols=150  Identities=19%  Similarity=0.237  Sum_probs=113.6

Q ss_pred             EEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEeccccCCCCCCCCCCCCCCccCCCCCCCceEEEE
Q 045516          445 DVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFI  523 (675)
Q Consensus       445 ~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV  523 (675)
                      .+.|+++.. +++|||||+|.+.+.|++||. +++....+..+.+.............     ............++|||
T Consensus         2 ~~kl~ln~~-~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~l~v   75 (158)
T 2kn4_A            2 QYKLILNGK-TLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGS-----HHHHHHMDVEGMTSLKV   75 (158)
T ss_dssp             EEEEEEECS-SCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEECCC-----CCSSCCCCCCBCCEEEE
T ss_pred             cEEEEecCc-cccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCccccccccccc-----cccccccCCCCCCEEEE
Confidence            456666543 689999999999999999997 77654444444433222111000000     00011112344789999


Q ss_pred             ecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEeccccCC
Q 045516          524 KGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVDEAKQRG  602 (675)
Q Consensus       524 ~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~~a~~r~  602 (675)
                      +|||+.+++++    |+.+|..||.|..|+|+++..+|.++|||||+|.+.+.|..||. |||..|+|+.|+|.++.++.
T Consensus        76 ~nl~~~~~~~~----l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  151 (158)
T 2kn4_A           76 DNLTYRTSPDT----LRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGR  151 (158)
T ss_dssp             ESCCTTCCHHH----HHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSS
T ss_pred             eCCCCCCCHHH----HHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCC
Confidence            99999999998    77888999999999999999999999999999999999999998 99999999999999998765


Q ss_pred             CC
Q 045516          603 DF  604 (675)
Q Consensus       603 ~~  604 (675)
                      ..
T Consensus       152 ~~  153 (158)
T 2kn4_A          152 PP  153 (158)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.83  E-value=3.9e-21  Score=211.17  Aligned_cols=86  Identities=24%  Similarity=0.456  Sum_probs=79.6

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      .+.++|||+||++.+++.+    |..||..||.|..|.|+.+..+|.++|||||+|.+.+.|..||. |||..|+|+.|.
T Consensus       100 ~~~~~lfV~nL~~~~te~~----L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~  175 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESK----LRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVL  175 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEE
Confidence            3468999999999999998    78899999999999999999999999999999999999999997 999999999999


Q ss_pred             EeccccCCCCC
Q 045516          595 VDEAKQRGDFG  605 (675)
Q Consensus       595 V~~a~~r~~~~  605 (675)
                      |.|+.++...+
T Consensus       176 V~~a~~~~~~~  186 (437)
T 3pgw_S          176 VDVERGRTVKG  186 (437)
T ss_pred             EEEeCCCCCCC
Confidence            99998766543

>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=99.83  E-value=9e-21  Score=169.97  Aligned_cols=108  Identities=28%  Similarity=0.502  Sum_probs=74.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEeccc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~  493 (675)
                      ..++|||+|||+++++++|++||+.||.|..|+|+++. +.++|||||+|.+.++|.+||. ||++.|.|+.|+|.++..
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~-~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~   82 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE-NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   82 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET-TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSC
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC-CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            35789999999999999999999999999999999986 4479999999999999999997 999999999999999876


Q ss_pred             cCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHH
Q 045516          494 RGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGED  533 (675)
Q Consensus       494 ~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~  533 (675)
                      +.......          ........+|||+|||+.+|++
T Consensus        83 ~~~~~~~~----------~~~~~~~~~lyv~Nl~~~~T~~  112 (115)
T 4f25_A           83 RKEREAEL----------GARAKEFTNVYIKNFGPGSTRA  112 (115)
T ss_dssp             CCC-------------------------------------
T ss_pred             cccccccc----------ccccCCCCceEeCCCCCCcccc
Confidence            54322111          1112235679999999999875

>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=99.79  E-value=2.8e-19  Score=155.81  Aligned_cols=80  Identities=34%  Similarity=0.602  Sum_probs=76.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      -+.++|||+|||+++|+++|+++|++||.|..|+|++++ +|+++|||||+|.+.++|.+||. |||..|.|+.|+|.++
T Consensus        17 ~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~A   96 (99)
T 4fxv_A           17 FQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYA   96 (99)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            356899999999999999999999999999999999997 89999999999999999999997 9999999999999998


Q ss_pred             cc
Q 045516          492 RE  493 (675)
Q Consensus       492 ~~  493 (675)
                      ++
T Consensus        97 kP   98 (99)
T 4fxv_A           97 RP   98 (99)
T ss_dssp             CB
T ss_pred             eC
Confidence            64

>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=99.78  E-value=1.3e-19  Score=182.36  Aligned_cols=79  Identities=22%  Similarity=0.327  Sum_probs=74.7

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccC--cEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCG--EITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G--~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      .++|||+||++.+++++    |+++|..||  .|..|+|+++..+|+++|||||+|.+.++|.+||. ||+..|+|+.|+
T Consensus        68 ~~~lfVgnL~~~~te~~----L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~  143 (229)
T 3q2s_C           68 RIALYIGNLTWWTTDED----LTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPV  143 (229)
T ss_dssp             -CEEEEESCCTTCCHHH----HHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCE
T ss_pred             ccEEEEeCCCCCCCHHH----HHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeE
Confidence            67999999999999998    778899999  99999999999999999999999999999999998 999999999999


Q ss_pred             Eecccc
Q 045516          595 VDEAKQ  600 (675)
Q Consensus       595 V~~a~~  600 (675)
                      |.++.+
T Consensus       144 V~~a~~  149 (229)
T 3q2s_C          144 VTPVNK  149 (229)
T ss_dssp             EEECCH
T ss_pred             EEECCC
Confidence            999864

>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=99.78  E-value=2.8e-19  Score=179.85  Aligned_cols=80  Identities=18%  Similarity=0.380  Sum_probs=74.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCC--CeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEE
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVA--EVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLD  489 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G--~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~  489 (675)
                      ...++|||+|||+++|+++|++||..||  .|..|+|++++ +++++|||||+|.+.++|.+||. ||++.|.|+.|+|.
T Consensus        66 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~  145 (229)
T 3q2s_C           66 GKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVT  145 (229)
T ss_dssp             ---CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEE
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEE
Confidence            3678999999999999999999999999  99999999997 89999999999999999999998 99999999999999


Q ss_pred             eccc
Q 045516          490 FARE  493 (675)
Q Consensus       490 ~a~~  493 (675)
                      ++..
T Consensus       146 ~a~~  149 (229)
T 3q2s_C          146 PVNK  149 (229)
T ss_dssp             ECCH
T ss_pred             ECCC
Confidence            9864

>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=99.77  E-value=7.8e-19  Score=164.84  Aligned_cols=137  Identities=18%  Similarity=0.266  Sum_probs=111.4

Q ss_pred             CCcccEEEEEecCHHHHHHHHH-h-CCcccCCeeEEEEeccccCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcC
Q 045516          454 GRFKGYGHVEFASVEDAHKAIE-L-NGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVG  531 (675)
Q Consensus       454 g~~kG~afV~F~~~e~A~~Al~-l-~g~~~~gr~i~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~t  531 (675)
                      ...+|+++|+|.+.+.|++||. | ||..|.| .|.+.++..+.........  .............++|||+|||+.++
T Consensus        10 ~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~~--~~~~~~~~~~~~~~~l~V~nl~~~~t   86 (150)
T 2i2y_A           10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGSHH--HHHHMHRDSCPLDCKVYVGNLGNNGN   86 (150)
T ss_dssp             SSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSSSS--CCCCSCSSSSTTSCEEEEESCCSCCS
T ss_pred             ccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCcccccccccc--ccccccccCCCCCCEEEEeCCCCCCC
Confidence            4679999999999999999997 8 9999999 9999988654321111000  00111122334579999999999999


Q ss_pred             HHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEeccccCC
Q 045516          532 EDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVDEAKQRG  602 (675)
Q Consensus       532 e~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~~a~~r~  602 (675)
                      +++    |+.+|..||.|..|+|+++     ++|||||+|.+.++|..||. |||..|+|+.|+|.|+.++.
T Consensus        87 ~~~----l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  149 (150)
T 2i2y_A           87 KTE----LERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEK  149 (150)
T ss_dssp             CHH----HHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCCC
T ss_pred             HHH----HHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCCC
Confidence            998    7788899999999999987     58999999999999999998 99999999999999998753

>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=99.75  E-value=3.5e-18  Score=161.49  Aligned_cols=80  Identities=31%  Similarity=0.512  Sum_probs=75.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ...++|||+|||+++++++|++||..||.|..|+|+.+. ++.++|||||+|.+.++|.+||. ||+..|.|+.|+|.++
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  116 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD  116 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            457899999999999999999999999999999999998 79999999999999999999998 9999999999999988


Q ss_pred             cc
Q 045516          492 RE  493 (675)
Q Consensus       492 ~~  493 (675)
                      ..
T Consensus       117 ~~  118 (156)
T 1h2v_Z          117 AG  118 (156)
T ss_dssp             SC
T ss_pred             CC
Confidence            53

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.75  E-value=4.9e-18  Score=150.84  Aligned_cols=79  Identities=16%  Similarity=0.205  Sum_probs=75.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~  492 (675)
                      ..++|||+|||+++++++|+++|++||.|..|+|+++. +++++|||||+|.+.++|.+||. |||..|.|+.|+|.++.
T Consensus         5 p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a~   84 (110)
T 3s8s_A            5 PLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDI   84 (110)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            46899999999999999999999999999999999998 79999999999999999999997 99999999999999985


Q ss_pred             c
Q 045516          493 E  493 (675)
Q Consensus       493 ~  493 (675)
                      .
T Consensus        85 ~   85 (110)
T 3s8s_A           85 K   85 (110)
T ss_dssp             T
T ss_pred             C
Confidence            4

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.74  E-value=1.1e-18  Score=149.56  Aligned_cols=80  Identities=19%  Similarity=0.405  Sum_probs=74.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhhCC-CeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-h-CCcccCCeeEEEEec
Q 045516          416 SKTLFVGNLPFSVEQADVQNFFSEVA-EVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-L-NGQMLGNRAIRLDFA  491 (675)
Q Consensus       416 ~~tlfV~nLp~~~te~~L~~~F~~~G-~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l-~g~~~~gr~i~V~~a  491 (675)
                      +++|||+|||+++|+++|+++|++|| .|.+|+|++++ +|+++|||||+|.+.++|.+||+ | |+..|+|++|+|.++
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a   80 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEc
Confidence            47999999999999999999999999 89999999997 89999999999999999999997 5 567899999999999


Q ss_pred             cccC
Q 045516          492 RERG  495 (675)
Q Consensus       492 ~~~~  495 (675)
                      .++.
T Consensus        81 ~~~~   84 (91)
T 2lxi_A           81 DPKP   84 (91)
T ss_dssp             CSCC
T ss_pred             CCCC
Confidence            7654

>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=99.74  E-value=6e-18  Score=159.87  Aligned_cols=84  Identities=17%  Similarity=0.313  Sum_probs=78.5

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      ...++|||+|||..+++++    |+.+|..||.|..|.|+++..++.++|||||+|.+.++|..||. ||+..|+|+.|+
T Consensus        37 ~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~  112 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQ----IYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIR  112 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHH----HHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            3479999999999999998    78899999999999999999999999999999999999999998 999999999999


Q ss_pred             EeccccCCC
Q 045516          595 VDEAKQRGD  603 (675)
Q Consensus       595 V~~a~~r~~  603 (675)
                      |.|+.+...
T Consensus       113 V~~a~~~~~  121 (156)
T 1h2v_Z          113 TDWDAGFKE  121 (156)
T ss_dssp             EEEESCCCT
T ss_pred             EEECCCCCC
Confidence            999986544

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=1.5e-17  Score=144.45  Aligned_cols=84  Identities=20%  Similarity=0.472  Sum_probs=79.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a  491 (675)
                      ....++|||+|||+++++++|+++|..||.|..|+|+++. +++++|||||+|.+.++|.+||.||+..|.|+.|+|.++
T Consensus         7 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~l~V~~a   86 (99)
T 2dgs_A            7 GSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDIMGKKVEVKRA   86 (99)
T ss_dssp             CSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHHHCCCBSSSCBCEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            4567999999999999999999999999999999999997 799999999999999999999999999999999999999


Q ss_pred             cccCC
Q 045516          492 RERGA  496 (675)
Q Consensus       492 ~~~~~  496 (675)
                      ..+..
T Consensus        87 ~~~~~   91 (99)
T 2dgs_A           87 EPRDS   91 (99)
T ss_dssp             CCCCC
T ss_pred             CCCcc
Confidence            87653

>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=99.74  E-value=1.8e-17  Score=145.55  Aligned_cols=85  Identities=27%  Similarity=0.408  Sum_probs=79.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCC---eeEEE
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGN---RAIRL  488 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~g---r~i~V  488 (675)
                      ....++|||+|||+++++++|+++|..||.|..|+|+++.+++++|||||+|.+.++|.+||. ||+..|.|   +.|+|
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V   91 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVV   91 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEE
Confidence            345799999999999999999999999999999999999999999999999999999999997 99999998   99999


Q ss_pred             EeccccCCC
Q 045516          489 DFARERGAY  497 (675)
Q Consensus       489 ~~a~~~~~~  497 (675)
                      .++......
T Consensus        92 ~~a~~~~~~  100 (105)
T 2dnh_A           92 KFADTDKES  100 (105)
T ss_dssp             EESCSSCCC
T ss_pred             EECccCccc
Confidence            999876543

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.73  E-value=2.1e-17  Score=143.94  Aligned_cols=83  Identities=24%  Similarity=0.454  Sum_probs=78.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ....++|||+|||+++++++|+++|..||.|..|+|+.+.+++++|||||+|.+.++|.+||. ||+..|.|+.|+|.++
T Consensus        14 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   93 (100)
T 2do4_A           14 SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAIS   93 (100)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            456789999999999999999999999999999999999999999999999999999999997 9999999999999999


Q ss_pred             cccC
Q 045516          492 RERG  495 (675)
Q Consensus       492 ~~~~  495 (675)
                      .++.
T Consensus        94 ~~~~   97 (100)
T 2do4_A           94 NSGP   97 (100)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            7653

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.73  E-value=3.7e-18  Score=147.32  Aligned_cols=80  Identities=23%  Similarity=0.373  Sum_probs=73.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCC--eEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCc----ccCCee
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAE--VVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQ----MLGNRA  485 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~--I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~----~~~gr~  485 (675)
                      ....||||+|||+++|+++|+++|++||.  |.+|+|++++ +|+++|||||+|.+.++|.+||+ |||.    .|+||+
T Consensus         7 ~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~   86 (95)
T 2lkz_A            7 HHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKT   86 (95)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEE
T ss_pred             CccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEE
Confidence            45689999999999999999999999995  6799999998 89999999999999999999998 9987    489999


Q ss_pred             EEEEeccc
Q 045516          486 IRLDFARE  493 (675)
Q Consensus       486 i~V~~a~~  493 (675)
                      |.|.|++.
T Consensus        87 i~V~~Aks   94 (95)
T 2lkz_A           87 IGVDFAKS   94 (95)
T ss_dssp             EEEEECCC
T ss_pred             EEEEEccC
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=99.73  E-value=1.5e-17  Score=139.39  Aligned_cols=79  Identities=32%  Similarity=0.603  Sum_probs=75.4

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEeccc
Q 045516          416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       416 ~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~  493 (675)
                      +++|||+|||+++++++|+++|..||.|..|+|+++. +++++|||||+|.+.++|.+||. |||..|.|+.|+|.++.+
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   80 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK   80 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCc
Confidence            4799999999999999999999999999999999996 89999999999999999999998 999999999999999976


Q ss_pred             c
Q 045516          494 R  494 (675)
Q Consensus       494 ~  494 (675)
                      +
T Consensus        81 ~   81 (83)
T 3md1_A           81 L   81 (83)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.73  E-value=2.4e-17  Score=141.99  Aligned_cols=83  Identities=35%  Similarity=0.627  Sum_probs=78.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ...++|||+|||+.+++++|+++|..||.|..|+|+++. +++++|||||+|.+.++|.+||. ||+..|.|+.|+|.++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   82 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHV   82 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            357899999999999999999999999999999999997 79999999999999999999998 9999999999999999


Q ss_pred             cccCC
Q 045516          492 RERGA  496 (675)
Q Consensus       492 ~~~~~  496 (675)
                      ..+..
T Consensus        83 ~~~~~   87 (95)
T 2dnz_A           83 TERLD   87 (95)
T ss_dssp             SCCCC
T ss_pred             ccccC
Confidence            77643

>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=99.73  E-value=2.6e-17  Score=142.96  Aligned_cols=84  Identities=27%  Similarity=0.451  Sum_probs=78.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      ....++|||+|||+++++++|+++|..||.|..|+|+++. +++++|||||+|.+.++|.+||. ||+..|.|+.|+|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   84 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            3467999999999999999999999999999999999998 89999999999999999999996 999999999999999


Q ss_pred             ccccCC
Q 045516          491 ARERGA  496 (675)
Q Consensus       491 a~~~~~  496 (675)
                      +..+..
T Consensus        85 a~~~~~   90 (99)
T 1whw_A           85 STIKKE   90 (99)
T ss_dssp             CCCCST
T ss_pred             cCCCcc
Confidence            987654

>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=99.73  E-value=1.3e-17  Score=141.08  Aligned_cols=81  Identities=36%  Similarity=0.623  Sum_probs=74.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ...++|||+|||+++++++|+++|+.||.|..|+|+++. +++++|||||+|.+.++|.+||. |||..|.|+.|+|.++
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA   83 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEec
Confidence            356899999999999999999999999999999999997 89999999999999999999998 9999999999999998


Q ss_pred             ccc
Q 045516          492 RER  494 (675)
Q Consensus       492 ~~~  494 (675)
                      ..+
T Consensus        84 ~~k   86 (87)
T 3bs9_A           84 TRK   86 (87)
T ss_dssp             C--
T ss_pred             CCC
Confidence            754

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=8.8e-18  Score=147.32  Aligned_cols=80  Identities=20%  Similarity=0.414  Sum_probs=75.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEeccc
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a~~  493 (675)
                      ...++|||+|||+++|+++|+++|++||.|..|+|+++..|+++|||||+|.+.++|.+||.+|+..|.|+.|.|.++..
T Consensus         9 ~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~~~~~~~~gr~l~V~~~~~   88 (103)
T 1s79_A            9 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKDD   88 (103)
T ss_dssp             SGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHTSSCCCCTTTTCEEEEHHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHHcCCCEECCEEEEEEEchH
Confidence            34689999999999999999999999999999999999889999999999999999999999999999999999998764

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=1.4e-17  Score=145.79  Aligned_cols=84  Identities=24%  Similarity=0.430  Sum_probs=79.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      ....++|||+|||+++++++|++||..||.|..|+|+++. +++++|||||+|.+.++|.+||. ||+..|.|+.|+|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (103)
T 2cq0_A           12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   91 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            3467999999999999999999999999999999999997 89999999999999999999998 999999999999999


Q ss_pred             ccccCC
Q 045516          491 ARERGA  496 (675)
Q Consensus       491 a~~~~~  496 (675)
                      +..+..
T Consensus        92 a~~~~~   97 (103)
T 2cq0_A           92 AKPSTN   97 (103)
T ss_dssp             SSCCCC
T ss_pred             CCCCCC
Confidence            987653

>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=99.72  E-value=1.9e-17  Score=140.19  Aligned_cols=79  Identities=27%  Similarity=0.556  Sum_probs=74.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a  491 (675)
                      ....++|||+|||+++++++|+++|.+||.|..|+|+++. +|+++|||||+|.+.++|.+||.+++..|.|+.|.|.++
T Consensus         8 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~i~v~~A   87 (87)
T 3s7r_A            8 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKEHRLDGRVIDPKKA   87 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHSSCEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            4567999999999999999999999999999999999997 799999999999999999999998999999999999875

>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=99.72  E-value=3e-17  Score=145.62  Aligned_cols=85  Identities=25%  Similarity=0.425  Sum_probs=79.2

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hC------CcccCC
Q 045516          412 QSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LN------GQMLGN  483 (675)
Q Consensus       412 ~~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~------g~~~~g  483 (675)
                      .....++|||+|||+++++++|+.+|..||.|..|+|+++. +++++|||||+|.+.++|.+||. ||      +..|.|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g   90 (111)
T 1x4h_A           11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   90 (111)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             cCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcC
Confidence            34568999999999999999999999999999999999997 79999999999999999999998 99      999999


Q ss_pred             eeEEEEeccccCC
Q 045516          484 RAIRLDFARERGA  496 (675)
Q Consensus       484 r~i~V~~a~~~~~  496 (675)
                      +.|+|.++..+..
T Consensus        91 ~~l~v~~a~~~~~  103 (111)
T 1x4h_A           91 RQLKVDLAVTRDE  103 (111)
T ss_dssp             CEEEEECCCCCCC
T ss_pred             EEEEEEECCCCcc
Confidence            9999999987643

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.72  E-value=5e-17  Score=145.26  Aligned_cols=84  Identities=33%  Similarity=0.594  Sum_probs=79.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      ....++|||+|||+.+++++|++||..||.|..|+|+++. ++.++|||||+|.+.++|.+||. ||+..|.|+.|+|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (115)
T 2dgo_A           12 TSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNW   91 (115)
T ss_dssp             STTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4567999999999999999999999999999999999997 89999999999999999999997 999999999999999


Q ss_pred             ccccCC
Q 045516          491 ARERGA  496 (675)
Q Consensus       491 a~~~~~  496 (675)
                      +..+..
T Consensus        92 a~~~~~   97 (115)
T 2dgo_A           92 ATRKPP   97 (115)
T ss_dssp             SSCCCC
T ss_pred             ccCCCC
Confidence            987654

>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=99.72  E-value=2.3e-17  Score=147.48  Aligned_cols=84  Identities=23%  Similarity=0.423  Sum_probs=78.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      ....++|||+|||+++++++|++||..||.|..|+|+++. +++++|||||+|.+.++|.+||. ||+..|.|+.|+|.+
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  101 (115)
T 2cpz_A           22 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQL  101 (115)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            3457899999999999999999999999999999999998 89999999999999999999997 999999999999999


Q ss_pred             ccccCC
Q 045516          491 ARERGA  496 (675)
Q Consensus       491 a~~~~~  496 (675)
                      +..+..
T Consensus       102 a~~~~~  107 (115)
T 2cpz_A          102 KRSKND  107 (115)
T ss_dssp             CCCSCC
T ss_pred             cCCCCc
Confidence            987654

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=1.9e-17  Score=144.96  Aligned_cols=84  Identities=26%  Similarity=0.418  Sum_probs=78.9

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEE
Q 045516          412 QSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLD  489 (675)
Q Consensus       412 ~~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~  489 (675)
                      .....++|||+|||+++++++|++||..||.|..|+|+++. +++++|||||+|.+.++|.+||. ||+..|.|+.|+|.
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2dnm_A            9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQ   88 (103)
T ss_dssp             CCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            35568999999999999999999999999999999999997 79999999999999999999998 99999999999999


Q ss_pred             eccccC
Q 045516          490 FARERG  495 (675)
Q Consensus       490 ~a~~~~  495 (675)
                      ++....
T Consensus        89 ~a~~~~   94 (103)
T 2dnm_A           89 VARYGR   94 (103)
T ss_dssp             ECSSCC
T ss_pred             ECCcCC
Confidence            997654

>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=99.72  E-value=5.2e-18  Score=144.88  Aligned_cols=79  Identities=16%  Similarity=0.354  Sum_probs=70.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhCC--CeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecc
Q 045516          417 KTLFVGNLPFSVEQADVQNFFSEVA--EVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       417 ~tlfV~nLp~~~te~~L~~~F~~~G--~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~  492 (675)
                      .+|||+|||+++++++|+++|+.||  .|..|+|++++ +|+++|||||+|.+.++|.+||+ |||..|.|+.|+|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            5899999999999999999999999  99999999997 89999999999999999999997 99999999999999987


Q ss_pred             ccC
Q 045516          493 ERG  495 (675)
Q Consensus       493 ~~~  495 (675)
                      +..
T Consensus        82 ~~~   84 (90)
T 3p5t_L           82 KLE   84 (90)
T ss_dssp             ---
T ss_pred             CCc
Confidence            654

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=1.7e-17  Score=143.19  Aligned_cols=83  Identities=33%  Similarity=0.604  Sum_probs=78.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEE-EEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDV-RLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v-~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      ...++|||+|||+++++++|+++|..||.|..| +|+++. ++.++|||||+|.+.++|.+||. ||+..|.|+.|+|.+
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSY   82 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            357899999999999999999999999999999 999995 89999999999999999999998 999999999999999


Q ss_pred             ccccCC
Q 045516          491 ARERGA  496 (675)
Q Consensus       491 a~~~~~  496 (675)
                      +..+..
T Consensus        83 a~~~~~   88 (96)
T 1x5t_A           83 AFKKDS   88 (96)
T ss_dssp             SCCCCC
T ss_pred             ecccCC
Confidence            987653

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=2.6e-17  Score=144.77  Aligned_cols=83  Identities=34%  Similarity=0.525  Sum_probs=78.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      ....++|||+|||+.+++++|+++|..||.|..|+|+.+. +|.++|||||+|.+.++|.+||. |||..|.|+.|+|.+
T Consensus        20 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   99 (106)
T 1p27_B           20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW   99 (106)
T ss_dssp             BTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEe
Confidence            4567999999999999999999999999999999999997 79999999999999999999998 999999999999999


Q ss_pred             ccccC
Q 045516          491 ARERG  495 (675)
Q Consensus       491 a~~~~  495 (675)
                      +..+.
T Consensus       100 a~~~~  104 (106)
T 1p27_B          100 CFVRG  104 (106)
T ss_dssp             SEESS
T ss_pred             ecCCC
Confidence            97653

>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=99.72  E-value=3.4e-17  Score=143.79  Aligned_cols=84  Identities=31%  Similarity=0.476  Sum_probs=79.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      ....++|||+|||+++++++|++||.+||.|..|+|+++. +++++|||||+|.+.++|.+||. ||+..|.|+.|+|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   91 (105)
T 1x5u_A           12 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNK   91 (105)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            4567999999999999999999999999999999999998 89999999999999999999998 999999999999999


Q ss_pred             ccccCC
Q 045516          491 ARERGA  496 (675)
Q Consensus       491 a~~~~~  496 (675)
                      +.....
T Consensus        92 a~~~~~   97 (105)
T 1x5u_A           92 ASAHNK   97 (105)
T ss_dssp             TTTTSC
T ss_pred             CCCCCc
Confidence            976643

>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=99.71  E-value=1.8e-17  Score=139.62  Aligned_cols=79  Identities=29%  Similarity=0.525  Sum_probs=74.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ...++|||+|||+.+++++|+++|.+||.|..|+|+++. +++++|||||+|.+.++|.+||. |||..|.|+.|+|.++
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   84 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   84 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            457999999999999999999999999999999999985 89999999999999999999996 9999999999999987


Q ss_pred             c
Q 045516          492 R  492 (675)
Q Consensus       492 ~  492 (675)
                      +
T Consensus        85 k   85 (85)
T 3mdf_A           85 K   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.71  E-value=1.2e-17  Score=145.82  Aligned_cols=99  Identities=19%  Similarity=0.393  Sum_probs=82.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEeccccC
Q 045516          417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARERG  495 (675)
Q Consensus       417 ~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~~~  495 (675)
                      ++|||+|||+++++++|+++|++||.|..|+|+.+    ++|||||+|.+.++|.+||. ||+..|.|+.|+|.++....
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   76 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMP   76 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCC
Confidence            58999999999999999999999999999999976    79999999999999999998 99999999999999998765


Q ss_pred             CCCCCCCCCCCCCccCCCCCCCceEEEEecCC
Q 045516          496 AYTPYSGGNESNSFQKGGRGQAAHTIFIKGFD  527 (675)
Q Consensus       496 ~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp  527 (675)
                      ......        ....+.....+|||+||+
T Consensus        77 ~~~~~~--------~~~~~~~~~~~ifvg~L~  100 (101)
T 2hvz_A           77 RRSRFD--------RPPARRKLLEVLFNGPLE  100 (101)
T ss_dssp             CSSCCC--------SCCCSCCCCSCCCSCCCC
T ss_pred             CcccCC--------CCCccccCCCceecCCCC
Confidence            322111        011122336789999986

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.71  E-value=6e-18  Score=147.59  Aligned_cols=81  Identities=27%  Similarity=0.461  Sum_probs=76.6

Q ss_pred             CCCceEEEcCCCC------CCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCC-e
Q 045516          414 GGSKTLFVGNLPF------SVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGN-R  484 (675)
Q Consensus       414 ~~~~tlfV~nLp~------~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~g-r  484 (675)
                      +..++|||+|||+      .+++++|+++|++||.|..|+|+++. +|+++|||||+|.+.++|.+||. |||..|.| +
T Consensus         4 ~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r   83 (100)
T 3ns6_A            4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKH   83 (100)
T ss_dssp             CGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSC
T ss_pred             CcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCe
Confidence            4468999999999      99999999999999999999999998 69999999999999999999997 99999999 9


Q ss_pred             eEEEEecccc
Q 045516          485 AIRLDFARER  494 (675)
Q Consensus       485 ~i~V~~a~~~  494 (675)
                      .|+|.++.++
T Consensus        84 ~l~V~~a~~~   93 (100)
T 3ns6_A           84 RLFLYTMKDV   93 (100)
T ss_dssp             BCEEEESHHH
T ss_pred             EEEEEECchh
Confidence            9999998764

>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=99.71  E-value=2.1e-17  Score=142.28  Aligned_cols=80  Identities=30%  Similarity=0.449  Sum_probs=76.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ....++|||+|||+.+++++|+++|..||.|..|+|+++.+++++|||||+|.+.++|.+||. ||+..|.|+.|+|.++
T Consensus        13 ~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   92 (95)
T 2ywk_A           13 EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGP   92 (95)
T ss_dssp             TTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEEc
Confidence            346799999999999999999999999999999999999889999999999999999999998 9999999999999987


Q ss_pred             c
Q 045516          492 R  492 (675)
Q Consensus       492 ~  492 (675)
                      .
T Consensus        93 ~   93 (95)
T 2ywk_A           93 S   93 (95)
T ss_dssp             C
T ss_pred             C
Confidence            5

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=3e-17  Score=143.34  Aligned_cols=84  Identities=30%  Similarity=0.592  Sum_probs=78.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      ....++|||+|||+++++++|+++|..||.|..|+|+++. +++++|||||+|.+.++|.+||. ||+..|.|+.|+|.+
T Consensus         9 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   88 (102)
T 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQ   88 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            3467999999999999999999999999999999999987 78999999999999999999996 999999999999999


Q ss_pred             ccccCC
Q 045516          491 ARERGA  496 (675)
Q Consensus       491 a~~~~~  496 (675)
                      +.....
T Consensus        89 a~~~~~   94 (102)
T 1x5s_A           89 AGKSSD   94 (102)
T ss_dssp             EECCCC
T ss_pred             CCCCCC
Confidence            986643

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.71  E-value=4.7e-17  Score=143.36  Aligned_cols=84  Identities=30%  Similarity=0.574  Sum_probs=78.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeC-C-CCCcccEEEEEecCHHHHHHHHH-h-CCcccCCeeEEE
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-A-DGRFKGYGHVEFASVEDAHKAIE-L-NGQMLGNRAIRL  488 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~-~-~g~~kG~afV~F~~~e~A~~Al~-l-~g~~~~gr~i~V  488 (675)
                      ....++|||+|||+++++++|++||..||.|..|+|+++ . +++++|||||+|.+.++|.+||. | |+..|.|+.|+|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v   91 (107)
T 2cph_A           12 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   91 (107)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEEE
Confidence            456799999999999999999999999999999999998 4 89999999999999999999998 8 999999999999


Q ss_pred             EeccccCC
Q 045516          489 DFARERGA  496 (675)
Q Consensus       489 ~~a~~~~~  496 (675)
                      .++..+..
T Consensus        92 ~~a~~~~~   99 (107)
T 2cph_A           92 EWADSEVT   99 (107)
T ss_dssp             EECCCCCC
T ss_pred             EeCCCCCC
Confidence            99987643

>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=99.71  E-value=2.9e-17  Score=141.94  Aligned_cols=81  Identities=27%  Similarity=0.635  Sum_probs=76.9

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEeccc
Q 045516          416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       416 ~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~  493 (675)
                      +++|||+|||+.+++++|+++|+.||.|..|+|+.+. +|+++|||||+|.+.++|.+||. |||..|.|+.|+|.++..
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   81 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSN   81 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCC
Confidence            5899999999999999999999999999999999997 79999999999999999999997 999999999999999987


Q ss_pred             cCC
Q 045516          494 RGA  496 (675)
Q Consensus       494 ~~~  496 (675)
                      +..
T Consensus        82 ~~~   84 (96)
T 2x1f_A           82 SDI   84 (96)
T ss_dssp             SSG
T ss_pred             CCC
Confidence            643

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=3.7e-17  Score=140.68  Aligned_cols=81  Identities=30%  Similarity=0.404  Sum_probs=76.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      ....++|||+|||+.+++++|+++|..||.|..|+|+++. +++++|||||+|.+.++|.+||. ||+..|.|+.|+|.+
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (95)
T 2cqc_A           12 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSG   91 (95)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            4467999999999999999999999999999999999997 78999999999999999999998 999999999999999


Q ss_pred             ccc
Q 045516          491 ARE  493 (675)
Q Consensus       491 a~~  493 (675)
                      +..
T Consensus        92 a~~   94 (95)
T 2cqc_A           92 PSS   94 (95)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            853

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=5.1e-17  Score=142.21  Aligned_cols=83  Identities=25%  Similarity=0.491  Sum_probs=78.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ....++|||+|||+++++++|++||..||.|..|+|+.+ ++.++|||||+|.+.++|.+||. ||+..|.|+.|+|.++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   90 (103)
T 2d9p_A           12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALA   90 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEe
Confidence            346799999999999999999999999999999999999 89999999999999999999998 9999999999999999


Q ss_pred             cccCC
Q 045516          492 RERGA  496 (675)
Q Consensus       492 ~~~~~  496 (675)
                      ..+..
T Consensus        91 ~~~~~   95 (103)
T 2d9p_A           91 QRKEE   95 (103)
T ss_dssp             SSCCC
T ss_pred             ccccc
Confidence            87653

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.71  E-value=4.6e-17  Score=141.50  Aligned_cols=80  Identities=26%  Similarity=0.510  Sum_probs=75.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEE--------EEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccC
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVD--------VRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLG  482 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~--------v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~  482 (675)
                      ....++|||+|||+++++++|+++|+.||.|..        |+|++++ +|+++|||||+|.+.++|.+||. |||..|.
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~   89 (99)
T 2la6_A           10 HSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   89 (99)
T ss_dssp             CCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeC
Confidence            456799999999999999999999999999999        9999996 89999999999999999999997 9999999


Q ss_pred             CeeEEEEecc
Q 045516          483 NRAIRLDFAR  492 (675)
Q Consensus       483 gr~i~V~~a~  492 (675)
                      |+.|+|.++.
T Consensus        90 g~~l~V~~A~   99 (99)
T 2la6_A           90 GNPIKVSFAT   99 (99)
T ss_dssp             SSBCEEEECC
T ss_pred             CcEEEEEecC
Confidence            9999999873

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.71  E-value=4.1e-17  Score=140.23  Aligned_cols=80  Identities=29%  Similarity=0.471  Sum_probs=75.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      ....++|||+|||+.+++++|+++|..||.|..|+|+.+. +++++|||||+|.+.++|.+||. ||+..|.|+.|+|.+
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   92 (94)
T 2e5h_A           13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASI   92 (94)
T ss_dssp             CCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEe
Confidence            4567899999999999999999999999999999999997 68999999999999999999997 999999999999998


Q ss_pred             cc
Q 045516          491 AR  492 (675)
Q Consensus       491 a~  492 (675)
                      ++
T Consensus        93 ak   94 (94)
T 2e5h_A           93 AI   94 (94)
T ss_dssp             CC
T ss_pred             cC
Confidence            73

>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=99.71  E-value=8.4e-17  Score=176.67  Aligned_cols=82  Identities=22%  Similarity=0.470  Sum_probs=76.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      ....++|||+|||+.||+++|..||..||.|..|.|+.+. +|.++|||||+|.+.++|.+||. |||+.|.|+.|.|.|
T Consensus        99 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~  178 (437)
T 3pgw_S           99 GDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  178 (437)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            3456899999999999999999999999999999999996 89999999999999999999997 999999999999999


Q ss_pred             cccc
Q 045516          491 ARER  494 (675)
Q Consensus       491 a~~~  494 (675)
                      +...
T Consensus       179 a~~~  182 (437)
T 3pgw_S          179 ERGR  182 (437)
T ss_pred             eCCC
Confidence            8643

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=2.2e-17  Score=144.20  Aligned_cols=84  Identities=27%  Similarity=0.483  Sum_probs=78.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      ....++|||+|||+.+++++|+++|..||.|..|+|+++. +++++|||||+|.+.++|.+||. ||+..|.|+.|+|.+
T Consensus         9 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   88 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEe
Confidence            3467999999999999999999999999999999999986 89999999999999999999997 999999999999999


Q ss_pred             ccccCC
Q 045516          491 ARERGA  496 (675)
Q Consensus       491 a~~~~~  496 (675)
                      +.....
T Consensus        89 a~~~~~   94 (102)
T 2cqb_A           89 AKPMRI   94 (102)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            987643

>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=99.70  E-value=1.9e-17  Score=145.01  Aligned_cols=82  Identities=29%  Similarity=0.472  Sum_probs=76.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEecc
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a~  492 (675)
                      ....++|||+|||+.+++++|++||..|| |+.|+|+++.+++++|||||+|.+.++|.+||.+|+..|.||.|.|.++.
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G-~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~~~   90 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLNS   90 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESSSSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcC-ceEEEEEECCCCCEeeEEEEEECCHHHHHHHHHhCCCeECCcEEEEEECC
Confidence            45678999999999999999999999999 45999999999999999999999999999999999999999999999887


Q ss_pred             ccC
Q 045516          493 ERG  495 (675)
Q Consensus       493 ~~~  495 (675)
                      ...
T Consensus        91 ~~~   93 (102)
T 1wez_A           91 TAG   93 (102)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=99.70  E-value=6.1e-17  Score=145.20  Aligned_cols=83  Identities=23%  Similarity=0.441  Sum_probs=78.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecc
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~  492 (675)
                      ...++|||+|||+++++++|+++|+.||.|..|.|+.+.+|+++|||||+|.+.++|.+||. |||..|.|+.|.|.++.
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   84 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAK   84 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            45689999999999999999999999999999999999999999999999999999999997 99999999999999998


Q ss_pred             ccCC
Q 045516          493 ERGA  496 (675)
Q Consensus       493 ~~~~  496 (675)
                      ....
T Consensus        85 ~~~~   88 (116)
T 2fy1_A           85 KPSF   88 (116)
T ss_dssp             CSSC
T ss_pred             CCCC
Confidence            7653

>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=99.70  E-value=4.1e-17  Score=144.38  Aligned_cols=82  Identities=35%  Similarity=0.649  Sum_probs=77.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      ....++|||+|||+.+++++|+++|+.||.|..|+|+++. +|+++|||||+|.+.++|.+||. |||..|.|+.|+|.+
T Consensus        23 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~  102 (108)
T 2jrs_A           23 SAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGH  102 (108)
T ss_dssp             CSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            4577999999999999999999999999999999999986 79999999999999999999997 999999999999999


Q ss_pred             cccc
Q 045516          491 ARER  494 (675)
Q Consensus       491 a~~~  494 (675)
                      +..+
T Consensus       103 a~~k  106 (108)
T 2jrs_A          103 VTER  106 (108)
T ss_dssp             SCSS
T ss_pred             cccC
Confidence            8765

>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=99.70  E-value=9.5e-17  Score=140.48  Aligned_cols=83  Identities=31%  Similarity=0.581  Sum_probs=77.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ....++|||+|||+++++++|++||..||.|..|+|+++..+ ++|||||+|.+.++|.+||. ||+..|.|+.|+|.++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~-~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   90 (103)
T 2cq3_A           12 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   90 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCC-CcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            456799999999999999999999999999999999988754 89999999999999999997 9999999999999999


Q ss_pred             cccCC
Q 045516          492 RERGA  496 (675)
Q Consensus       492 ~~~~~  496 (675)
                      ..+..
T Consensus        91 ~~~~~   95 (103)
T 2cq3_A           91 TARVM   95 (103)
T ss_dssp             CSSCC
T ss_pred             ccCCC
Confidence            87643

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.70  E-value=1.2e-16  Score=142.37  Aligned_cols=82  Identities=30%  Similarity=0.487  Sum_probs=77.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ....++|||+|||+++++++|++||..||.|..|+|+++.+++++|||||+|.+.++|.+||. ||+..|.|+.|+|.++
T Consensus        12 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   91 (114)
T 2do0_A           12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMD   91 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEc
Confidence            345789999999999999999999999999999999999999999999999999999999998 9999999999999998


Q ss_pred             ccc
Q 045516          492 RER  494 (675)
Q Consensus       492 ~~~  494 (675)
                      ...
T Consensus        92 ~~~   94 (114)
T 2do0_A           92 ERA   94 (114)
T ss_dssp             SCC
T ss_pred             ccC
Confidence            754

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.70  E-value=5.2e-17  Score=142.24  Aligned_cols=82  Identities=37%  Similarity=0.710  Sum_probs=77.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a  491 (675)
                      ....++|||+|||+++++++|++||..|| |..|+|+++. +++++|||||+|.+.++|.+||.||+..|.|+.|+|.++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a   90 (103)
T 2dng_A           12 TEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVDIA   90 (103)
T ss_dssp             SSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHGGGTTCEETTEECEEEEC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHHhhCCCeECCeEEEEEEe
Confidence            34579999999999999999999999997 9999999998 799999999999999999999999999999999999999


Q ss_pred             cccC
Q 045516          492 RERG  495 (675)
Q Consensus       492 ~~~~  495 (675)
                      ..+.
T Consensus        91 ~~~~   94 (103)
T 2dng_A           91 EGRK   94 (103)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            7654

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.70  E-value=6.2e-17  Score=141.89  Aligned_cols=84  Identities=30%  Similarity=0.530  Sum_probs=78.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhh-CCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcc-cCCeeEEEE
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSE-VAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQM-LGNRAIRLD  489 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~-~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~-~~gr~i~V~  489 (675)
                      ....++|||+|||+++++++|+++|.. ||.|..|+|+++.+|+++|||||+|.+.++|.+||. ||+.. |.|+.|+|.
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~   85 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLS   85 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEE
Confidence            356789999999999999999999999 999999999999999999999999999999999998 99999 999999999


Q ss_pred             eccccCC
Q 045516          490 FARERGA  496 (675)
Q Consensus       490 ~a~~~~~  496 (675)
                      ++..+..
T Consensus        86 ~a~~~~~   92 (104)
T 2dhg_A           86 VAIPKAS   92 (104)
T ss_dssp             BCCCCCS
T ss_pred             EccCCCc
Confidence            9976543

>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=99.70  E-value=1.1e-16  Score=140.04  Aligned_cols=82  Identities=24%  Similarity=0.467  Sum_probs=76.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ....++|||+|||+.+++++|++||..||.|..|+|+++..+ ++|||||+|.+.++|.+||. ||+..|.|+.|+|.++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~-~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   90 (103)
T 2cqi_A           12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   90 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS-SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC-CCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEEC
Confidence            456799999999999999999999999999999999998644 69999999999999999998 9999999999999999


Q ss_pred             cccC
Q 045516          492 RERG  495 (675)
Q Consensus       492 ~~~~  495 (675)
                      ....
T Consensus        91 ~~~~   94 (103)
T 2cqi_A           91 TTPS   94 (103)
T ss_dssp             CCTT
T ss_pred             CCCc
Confidence            8754

>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=99.70  E-value=4.6e-17  Score=144.28  Aligned_cols=83  Identities=29%  Similarity=0.450  Sum_probs=78.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      ....++|||+|||+.+++++|+.+|..||.|..|+|+.+. +|.++|||||+|.+.++|.+||. |||..|.|+.|+|.+
T Consensus        23 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  102 (110)
T 1oo0_B           23 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW  102 (110)
T ss_dssp             BTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            4567999999999999999999999999999999999987 89999999999999999999998 999999999999999


Q ss_pred             ccccC
Q 045516          491 ARERG  495 (675)
Q Consensus       491 a~~~~  495 (675)
                      +..+.
T Consensus       103 a~~~~  107 (110)
T 1oo0_B          103 CFVKG  107 (110)
T ss_dssp             SEESS
T ss_pred             cccCC
Confidence            97654

>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=99.70  E-value=3.8e-17  Score=143.53  Aligned_cols=82  Identities=28%  Similarity=0.420  Sum_probs=76.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEE-EEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVD-VRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~-v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a  491 (675)
                      ....++|||+|||+.+++++|++||..||.|.. |+|+++.+|+++|||||+|.+.++|.+||.+|+..|+||.|.|.++
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~~~~~~~gr~i~v~~~   91 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKS   91 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHhCcchhCCcEEEEEEC
Confidence            456799999999999999999999999999998 9999888999999999999999999999988999999999999988


Q ss_pred             ccc
Q 045516          492 RER  494 (675)
Q Consensus       492 ~~~  494 (675)
                      ...
T Consensus        92 ~~~   94 (104)
T 1wg5_A           92 SRA   94 (104)
T ss_dssp             CTT
T ss_pred             CHH
Confidence            654

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=8.1e-17  Score=137.60  Aligned_cols=81  Identities=25%  Similarity=0.457  Sum_probs=77.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEecc
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a~  492 (675)
                      ....++|||+|||+++++++|++||..| .|..|+|+++.+|+++|||||+|.+.++|.+||.||+..|.|+.|.|.++.
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~~g~~~~gr~i~v~~a~   85 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALKCNREYMGGRYIEVFREK   85 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHHSCSEEETTEEEEEEEES
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHHhCCceeCCcEEEEEECC
Confidence            4567999999999999999999999999 999999999989999999999999999999999999999999999999987


Q ss_pred             cc
Q 045516          493 ER  494 (675)
Q Consensus       493 ~~  494 (675)
                      .+
T Consensus        86 ~~   87 (91)
T 2dgw_A           86 SG   87 (91)
T ss_dssp             SC
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=99.70  E-value=6.7e-17  Score=142.44  Aligned_cols=80  Identities=31%  Similarity=0.490  Sum_probs=76.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ....++|||+|||+.+++++|++||..||.|..|+|+++.+|+++|||||+|.+.++|.+||. ||+..|.|+.|+|.++
T Consensus        26 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  105 (107)
T 3ulh_A           26 VETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLV  105 (107)
T ss_dssp             CCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEe
Confidence            456799999999999999999999999999999999999999999999999999999999998 9999999999999987


Q ss_pred             c
Q 045516          492 R  492 (675)
Q Consensus       492 ~  492 (675)
                      .
T Consensus       106 ~  106 (107)
T 3ulh_A          106 T  106 (107)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=2.7e-17  Score=145.63  Aligned_cols=81  Identities=32%  Similarity=0.459  Sum_probs=75.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEecc
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a~  492 (675)
                      ..+.++|||+|||+++++++|++||+.| .|..|+|+++.+|+++|||||+|.+.++|.+||.||+..|+||.|.|..+.
T Consensus        13 ~~~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~a~   91 (109)
T 2dnn_A           13 NPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEALKRNRMLMIQRYVEVSPAT   91 (109)
T ss_dssp             CHHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHHHTTTEEETTEEEEEEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEEEECC
Confidence            3456899999999999999999999999 899999999989999999999999999999999999999999999998886


Q ss_pred             cc
Q 045516          493 ER  494 (675)
Q Consensus       493 ~~  494 (675)
                      ..
T Consensus        92 ~~   93 (109)
T 2dnn_A           92 ER   93 (109)
T ss_dssp             HH
T ss_pred             cc
Confidence            54

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=5.3e-17  Score=141.00  Aligned_cols=82  Identities=28%  Similarity=0.497  Sum_probs=77.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeE-EEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCee----
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVV-DVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRA----  485 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~-~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~----  485 (675)
                      ....++|||+|||+++++++|+++|.+||.|. .|+|++++ +++++|||||+|.+.++|.+||. |||..|.|+.    
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~   85 (99)
T 2div_A            6 SGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKR   85 (99)
T ss_dssp             CSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEE
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCccee
Confidence            34679999999999999999999999999999 99999997 89999999999999999999998 9999999999    


Q ss_pred             EEEEecccc
Q 045516          486 IRLDFARER  494 (675)
Q Consensus       486 i~V~~a~~~  494 (675)
                      |+|.++...
T Consensus        86 l~v~~a~~~   94 (99)
T 2div_A           86 FKLNYATYS   94 (99)
T ss_dssp             CCEEETTCC
T ss_pred             EEEeecCCC
Confidence            999998754

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.69  E-value=6e-17  Score=140.35  Aligned_cols=82  Identities=28%  Similarity=0.539  Sum_probs=75.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCC--C--CcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEE
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD--G--RFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRL  488 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~--g--~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V  488 (675)
                      .+.++|||+|||+++++++|+++|..||.|..|+|+++..  |  +++|||||+|.+.++|.+||. ||+..|.|+.|+|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   82 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEV   82 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            3578999999999999999999999999999999998763  4  889999999999999999998 9999999999999


Q ss_pred             EeccccC
Q 045516          489 DFARERG  495 (675)
Q Consensus       489 ~~a~~~~  495 (675)
                      .++....
T Consensus        83 ~~a~~~~   89 (98)
T 2cpf_A           83 RISERAT   89 (98)
T ss_dssp             ECSSCSS
T ss_pred             EEccCCC
Confidence            9997654

>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=99.69  E-value=1.5e-17  Score=148.42  Aligned_cols=82  Identities=33%  Similarity=0.467  Sum_probs=77.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEecc
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a~  492 (675)
                      ...++|||+|||+++++++|++||..||.|..|+|+.+. +++++|||||+|.+.++|.+||.||+..|.|+.|+|.++.
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~  102 (114)
T 2cq4_A           23 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQ  102 (114)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEEHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHHHcCCCEeCCeEEEEEecC
Confidence            456899999999999999999999999999999999998 6999999999999999999999999999999999999997


Q ss_pred             ccC
Q 045516          493 ERG  495 (675)
Q Consensus       493 ~~~  495 (675)
                      .+.
T Consensus       103 ~~~  105 (114)
T 2cq4_A          103 AEK  105 (114)
T ss_dssp             HHH
T ss_pred             CCc
Confidence            653

>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=99.69  E-value=5.2e-17  Score=137.98  Aligned_cols=79  Identities=22%  Similarity=0.483  Sum_probs=75.5

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEecccc
Q 045516          416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARER  494 (675)
Q Consensus       416 ~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a~~~  494 (675)
                      .++|||+|||+++++++|+++|..||.|..|+|+++. +++++|||||+|.+.++|.+||.||+..|.|+.|+|.++...
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~g~~~~g~~l~V~~a~~~   85 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALDESLFRGRQIKVIPKRTN   85 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHGGGTTCEETTEECEEEETTTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHhcCCCEECCcEEEEEEccCC
Confidence            5899999999999999999999999999999999997 899999999999999999999999999999999999998653

>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=99.69  E-value=2.2e-17  Score=147.60  Aligned_cols=82  Identities=23%  Similarity=0.349  Sum_probs=77.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCe-EEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEV-VDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I-~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a  491 (675)
                      ....++|||+|||+.+++++|++||..||.| ..|+|+++.+|+++|||||+|.+.++|.+||.+|+..|.|+.|.|.++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~v~~a   91 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHVV   91 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHhCCCccCCeEEEEEEC
Confidence            4567999999999999999999999999999 899999999999999999999999999999999999999999999998


Q ss_pred             ccc
Q 045516          492 RER  494 (675)
Q Consensus       492 ~~~  494 (675)
                      ...
T Consensus        92 ~~~   94 (114)
T 2cpy_A           92 TLE   94 (114)
T ss_dssp             CHH
T ss_pred             CHH
Confidence            754

>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=99.69  E-value=7.7e-17  Score=140.29  Aligned_cols=79  Identities=18%  Similarity=0.398  Sum_probs=75.6

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~  596 (675)
                      .++|||+|||+.+++++    |+++|..||.|..|+|+++..+|.++|||||+|.+.++|.+||. |||..|+|+.|+|.
T Consensus        19 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           19 GTNLIVNYLPQNMTQDE----LRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVS   94 (99)
T ss_dssp             CSEEEEESCCTTCCHHH----HHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCEEEEeCCCCCCCHHH----HHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            57899999999999998    77889999999999999999999999999999999999999998 99999999999999


Q ss_pred             cccc
Q 045516          597 EAKQ  600 (675)
Q Consensus       597 ~a~~  600 (675)
                      |++|
T Consensus        95 ~AkP   98 (99)
T 4fxv_A           95 YARP   98 (99)
T ss_dssp             ECCB
T ss_pred             EeeC
Confidence            9976

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=5.4e-17  Score=142.59  Aligned_cols=84  Identities=27%  Similarity=0.450  Sum_probs=78.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a  491 (675)
                      ....++|||+|||+.+++++|++||..||.|..|+|++++ +++++|||||+|.+.++|.+||.+|+..|.|+.|+|.++
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~V~~a   92 (105)
T 2dh8_A           13 ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLDGRNIDPKPC   92 (105)
T ss_dssp             SSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHHCSEEETTEEEBCCCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEc
Confidence            4567999999999999999999999999999999999996 899999999999999999999988999999999999999


Q ss_pred             cccCC
Q 045516          492 RERGA  496 (675)
Q Consensus       492 ~~~~~  496 (675)
                      ..+..
T Consensus        93 ~~~~~   97 (105)
T 2dh8_A           93 TPRGM   97 (105)
T ss_dssp             CCSSC
T ss_pred             cCCCC
Confidence            76653

>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=99.69  E-value=7.3e-17  Score=141.92  Aligned_cols=83  Identities=25%  Similarity=0.446  Sum_probs=77.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCccc---CCeeEE
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQML---GNRAIR  487 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~---~gr~i~  487 (675)
                      ....++|||+|||+++++++|+++|..||.|..|+|+++. +++++|||||+|.+.++|.+||. ||+..|   .|+.|+
T Consensus        10 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~   89 (106)
T 2dgp_A           10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQ   89 (106)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEE
Confidence            4567999999999999999999999999999999999987 79999999999999999999997 999988   899999


Q ss_pred             EEeccccC
Q 045516          488 LDFARERG  495 (675)
Q Consensus       488 V~~a~~~~  495 (675)
                      |.++....
T Consensus        90 v~~a~~~~   97 (106)
T 2dgp_A           90 VKPADSES   97 (106)
T ss_dssp             EEECCCCS
T ss_pred             EEECCccc
Confidence            99997654

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.69  E-value=4.8e-17  Score=153.61  Aligned_cols=80  Identities=23%  Similarity=0.485  Sum_probs=75.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCC--CeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVA--EVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G--~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      ..++|||+|||+++++++|++||..||  .|..|+|++++ +|+++|||||+|.+.++|.+||. |||..|.|+.|.|.+
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~  133 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP  133 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEE
Confidence            468999999999999999999999999  99999999997 89999999999999999999998 899999999999999


Q ss_pred             cccc
Q 045516          491 ARER  494 (675)
Q Consensus       491 a~~~  494 (675)
                      +...
T Consensus       134 a~~~  137 (156)
T 3n9u_C          134 ATRQ  137 (156)
T ss_dssp             CCHH
T ss_pred             cCCC
Confidence            8654

>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=99.69  E-value=7.2e-17  Score=141.58  Aligned_cols=81  Identities=35%  Similarity=0.678  Sum_probs=76.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-C-CCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEec
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-D-GRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFA  491 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~-g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a  491 (675)
                      ...++|||+|||+++++++|++||..|| |..|+|+++. + ++++|||||+|.+.++|.+||.||+..|.|+.|+|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a   91 (104)
T 1wi8_A           13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVDVA   91 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHHhcCCCEeCCcEEEEEEc
Confidence            4569999999999999999999999999 9999999998 4 89999999999999999999999999999999999999


Q ss_pred             cccC
Q 045516          492 RERG  495 (675)
Q Consensus       492 ~~~~  495 (675)
                      ..+.
T Consensus        92 ~~~~   95 (104)
T 1wi8_A           92 DQAQ   95 (104)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            8764

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.69  E-value=9.3e-17  Score=137.39  Aligned_cols=82  Identities=33%  Similarity=0.536  Sum_probs=76.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ....++|||+|||+++++++|+++|.+||.|..|+|+++ +++++|||||+|.+.++|.+||. ||+..|.|+.|+|.++
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~-~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a   83 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRID   83 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES-SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc-CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            346799999999999999999999999999999999984 78899999999999999999998 9999999999999999


Q ss_pred             cccC
Q 045516          492 RERG  495 (675)
Q Consensus       492 ~~~~  495 (675)
                      ....
T Consensus        84 ~~~~   87 (92)
T 2dgv_A           84 RNAS   87 (92)
T ss_dssp             SCCS
T ss_pred             CCCC
Confidence            7653

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=7.3e-17  Score=143.69  Aligned_cols=84  Identities=23%  Similarity=0.417  Sum_probs=78.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeE--------EEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccC
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVV--------DVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLG  482 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~--------~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~  482 (675)
                      ....++|||+|||+.+++++|++||..||.|.        .|+|+.++ +++++|||||+|.+.++|.+||. ||+..|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   91 (113)
T 2cpe_A           12 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ   91 (113)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCccC
Confidence            45679999999999999999999999999999        69999995 89999999999999999999998 9999999


Q ss_pred             CeeEEEEeccccCC
Q 045516          483 NRAIRLDFARERGA  496 (675)
Q Consensus       483 gr~i~V~~a~~~~~  496 (675)
                      |+.|+|.++..+..
T Consensus        92 g~~l~V~~a~~~~~  105 (113)
T 2cpe_A           92 GSKLKVSLARKKPP  105 (113)
T ss_dssp             TEECEEECSSCCCC
T ss_pred             CCEEEEEECCCCCC
Confidence            99999999987643

>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=99.69  E-value=7.5e-17  Score=146.54  Aligned_cols=86  Identities=33%  Similarity=0.502  Sum_probs=80.0

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEE
Q 045516          412 QSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLD  489 (675)
Q Consensus       412 ~~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~  489 (675)
                      .....++|||+|||+.+++++|+.||..||.|..|+|+.+. ++.++|||||+|.+.++|.+||. ||+..|.|+.|.|.
T Consensus        18 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   97 (126)
T 3ex7_B           18 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   97 (126)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            34568999999999999999999999999999999999997 89999999999999999999997 99999999999999


Q ss_pred             eccccCCC
Q 045516          490 FARERGAY  497 (675)
Q Consensus       490 ~a~~~~~~  497 (675)
                      ++......
T Consensus        98 ~a~~~~~~  105 (126)
T 3ex7_B           98 WCFVRGPP  105 (126)
T ss_dssp             ESEESSSC
T ss_pred             EecCCCCC
Confidence            99876543

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.69  E-value=1.4e-16  Score=147.40  Aligned_cols=86  Identities=26%  Similarity=0.491  Sum_probs=79.9

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEE
Q 045516          411 PQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRL  488 (675)
Q Consensus       411 ~~~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V  488 (675)
                      +.....++|||+|||+++++++|+++|..||.|..|+|+++. +++++|||||+|.+.++|.+||. ||+..|.|+.|+|
T Consensus        37 ~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  116 (139)
T 1u6f_A           37 PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKV  116 (139)
T ss_dssp             CCTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            335667999999999999999999999999999999999997 78999999999999999999998 9999999999999


Q ss_pred             EeccccCC
Q 045516          489 DFARERGA  496 (675)
Q Consensus       489 ~~a~~~~~  496 (675)
                      .++.....
T Consensus       117 ~~a~~~~~  124 (139)
T 1u6f_A          117 ALAASGHQ  124 (139)
T ss_dssp             EESSCCCC
T ss_pred             EECCCCCC
Confidence            99987654

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.69  E-value=3.3e-17  Score=147.36  Aligned_cols=82  Identities=28%  Similarity=0.415  Sum_probs=77.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCC---eEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEE
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAE---VVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLD  489 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~---I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~  489 (675)
                      ....++|||+|||+++|+++|++||..||.   |..|+|+++..|+++|||||+|.+.++|.+||.||+..|.||.|.|.
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V~   93 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALKKDRESMGHRYIEVF   93 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGGGTTEEETTEEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEEE
Confidence            456789999999999999999999999999   89999999988999999999999999999999999999999999999


Q ss_pred             ecccc
Q 045516          490 FARER  494 (675)
Q Consensus       490 ~a~~~  494 (675)
                      ++...
T Consensus        94 ~a~~~   98 (118)
T 2db1_A           94 KSHRT   98 (118)
T ss_dssp             EECHH
T ss_pred             ECCHH
Confidence            88643

>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=99.69  E-value=9.7e-17  Score=138.73  Aligned_cols=80  Identities=23%  Similarity=0.368  Sum_probs=74.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHH----HHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEE
Q 045516          414 GGSKTLFVGNLPFSVEQADVQ----NFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRL  488 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~----~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V  488 (675)
                      ...++|||+|||+++++++|+    ++|.+||.|..|+|+++..+  +|||||+|.+.++|.+||. |||..|.|+.|+|
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~--rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V   84 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY--QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILV   84 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST--TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC--CeEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            456899999999999999999    99999999999999988755  8999999999999999998 9999999999999


Q ss_pred             EeccccC
Q 045516          489 DFARERG  495 (675)
Q Consensus       489 ~~a~~~~  495 (675)
                      .++....
T Consensus        85 ~~a~~~~   91 (96)
T 2dgx_A           85 SLATGAS   91 (96)
T ss_dssp             EECCCSS
T ss_pred             EEcCCCC
Confidence            9997653

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.68  E-value=3e-17  Score=134.94  Aligned_cols=74  Identities=28%  Similarity=0.491  Sum_probs=71.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEec
Q 045516          418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFA  491 (675)
Q Consensus       418 tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a  491 (675)
                      +|||+|||+++++++|+++|++||.|..|+|+++. +++++|||||+|.+.++|.+||+||+..|.|+.|.|.++
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 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHSSSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHCCCCEECCEEEEEEeC
Confidence            59999999999999999999999999999999997 899999999999999999999999999999999999875

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=1.7e-16  Score=142.03  Aligned_cols=82  Identities=23%  Similarity=0.485  Sum_probs=76.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      ....++|||+|||+++++++|++||..||.|..|+|+++. +++++|||||+|.+.++|.+||. ||+ .|.|+.|+|.+
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~~   92 (116)
T 2cqd_A           14 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNL   92 (116)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEEE
Confidence            4567999999999999999999999999999999999997 79999999999999999999998 887 89999999999


Q ss_pred             ccccC
Q 045516          491 ARERG  495 (675)
Q Consensus       491 a~~~~  495 (675)
                      +....
T Consensus        93 a~~~~   97 (116)
T 2cqd_A           93 AYLGA   97 (116)
T ss_dssp             STTTC
T ss_pred             cccCC
Confidence            97543

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=7.7e-17  Score=144.32  Aligned_cols=82  Identities=22%  Similarity=0.469  Sum_probs=77.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEeccc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a~~  493 (675)
                      ..++|||+|||+++++++|++||..||.|..|+|+++. +++++|||||+|.+.++|.+||.+|+..|.|+.|+|.++..
T Consensus        26 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~V~~a~~  105 (116)
T 1x4b_A           26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVA  105 (116)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECCSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHhCCcEECCEEEEEEECCC
Confidence            45899999999999999999999999999999999997 79999999999999999999998899999999999999987


Q ss_pred             cCC
Q 045516          494 RGA  496 (675)
Q Consensus       494 ~~~  496 (675)
                      +..
T Consensus       106 ~~~  108 (116)
T 1x4b_A          106 REE  108 (116)
T ss_dssp             CCC
T ss_pred             Ccc
Confidence            654

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

Probab=99.68  E-value=6e-17  Score=145.42  Aligned_cols=80  Identities=23%  Similarity=0.433  Sum_probs=75.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      ....++|||+|||+++++++|++||..||.|..|+|+++. +|+++|||||+|.+.++|.+||. |||..|+|+.|+|.+
T Consensus        37 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~  116 (118)
T 2khc_A           37 GPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQL  116 (118)
T ss_dssp             CCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            3467999999999999999999999999999999999986 79999999999999999999998 999999999999998


Q ss_pred             cc
Q 045516          491 AR  492 (675)
Q Consensus       491 a~  492 (675)
                      ++
T Consensus       117 ak  118 (118)
T 2khc_A          117 KK  118 (118)
T ss_dssp             C-
T ss_pred             cC
Confidence            73

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.68  E-value=1e-16  Score=142.04  Aligned_cols=83  Identities=22%  Similarity=0.430  Sum_probs=74.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a  491 (675)
                      ....++|||+|||+++++++|+++|+.||.|..|+|+++. +|+++|||||+|.+.++|.+||.+++..|.|+.|.|.++
T Consensus        22 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~g~~l~V~~a  101 (109)
T 2rs2_A           22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVA  101 (109)
T ss_dssp             ----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSCEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCCCcCCCEEEEEEEc
Confidence            4567999999999999999999999999999999999997 799999999999999999999995579999999999999


Q ss_pred             cccC
Q 045516          492 RERG  495 (675)
Q Consensus       492 ~~~~  495 (675)
                      ..+.
T Consensus       102 ~~~~  105 (109)
T 2rs2_A          102 FPRR  105 (109)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            7654

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=7.8e-17  Score=140.91  Aligned_cols=78  Identities=17%  Similarity=0.313  Sum_probs=71.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hC--CcccCCeeEEEEe
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LN--GQMLGNRAIRLDF  490 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~--g~~~~gr~i~V~~  490 (675)
                      ...++|||+|||+.+++++|+++|++||.|.+|+|+++     +|||||+|.+.++|..||. |+  +..|.|++|+|.+
T Consensus        14 ~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~-----kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~   88 (105)
T 1sjq_A           14 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQF   88 (105)
T ss_dssp             CCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEE
Confidence            45689999999999999999999999999999999975     8999999999999999998 75  4789999999999


Q ss_pred             ccccCC
Q 045516          491 ARERGA  496 (675)
Q Consensus       491 a~~~~~  496 (675)
                      +..+..
T Consensus        89 A~~~~~   94 (105)
T 1sjq_A           89 SNHKEL   94 (105)
T ss_dssp             CSSSSC
T ss_pred             cCCCCC
Confidence            976643

>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=99.68  E-value=1.4e-16  Score=142.29  Aligned_cols=80  Identities=19%  Similarity=0.423  Sum_probs=73.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecc
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~  492 (675)
                      ..+++|||+|||+.+++++|+.+|+.||.|..|+|+++  +.++|||||+|.+.++|.+||. |||..|.|+.|.|.++.
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~--~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   83 (115)
T 3lqv_A            6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYN   83 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS--TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC--CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEec
Confidence            35689999999999999999999999999999999965  5569999999999999999998 99999999999999997


Q ss_pred             ccC
Q 045516          493 ERG  495 (675)
Q Consensus       493 ~~~  495 (675)
                      ...
T Consensus        84 ~~~   86 (115)
T 3lqv_A           84 ANR   86 (115)
T ss_dssp             HHH
T ss_pred             CCh
Confidence            653

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.68  E-value=2e-16  Score=143.47  Aligned_cols=86  Identities=28%  Similarity=0.429  Sum_probs=79.9

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          412 QSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       412 ~~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      .....++|||+|||+.+++++|+++|..||.|..|+|+.+.+|+++|||||+|.+.++|.+||. |||..|.|+.|+|.+
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  110 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  110 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            3456799999999999999999999999999999999999999999999999999999999998 999999999999999


Q ss_pred             ccccCCC
Q 045516          491 ARERGAY  497 (675)
Q Consensus       491 a~~~~~~  497 (675)
                      +......
T Consensus       111 a~~~~~~  117 (124)
T 2kt5_A          111 VASQIDL  117 (124)
T ss_dssp             ECCTTCC
T ss_pred             eCCCCCC
Confidence            9765443

>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=99.68  E-value=7.8e-17  Score=136.50  Aligned_cols=80  Identities=20%  Similarity=0.385  Sum_probs=74.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCC-cccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGR-FKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~-~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ..++|||+|||+++++++|+++|..||.|..|+|+.+. ++. ++|||||+|.+.++|.+||. |||..|.|+.|+|.++
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   82 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAV   82 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEEC
Confidence            46899999999999999999999999999999999887 344 89999999999999999998 9999999999999998


Q ss_pred             ccc
Q 045516          492 RER  494 (675)
Q Consensus       492 ~~~  494 (675)
                      .+.
T Consensus        83 ~~~   85 (88)
T 4a8x_A           83 LAP   85 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.68  E-value=1.5e-16  Score=151.81  Aligned_cols=139  Identities=24%  Similarity=0.339  Sum_probs=79.3

Q ss_pred             EEecCHHHHHHHHH-hCCcccC--CeeEEEEeccccC--CCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHH
Q 045516          462 VEFASVEDAHKAIE-LNGQMLG--NRAIRLDFARERG--AYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVR  536 (675)
Q Consensus       462 V~F~~~e~A~~Al~-l~g~~~~--gr~i~V~~a~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~  536 (675)
                      .+|.+.+++..++. |++..+.  |+.+.+.+.....  .+.....................++|||+|||+.+++++  
T Consensus        11 ee~e~~~d~e~~~~~~~~~~~~~kgr~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~--   88 (165)
T 1rk8_A           11 EEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDE--   88 (165)
T ss_dssp             -------------------------------------------------------CCCCC-CEEEEEESCCTTCCHHH--
T ss_pred             hhhhccccccccchhhccccccccCCCCCCCccccccccCccccccCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHH--
Confidence            78999999999997 8887765  7776665532211  000000000000111122344578999999999999998  


Q ss_pred             HHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEeccccCCCC
Q 045516          537 ASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVDEAKQRGDF  604 (675)
Q Consensus       537 ~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~~a~~r~~~  604 (675)
                        |+.+|..||.|..|.|+.+..+|.++|||||+|.+.+.|..||. |||..|+|+.|.|.|+.++...
T Consensus        89 --L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~  155 (165)
T 1rk8_A           89 --IQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPK  155 (165)
T ss_dssp             --HHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEECC--
T ss_pred             --HHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCCCC
Confidence              78899999999999999999999999999999999999999998 9999999999999999876654

>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=99.68  E-value=3.2e-17  Score=142.94  Aligned_cols=81  Identities=36%  Similarity=0.679  Sum_probs=74.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC--CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEe
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA--DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDF  490 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~--~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~  490 (675)
                      ....++|||+|||+++++++|++||..|| |..|+|+++.  +|+++|||||+|.+.++|.+||.|||..|.|+.|+|.+
T Consensus        16 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai~l~g~~~~g~~l~V~~   94 (100)
T 2j76_E           16 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNRRIRVDV   94 (100)
T ss_dssp             ----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHHHTTTCCBTTBCCCCEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHHhcCCCEECCeEEEEEe
Confidence            45689999999999999999999999999 9999999986  79999999999999999999999999999999999999


Q ss_pred             cccc
Q 045516          491 ARER  494 (675)
Q Consensus       491 a~~~  494 (675)
                      +..+
T Consensus        95 a~~~   98 (100)
T 2j76_E           95 ADQA   98 (100)
T ss_dssp             CCCS
T ss_pred             ccCC
Confidence            8754

>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=99.68  E-value=2.5e-16  Score=137.81  Aligned_cols=83  Identities=25%  Similarity=0.467  Sum_probs=76.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a  491 (675)
                      ....++|||+|||+++++++|++||..||.|..|+|+++. +++++|||||+|.+.++|.+||. +++.|.|+.|.|.++
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~g~~l~v~~a   90 (103)
T 2cqg_A           12 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS-QRHMIDGRWCDCKLP   90 (103)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH-SCEEETTEEEEEECC
T ss_pred             cCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH-cCCeeCCeEEEEEec
Confidence            3457899999999999999999999999999999999997 79999999999999999999998 577999999999999


Q ss_pred             cccCC
Q 045516          492 RERGA  496 (675)
Q Consensus       492 ~~~~~  496 (675)
                      ..+..
T Consensus        91 ~~~~~   95 (103)
T 2cqg_A           91 NSKQS   95 (103)
T ss_dssp             CTTCC
T ss_pred             CCCCc
Confidence            87643

>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=99.68  E-value=1.1e-16  Score=146.27  Aligned_cols=82  Identities=32%  Similarity=0.469  Sum_probs=77.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      ....++|||+|||+++++++|+++|..||.|..|+|+++. +++++|||||+|.+.++|.+||. |||..|.|+.|.|.+
T Consensus        43 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~  122 (129)
T 2kxn_B           43 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF  122 (129)
T ss_dssp             CCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4567999999999999999999999999999999999997 78999999999999999999998 999999999999999


Q ss_pred             cccc
Q 045516          491 ARER  494 (675)
Q Consensus       491 a~~~  494 (675)
                      +..+
T Consensus       123 a~~~  126 (129)
T 2kxn_B          123 SITK  126 (129)
T ss_dssp             CSSS
T ss_pred             ecCC
Confidence            8764

>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=99.68  E-value=2.9e-16  Score=138.92  Aligned_cols=81  Identities=23%  Similarity=0.432  Sum_probs=74.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ....++|||+|||+++++++|++||.+||.|..|+|+.  ++.++|||||+|.+.++|.+||. ||+..|.|+.|+|.++
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~--~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   96 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN--RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP   96 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC--SSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEE--CCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEc
Confidence            45679999999999999999999999999999999965  45689999999999999999996 9999999999999999


Q ss_pred             cccC
Q 045516          492 RERG  495 (675)
Q Consensus       492 ~~~~  495 (675)
                      ....
T Consensus        97 ~~~~  100 (109)
T 1x4a_A           97 RSGR  100 (109)
T ss_dssp             CCCC
T ss_pred             ccCC
Confidence            7654

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.68  E-value=9.3e-17  Score=141.27  Aligned_cols=82  Identities=23%  Similarity=0.401  Sum_probs=75.2

Q ss_pred             CCCCceEEEcCCCCCC------CHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCe-
Q 045516          413 SGGSKTLFVGNLPFSV------EQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNR-  484 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~------te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr-  484 (675)
                      ....++|||+|||+.+      ++++|+.+|++||.|..|+|+ ..+|+++|||||+|.+.++|.+||. |||..|.|+ 
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~-~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~   90 (105)
T 2nlw_A           12 DGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQH   90 (105)
T ss_dssp             CSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC-CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTC
T ss_pred             CCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee-CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCc
Confidence            4557899999999999      889999999999999999998 4589999999999999999999998 999999998 


Q ss_pred             eEEEEeccccC
Q 045516          485 AIRLDFARERG  495 (675)
Q Consensus       485 ~i~V~~a~~~~  495 (675)
                      .|+|.++....
T Consensus        91 ~l~V~~a~~~~  101 (105)
T 2nlw_A           91 TFRVNLFTDFD  101 (105)
T ss_dssp             EEEEECSCCCC
T ss_pred             eEEEEEcchHh
Confidence            99999987543

>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=99.67  E-value=7e-17  Score=141.48  Aligned_cols=81  Identities=38%  Similarity=0.683  Sum_probs=76.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~  492 (675)
                      ..++|||+|||+.+++++|+++|..||.|..|+|+++. +|+++|||||+|.+.++|.+||. |||..|.|+.|+|.++.
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   86 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCC
Confidence            45899999999999999999999999999999999997 89999999999999999999997 99999999999999997


Q ss_pred             ccC
Q 045516          493 ERG  495 (675)
Q Consensus       493 ~~~  495 (675)
                      ...
T Consensus        87 ~~~   89 (104)
T 1p1t_A           87 SEK   89 (104)
T ss_dssp             CTT
T ss_pred             Ccc
Confidence            653

>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=99.67  E-value=5e-17  Score=149.67  Aligned_cols=82  Identities=27%  Similarity=0.404  Sum_probs=77.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCC---eEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEE
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAE---VVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLD  489 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~---I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~  489 (675)
                      ....++|||+|||+++|+++|++||+.||.   |..|+|+++..|+++|||||+|.+.++|.+||.||+..|.||.|.|.
T Consensus        41 ~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~~~g~~l~gr~i~V~  120 (136)
T 2hgl_A           41 GGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALKKDRESMGHRYIEVF  120 (136)
T ss_dssp             CCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHTTTEEESSSSEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHhcCCCEECCEEEEEE
Confidence            456789999999999999999999999999   89999999988999999999999999999999999999999999999


Q ss_pred             ecccc
Q 045516          490 FARER  494 (675)
Q Consensus       490 ~a~~~  494 (675)
                      ++...
T Consensus       121 ~a~~~  125 (136)
T 2hgl_A          121 KSHRT  125 (136)
T ss_dssp             ECCHH
T ss_pred             ECChH
Confidence            88543

>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=99.67  E-value=8.2e-17  Score=140.51  Aligned_cols=78  Identities=9%  Similarity=0.188  Sum_probs=70.4

Q ss_pred             CCCCceEEEcCCCC-CCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCc--ccCCeeEEE
Q 045516          413 SGGSKTLFVGNLPF-SVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQ--MLGNRAIRL  488 (675)
Q Consensus       413 ~~~~~tlfV~nLp~-~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~--~~~gr~i~V  488 (675)
                      ...+++|||+|||+ .+++++|+++|.+||.|.+|+|+++     +|||||+|.+.++|..||. ||+.  .|.|++|+|
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V   86 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRV   86 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-----SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEE
Confidence            34678999999999 9999999999999999999999865     6999999999999999997 8754  599999999


Q ss_pred             EeccccC
Q 045516          489 DFARERG  495 (675)
Q Consensus       489 ~~a~~~~  495 (675)
                      .++....
T Consensus        87 ~~a~~~~   93 (102)
T 1x4d_A           87 HLSQKYK   93 (102)
T ss_dssp             EEECCCT
T ss_pred             EECCCCC
Confidence            9998644

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=3.2e-17  Score=138.22  Aligned_cols=79  Identities=23%  Similarity=0.371  Sum_probs=74.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ...++|||+|||+++++++|+++|..||.|..|+|+.+. +++++|||||+|.+.++|.+||. |||..|.|+.|+|.+.
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~   82 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGP   82 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCC
Confidence            457899999999999999999999999999999999997 89999999999999999999998 9999999999988765


Q ss_pred             c
Q 045516          492 R  492 (675)
Q Consensus       492 ~  492 (675)
                      .
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.67  E-value=1.2e-16  Score=144.72  Aligned_cols=81  Identities=22%  Similarity=0.462  Sum_probs=76.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEeccc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a~~  493 (675)
                      ..++|||+|||+++++++|++||.+||.|..|+|+++. +|.++|||||+|.+.++|.+||.|||..|.|+.|+|.++..
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~~  114 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMDETVFRGRTIKVLPKRT  114 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHHTTTTCEETTEECEEEESSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHHhcCCCeECCeEEEEEECCC
Confidence            35899999999999999999999999999999999986 89999999999999999999999999999999999999875


Q ss_pred             cC
Q 045516          494 RG  495 (675)
Q Consensus       494 ~~  495 (675)
                      ..
T Consensus       115 ~~  116 (124)
T 2jwn_A          115 NM  116 (124)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.67  E-value=2.8e-16  Score=135.20  Aligned_cols=85  Identities=31%  Similarity=0.547  Sum_probs=79.4

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEE
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVV  595 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V  595 (675)
                      +.++|||+|||..+++++    |+++|..||.|..|.|+++..++.++|||||+|.+.++|.+||. ||+..|+|+.|+|
T Consensus         4 ~~~~l~v~nlp~~~t~~~----l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   79 (95)
T 2dnz_A            4 GSSGLYVGSLHFNITEDM----LRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRV   79 (95)
T ss_dssp             CCCEEEEESCCTTCCHHH----HHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             CCcEEEEeCCCCCCCHHH----HHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEE
Confidence            478999999999999998    78899999999999999999999999999999999999999998 9999999999999


Q ss_pred             eccccCCCCC
Q 045516          596 DEAKQRGDFG  605 (675)
Q Consensus       596 ~~a~~r~~~~  605 (675)
                      .++.++...+
T Consensus        80 ~~a~~~~~~~   89 (95)
T 2dnz_A           80 GHVTERLDGG   89 (95)
T ss_dssp             EESSCCCCCC
T ss_pred             EEcccccCCC
Confidence            9998766543

>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=99.67  E-value=1.6e-16  Score=144.44  Aligned_cols=85  Identities=25%  Similarity=0.460  Sum_probs=79.3

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      ...++|||+|||+.+++++    |..+|..||.|..|.|+.+..+|.++|||||+|.+.++|..||. |||..|+|+.|+
T Consensus        20 ~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   95 (126)
T 3ex7_B           20 VEGWILFVTGVHEEATEED----IHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPIS   95 (126)
T ss_dssp             SSSEEEEEESCCTTCCHHH----HHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCE
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEE
Confidence            4478999999999999998    77889999999999999999999999999999999999999998 999999999999


Q ss_pred             EeccccCCCC
Q 045516          595 VDEAKQRGDF  604 (675)
Q Consensus       595 V~~a~~r~~~  604 (675)
                      |.|+.++...
T Consensus        96 v~~a~~~~~~  105 (126)
T 3ex7_B           96 VDWCFVRGPP  105 (126)
T ss_dssp             EEESEESSSC
T ss_pred             EEEecCCCCC
Confidence            9999877654

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.67  E-value=6.7e-17  Score=148.11  Aligned_cols=82  Identities=16%  Similarity=0.345  Sum_probs=76.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEE--EEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCc----ccCCe
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVD--VRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQ----MLGNR  484 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~--v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~----~~~gr  484 (675)
                      ....++|||+|||+++++++|+++|..||.|..  |+|++++ +|+++|||||+|.+. +|.+||. |||.    .|.|+
T Consensus        20 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr   98 (131)
T 2m2b_A           20 ENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGK   98 (131)
T ss_dssp             SCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCE
Confidence            346789999999999999999999999999976  9999998 999999999999999 9999997 9999    99999


Q ss_pred             eEEEEeccccC
Q 045516          485 AIRLDFARERG  495 (675)
Q Consensus       485 ~i~V~~a~~~~  495 (675)
                      .|+|.++....
T Consensus        99 ~l~V~~a~~~~  109 (131)
T 2m2b_A           99 TINVEFAKGSK  109 (131)
T ss_dssp             CCCCEECCCSC
T ss_pred             EEEEEECCCCC
Confidence            99999997654

>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=99.67  E-value=8.4e-17  Score=139.43  Aligned_cols=81  Identities=25%  Similarity=0.378  Sum_probs=74.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ...++|||+|||+++++++|++||..||.|..|.|+.+. +|+++|||||+|.+.++|.+||. ||+..|.|+.|+|.++
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   92 (98)
T 2cqp_A           13 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   92 (98)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEc
Confidence            456899999999999999999999999999988877775 89999999999999999999996 9999999999999998


Q ss_pred             ccc
Q 045516          492 RER  494 (675)
Q Consensus       492 ~~~  494 (675)
                      ..+
T Consensus        93 ~~~   95 (98)
T 2cqp_A           93 SGP   95 (98)
T ss_dssp             SCS
T ss_pred             CCC
Confidence            644

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=4.9e-17  Score=147.08  Aligned_cols=80  Identities=26%  Similarity=0.377  Sum_probs=74.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCe----EEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEE
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEV----VDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLD  489 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I----~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~  489 (675)
                      ...++|||+||||++|+++|++||+.||.|    ..|+|+++.+|+++|||||+|.+.++|.+||.+|+..|.||.|.|.
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~~~~~l~gR~i~V~  100 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIELF  100 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTTTTEESSSCEECCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHhCCCeeCCeEEEEE
Confidence            346899999999999999999999999986    6899999999999999999999999999999989999999999998


Q ss_pred             eccc
Q 045516          490 FARE  493 (675)
Q Consensus       490 ~a~~  493 (675)
                      ++..
T Consensus       101 ~a~~  104 (123)
T 2dha_A          101 RSTA  104 (123)
T ss_dssp             EECH
T ss_pred             ECCH
Confidence            8754

>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=99.67  E-value=1.8e-16  Score=151.24  Aligned_cols=85  Identities=28%  Similarity=0.446  Sum_probs=78.4

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEE
Q 045516          412 QSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLD  489 (675)
Q Consensus       412 ~~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~  489 (675)
                      .....++|||+|||+.+++++|+.||..||.|..|+|+.+. +|.++|||||+|.+.++|.+||. |||..|.|+.|.|.
T Consensus        68 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  147 (165)
T 1rk8_A           68 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD  147 (165)
T ss_dssp             CCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999996 89999999999999999999997 99999999999999


Q ss_pred             eccccCC
Q 045516          490 FARERGA  496 (675)
Q Consensus       490 ~a~~~~~  496 (675)
                      |+.....
T Consensus       148 ~a~~~~~  154 (165)
T 1rk8_A          148 WCFVKGP  154 (165)
T ss_dssp             ESEECC-
T ss_pred             EecCCCC
Confidence            9987653

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.67  E-value=1.4e-16  Score=133.37  Aligned_cols=73  Identities=22%  Similarity=0.289  Sum_probs=69.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~  492 (675)
                      .+..|||+||++.+|+++|+++|.+||+|.+++|..     ++|||||+|.+.++|.+||. ||+..|.||.|+|.++.
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~-----~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL-----NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET-----TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC-----CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            467999999999999999999999999999999975     59999999999999999998 99999999999999884

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.66  E-value=3e-16  Score=145.11  Aligned_cols=85  Identities=21%  Similarity=0.323  Sum_probs=78.7

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      ...++|||+|||..+++++    |+.+|..||.|..|.|+++..+|.++|||||+|.+.++|.+||. ||+..|+|+.|+
T Consensus        40 ~~~~~l~V~nLp~~~~~~~----l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  115 (139)
T 1u6f_A           40 DVLRNLMVNYIPTTVDEVQ----LRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLK  115 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHH----HHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            4478999999999999998    77888899999999999999999999999999999999999998 999999999999


Q ss_pred             EeccccCCCC
Q 045516          595 VDEAKQRGDF  604 (675)
Q Consensus       595 V~~a~~r~~~  604 (675)
                      |.++.++..+
T Consensus       116 v~~a~~~~~~  125 (139)
T 1u6f_A          116 VALAASGHQR  125 (139)
T ss_dssp             EEESSCCCCC
T ss_pred             EEECCCCCCC
Confidence            9999876543

>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=99.66  E-value=5.6e-17  Score=139.63  Aligned_cols=78  Identities=26%  Similarity=0.392  Sum_probs=72.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~  492 (675)
                      ..++|||+|||+.+++++|++||.+||.|..|+|+.+. +++++|||||+|.+.++|.+||. ||+..|.|+.|+|.++.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a~   93 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPS   93 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEecc
Confidence            45899999999999999999999999999988888776 88999999999999999999998 99999999999999875

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.66  E-value=2.1e-16  Score=136.83  Aligned_cols=76  Identities=18%  Similarity=0.215  Sum_probs=69.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcc--cCCeeEEEEe
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQM--LGNRAIRLDF  490 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~--~~gr~i~V~~  490 (675)
                      ..+++|||+|||+.+++++|+.+|++||.|.+|+|++     .+|||||+|.+.++|.+||. ||+..  |.|++|+|.|
T Consensus        19 ~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~-----~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~   93 (100)
T 3r27_A           19 PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP-----KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNY   93 (100)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET-----TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc-----CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEe
Confidence            4578999999999999999999999999999999985     48999999999999999997 88875  7899999999


Q ss_pred             cccc
Q 045516          491 ARER  494 (675)
Q Consensus       491 a~~~  494 (675)
                      +..+
T Consensus        94 S~~k   97 (100)
T 3r27_A           94 STSQ   97 (100)
T ss_dssp             CSCS
T ss_pred             cccc
Confidence            9754

>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=99.66  E-value=3.9e-17  Score=144.22  Aligned_cols=82  Identities=24%  Similarity=0.355  Sum_probs=77.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCC---eEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEE
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAE---VVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLD  489 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~---I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~  489 (675)
                      ....++|||+|||+++++++|++||..||.   |..|+|+++..|+++|||||+|.+.++|.+||.||+..|+||.|.|.
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~   87 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALEKHRMYMGQRYVEVY   87 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHTTTTCCSSSSCCCCE
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHhCcceeCCeEEEEE
Confidence            456799999999999999999999999998   99999999988999999999999999999999999999999999999


Q ss_pred             ecccc
Q 045516          490 FARER  494 (675)
Q Consensus       490 ~a~~~  494 (675)
                      ++...
T Consensus        88 ~a~~~   92 (107)
T 2lmi_A           88 EINNE   92 (107)
T ss_dssp             ECCHH
T ss_pred             ECCHH
Confidence            88653

>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=99.66  E-value=4.4e-16  Score=138.82  Aligned_cols=82  Identities=22%  Similarity=0.516  Sum_probs=75.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCccc--------CC
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQML--------GN  483 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~--------~g  483 (675)
                      ....++|||+|||+++++++|+++|..||.|..|+|+++.++.++|||||+|.+.++|.+||. |||..|        .+
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~  101 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT  101 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCC
Confidence            346789999999999999999999999999999999999999999999999999999999998 999999        57


Q ss_pred             eeEEEEecccc
Q 045516          484 RAIRLDFARER  494 (675)
Q Consensus       484 r~i~V~~a~~~  494 (675)
                      ++|.|.|+.++
T Consensus       102 ~~l~v~~a~p~  112 (114)
T 1x5o_A          102 EPLLCKFSGPS  112 (114)
T ss_dssp             SCBEEEECCCS
T ss_pred             CceeEEccCCC
Confidence            88999988643

>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=99.66  E-value=7.3e-16  Score=133.73  Aligned_cols=86  Identities=22%  Similarity=0.369  Sum_probs=79.9

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      ...++|||+|||..+++++    |+.+|..||.|..|.|+++..+|.++|||||+|.+.++|.+||. ||+..|+|+.|+
T Consensus         6 ~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   81 (99)
T 1whw_A            6 SGSGRLFVRNLSYTSSEED----LEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLH   81 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHH----HHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEE
Confidence            3479999999999999998    77889999999999999999899999999999999999999997 999999999999


Q ss_pred             EeccccCCCCC
Q 045516          595 VDEAKQRGDFG  605 (675)
Q Consensus       595 V~~a~~r~~~~  605 (675)
                      |.++.++....
T Consensus        82 V~~a~~~~~~~   92 (99)
T 1whw_A           82 VLPSTIKKEAS   92 (99)
T ss_dssp             EEECCCCSTTC
T ss_pred             EEEcCCCcccc
Confidence            99999876653

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.66  E-value=7.3e-16  Score=133.80  Aligned_cols=86  Identities=26%  Similarity=0.452  Sum_probs=80.2

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVV  595 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V  595 (675)
                      ...++|||+|||..+++++    |+++|..||.|..|.|+++..++.++|||||+|.+.++|.+||.||+..|+|+.|+|
T Consensus         8 ~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~l~V   83 (99)
T 2dgs_A            8 SKSNKIFVGGIPHNCGETE----LREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDIMGKKVEV   83 (99)
T ss_dssp             SSCCEEEEESCCSSCCHHH----HHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHHHCCCBSSSCBCEE
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHHhCCCEECCeEEEE
Confidence            3479999999999999998    788999999999999999999999999999999999999999999999999999999


Q ss_pred             eccccCCCCC
Q 045516          596 DEAKQRGDFG  605 (675)
Q Consensus       596 ~~a~~r~~~~  605 (675)
                      .++.++....
T Consensus        84 ~~a~~~~~~~   93 (99)
T 2dgs_A           84 KRAEPRDSKS   93 (99)
T ss_dssp             EECCCCCCCC
T ss_pred             EECCCCcccC
Confidence            9998776554

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=1.7e-16  Score=140.53  Aligned_cols=81  Identities=31%  Similarity=0.580  Sum_probs=75.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ....++|||+|||+++++++|+++|+.||.|..|+|+++.. .++|||||+|.+.++|.+||. |||..|.|+.|+|.++
T Consensus        26 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  104 (109)
T 2err_A           26 KSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER-GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA  104 (109)
T ss_dssp             TTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTT-BCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCC-CCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            45679999999999999999999999999999999998864 489999999999999999998 9999999999999998


Q ss_pred             ccc
Q 045516          492 RER  494 (675)
Q Consensus       492 ~~~  494 (675)
                      ..+
T Consensus       105 ~~~  107 (109)
T 2err_A          105 TAR  107 (109)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            754

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.66  E-value=3e-16  Score=136.78  Aligned_cols=80  Identities=39%  Similarity=0.672  Sum_probs=73.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ....++|||+|||+++++++|++||.+||.|   +|+.+.+++++|||||+|.+.++|.+||. ||+..|.|+.|+|.++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   88 (101)
T 2fc9_A           12 SGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQ   88 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEc
Confidence            4567999999999999999999999999977   56666789999999999999999999998 9999999999999999


Q ss_pred             cccC
Q 045516          492 RERG  495 (675)
Q Consensus       492 ~~~~  495 (675)
                      ..+.
T Consensus        89 ~~~~   92 (101)
T 2fc9_A           89 GPRG   92 (101)
T ss_dssp             SSCC
T ss_pred             CCCC
Confidence            7764

>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=99.65  E-value=5.6e-16  Score=135.96  Aligned_cols=79  Identities=16%  Similarity=0.213  Sum_probs=70.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCC--cccCCeeEEEEe
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNG--QMLGNRAIRLDF  490 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g--~~~~gr~i~V~~  490 (675)
                      ..+++|||+|||+.+++++|+++|++||.|..|+|+++     +|||||+|.+.++|.+||. ||+  ..|.|++|+|.|
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~   87 (104)
T 1wex_A           13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNY   87 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEE
Confidence            45789999999999999999999999999999999864     8999999999999999997 765  459999999999


Q ss_pred             ccccCCC
Q 045516          491 ARERGAY  497 (675)
Q Consensus       491 a~~~~~~  497 (675)
                      +..+...
T Consensus        88 a~~~~~~   94 (104)
T 1wex_A           88 STSKRIT   94 (104)
T ss_dssp             CSSSSCC
T ss_pred             ccCcccc
Confidence            9876543

>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=99.65  E-value=3.7e-16  Score=138.14  Aligned_cols=83  Identities=28%  Similarity=0.380  Sum_probs=75.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCC-eEEEEEe-eCC-CCCcccEEEEEecCHHHHHHHHH-hC--CcccCCeeEE
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAE-VVDVRLS-SDA-DGRFKGYGHVEFASVEDAHKAIE-LN--GQMLGNRAIR  487 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~-I~~v~i~-~~~-~g~~kG~afV~F~~~e~A~~Al~-l~--g~~~~gr~i~  487 (675)
                      ...++|||+|||+++++++|+++|..||. |..|+|+ .+. +|+++|||||+|.+.++|.+||. ||  +..|.|+.|+
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~   85 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIA   85 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCE
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEE
Confidence            45789999999999999999999999998 9999998 565 78999999999999999999998 86  5899999999


Q ss_pred             EEeccccCC
Q 045516          488 LDFARERGA  496 (675)
Q Consensus       488 V~~a~~~~~  496 (675)
                      |.++.++..
T Consensus        86 V~~a~~~~~   94 (109)
T 2dis_A           86 VDWAEPEID   94 (109)
T ss_dssp             EEESCSSCS
T ss_pred             EEEcCCCCC
Confidence            999987654

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.65  E-value=6.7e-16  Score=131.63  Aligned_cols=77  Identities=26%  Similarity=0.501  Sum_probs=71.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ....++|||+|||+++++++|+++|.+||.|..|+|+       +|||||+|.+.++|.+||. ||+..|.|+.|+|.++
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   77 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEAS   77 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE-------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECS
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEEC
Confidence            3467999999999999999999999999999999998       7899999999999999997 9999999999999999


Q ss_pred             cccCC
Q 045516          492 RERGA  496 (675)
Q Consensus       492 ~~~~~  496 (675)
                      ..+..
T Consensus        78 ~~~~~   82 (90)
T 2dnq_A           78 KNKSK   82 (90)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            87643

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.65  E-value=9.8e-17  Score=132.39  Aligned_cols=74  Identities=23%  Similarity=0.475  Sum_probs=70.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       417 ~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ++|||+|||+++++++|+++|++||.|..|+|++++ +|+++|||||+|.+.++|.+||. +| ..|.|+.|.|.++
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            589999999999999999999999999999999997 79999999999999999999998 77 9999999999886

>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=99.65  E-value=3.8e-16  Score=136.21  Aligned_cols=78  Identities=19%  Similarity=0.284  Sum_probs=71.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-h--CCcccCCeeEEEEe
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-L--NGQMLGNRAIRLDF  490 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l--~g~~~~gr~i~V~~  490 (675)
                      ..+++|||+|||+.+++++|+++|.+||.|..|+|+++     +|||||+|.+.++|..||. |  ++..|.|++|+|.|
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~   87 (101)
T 2cq1_A           13 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQY   87 (101)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEE
Confidence            45689999999999999999999999999999999864     8999999999999999997 5  57789999999999


Q ss_pred             ccccCC
Q 045516          491 ARERGA  496 (675)
Q Consensus       491 a~~~~~  496 (675)
                      +..+..
T Consensus        88 a~~~~~   93 (101)
T 2cq1_A           88 SNHKEL   93 (101)
T ss_dssp             CSCSSC
T ss_pred             cCcccC
Confidence            986643

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=1.3e-15  Score=133.29  Aligned_cols=86  Identities=30%  Similarity=0.445  Sum_probs=80.5

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      ...++|||+|||..+++++    |+.+|..||.|..|.|+++..+|.++|||||+|.+.++|.+||. ||+..|+|+.|+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~----l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   88 (103)
T 2cq0_A           13 DDNATIRVTNLSEDTRETD----LQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILN   88 (103)
T ss_dssp             SSSEEEEEESCCTTCCHHH----HHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEE
Confidence            4479999999999999998    88999999999999999999999999999999999999999998 999999999999


Q ss_pred             EeccccCCCCC
Q 045516          595 VDEAKQRGDFG  605 (675)
Q Consensus       595 V~~a~~r~~~~  605 (675)
                      |.|+.++...+
T Consensus        89 v~~a~~~~~~~   99 (103)
T 2cq0_A           89 VEWAKPSTNSG   99 (103)
T ss_dssp             EEESSCCCCSC
T ss_pred             EEECCCCCCCC
Confidence            99998876554

>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=99.65  E-value=6.8e-17  Score=132.71  Aligned_cols=74  Identities=22%  Similarity=0.421  Sum_probs=70.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEec
Q 045516          418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFA  491 (675)
Q Consensus       418 tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a  491 (675)
                      +|||+|||+++++++|+++|++||.|..|+|+++. +++++|||||+|.+.++|.+||.+++..|.|+.|.|.++
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 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTTSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEC
Confidence            69999999999999999999999999999999987 799999999999999999999999999999999999874

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

Probab=99.65  E-value=3.2e-16  Score=142.55  Aligned_cols=81  Identities=17%  Similarity=0.307  Sum_probs=73.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHH----HHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEE
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQ----NFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIR  487 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~----~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~  487 (675)
                      ....++|||+|||+.+++++|+    ++|++||.|..|.|..  +++++|||||+|.+.++|..||. |||..|.|+.|+
T Consensus        26 ~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~--~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~  103 (127)
T 2a3j_A           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL--SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLV  103 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC--CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc--CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEE
Confidence            3457899999999999999876    7999999999998854  67899999999999999999997 999999999999


Q ss_pred             EEeccccC
Q 045516          488 LDFARERG  495 (675)
Q Consensus       488 V~~a~~~~  495 (675)
                      |.|+..+.
T Consensus       104 V~~a~~~~  111 (127)
T 2a3j_A          104 ITFSETPQ  111 (127)
T ss_dssp             EEECCCCC
T ss_pred             EEEccCcc
Confidence            99997654

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.65  E-value=1.2e-16  Score=133.61  Aligned_cols=72  Identities=25%  Similarity=0.439  Sum_probs=67.4

Q ss_pred             CceEEEcCCCCCC------CHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCe-eEE
Q 045516          416 SKTLFVGNLPFSV------EQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNR-AIR  487 (675)
Q Consensus       416 ~~tlfV~nLp~~~------te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr-~i~  487 (675)
                      +++|||+|||+.+      ++++|+++|++||.|..|+|+ ..+|+++|||||+|.+.++|.+||. |||..|.|+ .|+
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~-~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~   79 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFR   79 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC-CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec-CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEE
Confidence            3799999999999      789999999999999999988 4588999999999999999999998 999999999 887


Q ss_pred             E
Q 045516          488 L  488 (675)
Q Consensus       488 V  488 (675)
                      |
T Consensus        80 V   80 (81)
T 2krb_A           80 V   80 (81)
T ss_dssp             C
T ss_pred             e
Confidence            6

>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=99.65  E-value=1.1e-16  Score=145.25  Aligned_cols=82  Identities=27%  Similarity=0.468  Sum_probs=74.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEE-EEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVD-VRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~-v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a  491 (675)
                      ....++|||+|||+++++++|++||..||.|.. +.|+.+.+|+++|||||+|.+.++|.+||.||+..|.|+.|.|.++
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V~~a  101 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPI  101 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHHhCCCeECCcEEEEEEC
Confidence            446789999999999999999999999999988 4455555999999999999999999999999999999999999998


Q ss_pred             ccc
Q 045516          492 RER  494 (675)
Q Consensus       492 ~~~  494 (675)
                      ...
T Consensus       102 ~~~  104 (124)
T 1wel_A          102 TKK  104 (124)
T ss_dssp             CHH
T ss_pred             CHH
Confidence            653

>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=99.65  E-value=4.6e-16  Score=139.36  Aligned_cols=79  Identities=16%  Similarity=0.301  Sum_probs=71.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hC--CcccCCeeEEEEe
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LN--GQMLGNRAIRLDF  490 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~--g~~~~gr~i~V~~  490 (675)
                      ..+++|||+|||+.+++++|+++|++||.|..|+|+++     +|||||+|.+.++|.+||. |+  +..|.|++|+|.+
T Consensus        29 ~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~-----kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~  103 (119)
T 2ad9_A           29 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQF  103 (119)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG-----GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEE
Confidence            35689999999999999999999999999999999975     8999999999999999997 76  4689999999999


Q ss_pred             ccccCCC
Q 045516          491 ARERGAY  497 (675)
Q Consensus       491 a~~~~~~  497 (675)
                      +..+...
T Consensus       104 a~~k~~~  110 (119)
T 2ad9_A          104 SNHKELK  110 (119)
T ss_dssp             CSSSSCC
T ss_pred             ccCCCCC
Confidence            9876543

>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=99.65  E-value=8.2e-16  Score=135.88  Aligned_cols=78  Identities=26%  Similarity=0.364  Sum_probs=72.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCC-----eeE
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGN-----RAI  486 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~g-----r~i  486 (675)
                      ....++|||+|||+++++++|++||..||.|..|+|+.+      |||||+|.+.++|.+||. ||+..|.|     +.|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i   85 (108)
T 1x4c_A           12 RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   85 (108)
T ss_dssp             CSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEE
Confidence            456799999999999999999999999999999999975      999999999999999998 99999999     999


Q ss_pred             EEEeccccCC
Q 045516          487 RLDFARERGA  496 (675)
Q Consensus       487 ~V~~a~~~~~  496 (675)
                      +|.++..+..
T Consensus        86 ~V~~a~~~~~   95 (108)
T 1x4c_A           86 RVKVDGPRSP   95 (108)
T ss_dssp             EEEESSCCSC
T ss_pred             EEEeCCCCCC
Confidence            9999987643

>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=99.65  E-value=1.3e-16  Score=144.64  Aligned_cols=81  Identities=30%  Similarity=0.492  Sum_probs=74.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeE--EEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEe
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVV--DVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDF  490 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~--~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~  490 (675)
                      ....++|||+||||++|+++|++||+.| .|+  .|+|++++.|+++|||||+|.+.++|.+||.+++..|.||.|.|.+
T Consensus        39 ~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~~~~~~l~gR~I~V~~  117 (126)
T 2hgm_A           39 SANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGKHKERIGHRYIEVFK  117 (126)
T ss_dssp             SSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHTTTTCCBTTBCCCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHHHCCCEECCEEEEEEE
Confidence            4567899999999999999999999999 677  9999999889999999999999999999999888999999999988


Q ss_pred             cccc
Q 045516          491 ARER  494 (675)
Q Consensus       491 a~~~  494 (675)
                      +...
T Consensus       118 a~~~  121 (126)
T 2hgm_A          118 SSQE  121 (126)
T ss_dssp             ECHH
T ss_pred             CCHH
Confidence            7543

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=4.9e-16  Score=133.95  Aligned_cols=85  Identities=29%  Similarity=0.500  Sum_probs=78.9

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEE-EecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRI-SVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v-~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      +.++|||+|||..+++++    |+.+|..||.|..| +|+++..+|.++|||||+|.+.++|..||. ||+..|+|+.|+
T Consensus         4 ~~~~l~V~nLp~~~t~~~----l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   79 (96)
T 1x5t_A            4 GSSGIFIGNLDPEIDEKL----LYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPIT   79 (96)
T ss_dssp             CCCEEEEECCCTTCCHHH----HHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECE
T ss_pred             CCCEEEEeCCCCCCCHHH----HHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            479999999999999998    77889999999999 999998999999999999999999999999 999999999999


Q ss_pred             EeccccCCCCC
Q 045516          595 VDEAKQRGDFG  605 (675)
Q Consensus       595 V~~a~~r~~~~  605 (675)
                      |.++.++...+
T Consensus        80 v~~a~~~~~~~   90 (96)
T 1x5t_A           80 VSYAFKKDSKG   90 (96)
T ss_dssp             EEESCCCCCCC
T ss_pred             EEEecccCCCC
Confidence            99998766543

>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=99.65  E-value=5.4e-16  Score=146.57  Aligned_cols=83  Identities=27%  Similarity=0.481  Sum_probs=78.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      ....++|||+|||+++++++|+++|+.||.|..|+|+++. +|+++|||||+|.+.++|.+||. |||..|.|+.|+|.+
T Consensus        67 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  146 (158)
T 2kn4_A           67 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM  146 (158)
T ss_dssp             CCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            3457899999999999999999999999999999999997 89999999999999999999997 999999999999999


Q ss_pred             ccccC
Q 045516          491 ARERG  495 (675)
Q Consensus       491 a~~~~  495 (675)
                      +....
T Consensus       147 a~~~~  151 (158)
T 2kn4_A          147 ARYGR  151 (158)
T ss_dssp             ECCSS
T ss_pred             CCCCC
Confidence            97654

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.64  E-value=1.5e-15  Score=132.85  Aligned_cols=85  Identities=26%  Similarity=0.433  Sum_probs=78.7

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVV  595 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V  595 (675)
                      .+.++|||+|||+.+++++    |+++|..|| |..|+|+++..+|+++|||||+|.+.++|.+||.||+..|+|+.|+|
T Consensus        13 ~~~~~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           13 EPPYTAYVGNLPFNTVQGD----IDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRV   87 (103)
T ss_dssp             SSCEEEEEESCCTTCCHHH----HHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHGGGTTCEETTEECEE
T ss_pred             CCCeEEEEeCCCCCCCHHH----HHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHHhhCCCeECCeEEEE
Confidence            4479999999999999998    788999997 99999999999999999999999999999999999999999999999


Q ss_pred             eccccCCCCC
Q 045516          596 DEAKQRGDFG  605 (675)
Q Consensus       596 ~~a~~r~~~~  605 (675)
                      .++.++....
T Consensus        88 ~~a~~~~~~~   97 (103)
T 2dng_A           88 DIAEGRKQDK   97 (103)
T ss_dssp             EECCCCCCCC
T ss_pred             EEecCCCCCC
Confidence            9998765543

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=9.9e-16  Score=131.13  Aligned_cols=77  Identities=23%  Similarity=0.409  Sum_probs=71.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ....++|||+|||+++++++|+++|+.||.|..|+|+       ++||||+|.+.++|.+||. ||+..|.|+.|+|.++
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~-------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   79 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV-------KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLS   79 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC-------SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE-------CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            4567999999999999999999999999999999998       5599999999999999997 9999999999999999


Q ss_pred             cccCC
Q 045516          492 RERGA  496 (675)
Q Consensus       492 ~~~~~  496 (675)
                      ..+..
T Consensus        80 ~~~~~   84 (92)
T 2dgt_A           80 TSRLR   84 (92)
T ss_dssp             SCCCS
T ss_pred             cCCCC
Confidence            87643

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.64  E-value=7.7e-16  Score=136.59  Aligned_cols=82  Identities=15%  Similarity=0.183  Sum_probs=77.2

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      .+.++|||+||++.+++++    |+++|.+||.|..|.|+++..||+++|||||+|.+.++|.+||. |||..|+|+.|+
T Consensus         4 ~p~~~lfV~nL~~~~te~~----L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~   79 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETF----LKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIH   79 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHH----HHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCcEEEEECCCCCCCHHH----HHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            3478999999999999998    78899999999999999999999999999999999999999998 999999999999


Q ss_pred             EeccccC
Q 045516          595 VDEAKQR  601 (675)
Q Consensus       595 V~~a~~r  601 (675)
                      |.++..+
T Consensus        80 V~~a~~~   86 (110)
T 3s8s_A           80 AQLDIKG   86 (110)
T ss_dssp             EEECSTT
T ss_pred             EEECCCC
Confidence            9998654

>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=99.64  E-value=1.3e-15  Score=133.54  Aligned_cols=85  Identities=27%  Similarity=0.467  Sum_probs=78.9

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCC-CCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDT-GSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~t-G~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~  594 (675)
                      .+.++|||+|||+.+++++    |+.+|..|| |..|+|+++..+ |+++|||||+|.+.+.|.+||.||+..|+|+.|+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~----l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~   87 (104)
T 1wi8_A           13 SPPYTAFLGNLPYDVTEES----IKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIR   87 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHH----HHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECE
T ss_pred             CCCCEEEEeCCCCcCCHHH----HHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHHhcCCCEeCCcEEE
Confidence            3479999999999999998    788999999 999999999988 9999999999999999999999999999999999


Q ss_pred             EeccccCCCCC
Q 045516          595 VDEAKQRGDFG  605 (675)
Q Consensus       595 V~~a~~r~~~~  605 (675)
                      |.++.++....
T Consensus        88 V~~a~~~~~~~   98 (104)
T 1wi8_A           88 VDVADQAQDKD   98 (104)
T ss_dssp             EEECCCCCCCC
T ss_pred             EEEccCCCCCC
Confidence            99998866543

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.64  E-value=1.8e-16  Score=135.67  Aligned_cols=83  Identities=13%  Similarity=0.350  Sum_probs=75.5

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccC-cEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-h-CCceeCCeeeE
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCG-EITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-M-SGTEIGGYSLV  594 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G-~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-l-ng~~~~Gr~l~  594 (675)
                      +++|||+|||+.+++++    |+++|..|| .|..|+|++++.+|.++|||||+|.+.++|.+||+ | |+..|+|+.|+
T Consensus         1 S~~i~v~nLp~~~te~~----l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~   76 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDD----IRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVS   76 (91)
T ss_dssp             CCEEEEETCCSSCCHHH----HHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEE
T ss_pred             CCEEEEeCCCCCCCHHH----HHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEE
Confidence            47899999999999999    678888889 89999999999999999999999999999999998 6 56689999999


Q ss_pred             EeccccCCCC
Q 045516          595 VDEAKQRGDF  604 (675)
Q Consensus       595 V~~a~~r~~~  604 (675)
                      |.|+.++...
T Consensus        77 V~~a~~~~~~   86 (91)
T 2lxi_A           77 MHYSDPKPKI   86 (91)
T ss_dssp             EECCCSCCCC
T ss_pred             EEEcCCCCCC
Confidence            9999887544

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=2.4e-15  Score=134.49  Aligned_cols=83  Identities=22%  Similarity=0.322  Sum_probs=76.5

Q ss_pred             CCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeee
Q 045516          515 GQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSL  593 (675)
Q Consensus       515 ~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l  593 (675)
                      ....++|||+|||..+++++    |+++|..||.|..|+|+++..++.++|||||+|.+.++|.+||. ||+ .|+|+.|
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l   88 (116)
T 2cqd_A           14 DTTFTKIFVGGLPYHTTDAS----LRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKA   88 (116)
T ss_dssp             SCSSSEEEEECCCSSCCHHH----HHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHH----HHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEE
Confidence            34579999999999999998    77889999999999999999999999999999999999999999 887 8999999


Q ss_pred             EEeccccCC
Q 045516          594 VVDEAKQRG  602 (675)
Q Consensus       594 ~V~~a~~r~  602 (675)
                      +|.++.+..
T Consensus        89 ~V~~a~~~~   97 (116)
T 2cqd_A           89 NVNLAYLGA   97 (116)
T ss_dssp             EEEESTTTC
T ss_pred             EEEEcccCC
Confidence            999997643

>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=99.64  E-value=6.4e-17  Score=137.88  Aligned_cols=78  Identities=31%  Similarity=0.531  Sum_probs=71.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecccc
Q 045516          417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARER  494 (675)
Q Consensus       417 ~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~~  494 (675)
                      ++|||+|||+++++++|+++|+.||.|..|+|+++. +|+++|||||+|.+.+ |.+|+. |||..|.|+.|+|.++...
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~   80 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPK   80 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC---
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            689999999999999999999999999999999997 7999999999999999 999998 9999999999999999765


Q ss_pred             C
Q 045516          495 G  495 (675)
Q Consensus       495 ~  495 (675)
                      .
T Consensus        81 ~   81 (90)
T 2ki2_A           81 K   81 (90)
T ss_dssp             -
T ss_pred             C
Confidence            4

>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=99.64  E-value=2.3e-16  Score=140.21  Aligned_cols=83  Identities=17%  Similarity=0.289  Sum_probs=75.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHH---HHhhhCCCeEEEEEeeCC-C---CCcccEEEEEecCHHHHHHHHH-hCCcccCCe
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQ---NFFSEVAEVVDVRLSSDA-D---GRFKGYGHVEFASVEDAHKAIE-LNGQMLGNR  484 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~---~~F~~~G~I~~v~i~~~~-~---g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr  484 (675)
                      ....++|||+|||+.+++++|+   ++|.+||.|..|+|+++. +   ++++|||||+|.+.++|.+||. |||..|.|+
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr   91 (111)
T 2cpi_A           12 VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGR   91 (111)
T ss_dssp             CCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             ccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCE
Confidence            3457899999999999999999   999999999999999886 3   3567999999999999999998 999999999


Q ss_pred             eEEEEeccccC
Q 045516          485 AIRLDFARERG  495 (675)
Q Consensus       485 ~i~V~~a~~~~  495 (675)
                      .|+|.++..+.
T Consensus        92 ~l~V~~a~~k~  102 (111)
T 2cpi_A           92 TLKASLGTTKY  102 (111)
T ss_dssp             EEEEESCCCCS
T ss_pred             EEEEEeccccc
Confidence            99999998764

>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=99.64  E-value=1.2e-15  Score=133.90  Aligned_cols=86  Identities=24%  Similarity=0.406  Sum_probs=79.8

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      ...++|||+|||..+++++    |+.+|..||.|..|.|+++..++.++|||||+|.+.++|.+||. ||+..|+|+.|+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   88 (105)
T 1x5u_A           13 NQDATVYVGGLDEKVSEPL----LWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIR   88 (105)
T ss_dssp             CTTTEEEEECCCTTCCHHH----HHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCE
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEE
Confidence            3479999999999999998    77899999999999999999899999999999999999999998 999999999999


Q ss_pred             EeccccCCCCC
Q 045516          595 VDEAKQRGDFG  605 (675)
Q Consensus       595 V~~a~~r~~~~  605 (675)
                      |.++.++....
T Consensus        89 v~~a~~~~~~~   99 (105)
T 1x5u_A           89 VNKASAHNKNL   99 (105)
T ss_dssp             EEETTTTSCCC
T ss_pred             EEECCCCCcCC
Confidence            99998766543

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=9e-16  Score=130.82  Aligned_cols=76  Identities=25%  Similarity=0.500  Sum_probs=70.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ....++|||+|||+++++++|+.+|.+||.|..|+|+       ++||||+|.+.++|.+||. ||+..|.|+.|+|.++
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~-------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   78 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV-------KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELS   78 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC-------SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            3467899999999999999999999999999999998       5699999999999999998 9999999999999999


Q ss_pred             cccC
Q 045516          492 RERG  495 (675)
Q Consensus       492 ~~~~  495 (675)
                      ....
T Consensus        79 ~~~~   82 (90)
T 2dnp_A           79 TKGQ   82 (90)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.63  E-value=2.3e-16  Score=145.41  Aligned_cols=83  Identities=27%  Similarity=0.481  Sum_probs=78.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      ....++|||+|||+++++++|+++|+.||.|..|+|+.+. +++++|||||+|.+.++|.+||. ||+..|.|+.|+|.+
T Consensus        44 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~  123 (135)
T 2lea_A           44 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM  123 (135)
T ss_dssp             GGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            4567899999999999999999999999999999999987 89999999999999999999997 999999999999999


Q ss_pred             ccccC
Q 045516          491 ARERG  495 (675)
Q Consensus       491 a~~~~  495 (675)
                      +....
T Consensus       124 a~~~~  128 (135)
T 2lea_A          124 ARYGR  128 (135)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            97653

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.63  E-value=2.7e-16  Score=144.87  Aligned_cols=124  Identities=18%  Similarity=0.297  Sum_probs=79.6

Q ss_pred             cEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEeccccCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHH
Q 045516          458 GYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVR  536 (675)
Q Consensus       458 G~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~  536 (675)
                      -|+|++|.+...+..||. ++|....|+.. +.+..+                  .......++|||+|||..+++++  
T Consensus         5 ~~~~~~~~~~~~~~~a~~~~~g~~~~g~~~-~~~~~~------------------~~~~~~~~~l~V~nLp~~~te~~--   63 (135)
T 2lea_A            5 HHHHHHSSGLVPRGSHMASMTGGQQMGRGS-MSYGRP------------------PPDVEGMTSLKVDNLTYRTSPDT--   63 (135)
T ss_dssp             -------------------------------CCSCCS------------------CSSGGGCCCEEEECCCSSCHHHH--
T ss_pred             ccccccccCCCchhhhhhhccCCCCCCCCC-CCcCCC------------------CCCCCCCCEEEEeCCCCCCCHHH--
Confidence            366777778888888887 88777666541 111111                  11122368999999999999998  


Q ss_pred             HHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEeccccCCCC
Q 045516          537 ASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVDEAKQRGDF  604 (675)
Q Consensus       537 ~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~~a~~r~~~  604 (675)
                        |+.+|..||.|..|.|+++..++.++|||||+|.+.++|.+||. ||+..|+|+.|+|.|+++....
T Consensus        64 --L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~~~  130 (135)
T 2lea_A           64 --LRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPP  130 (135)
T ss_dssp             --HHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCCCCC
T ss_pred             --HHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCCC
Confidence              77899999999999999999999999999999999999999998 9999999999999999875543

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.63  E-value=4.6e-15  Score=132.42  Aligned_cols=86  Identities=21%  Similarity=0.404  Sum_probs=79.8

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      ...++|||+|||..+++++    |+.+|..||.|..|+|+++..+|.++|||||+|.+.++|.+||. ||+..|+|+.|+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   88 (115)
T 2dgo_A           13 SNHFHVFVGDLSPEITTED----IKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIR   88 (115)
T ss_dssp             TTCEEEEEESCCTTCCHHH----HHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECE
T ss_pred             CCCcEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            3479999999999999998    77899999999999999998899999999999999999999998 999999999999


Q ss_pred             EeccccCCCCC
Q 045516          595 VDEAKQRGDFG  605 (675)
Q Consensus       595 V~~a~~r~~~~  605 (675)
                      |.|+.++....
T Consensus        89 V~~a~~~~~~~   99 (115)
T 2dgo_A           89 TNWATRKPPAP   99 (115)
T ss_dssp             EEESSCCCCCS
T ss_pred             EEEccCCCCCC
Confidence            99998776543

>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=99.63  E-value=1.6e-15  Score=131.11  Aligned_cols=85  Identities=14%  Similarity=0.235  Sum_probs=79.1

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEE
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVV  595 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V  595 (675)
                      ..++|||+|||+.+++++|+.+|+.+|..||.|..|+|+++..+   +|||||+|.+.++|.+||. |||..|+|+.|+|
T Consensus         8 ~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V   84 (96)
T 2dgx_A            8 NGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILV   84 (96)
T ss_dssp             SCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            36899999999999999999999999999999999999998765   8999999999999999998 9999999999999


Q ss_pred             eccccCCCC
Q 045516          596 DEAKQRGDF  604 (675)
Q Consensus       596 ~~a~~r~~~  604 (675)
                      .+++++...
T Consensus        85 ~~a~~~~~~   93 (96)
T 2dgx_A           85 SLATGASGP   93 (96)
T ss_dssp             EECCCSSCC
T ss_pred             EEcCCCCCC
Confidence            999876543

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=7.7e-16  Score=134.35  Aligned_cols=86  Identities=27%  Similarity=0.511  Sum_probs=79.4

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      ...++|||+|||+.+++++    |+++|..||.|..|.|+++..++.++|||||+|.+.++|..||. ||+..|+|+.|+
T Consensus        10 ~~~~~l~v~nLp~~~t~~~----l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   85 (102)
T 1x5s_A           10 SDEGKLFVGGLSFDTNEQS----LEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIR   85 (102)
T ss_dssp             CCCSEEEEESCCTTCCHHH----HHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCE
T ss_pred             CCCCEEEEECCCCCCCHHH----HHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            4479999999999999998    77888889999999999999999999999999999999999997 999999999999


Q ss_pred             EeccccCCCCC
Q 045516          595 VDEAKQRGDFG  605 (675)
Q Consensus       595 V~~a~~r~~~~  605 (675)
                      |.++.++....
T Consensus        86 v~~a~~~~~~~   96 (102)
T 1x5s_A           86 VDQAGKSSDNR   96 (102)
T ss_dssp             EEEEECCCCCC
T ss_pred             EEECCCCCCCC
Confidence            99998776543

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.63  E-value=7e-16  Score=142.50  Aligned_cols=79  Identities=29%  Similarity=0.518  Sum_probs=74.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      ....++|||+|||+.+++++|+++|..||.|..|+|++++ +++++|||||+|.+.++|.+||. |||..|.|+.|+|.+
T Consensus        60 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  139 (140)
T 2ku7_A           60 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL  139 (140)
T ss_dssp             CSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEEC
T ss_pred             CCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            3467999999999999999999999999999999999996 89999999999999999999997 999999999999987


Q ss_pred             c
Q 045516          491 A  491 (675)
Q Consensus       491 a  491 (675)
                      +
T Consensus       140 A  140 (140)
T 2ku7_A          140 A  140 (140)
T ss_dssp             -
T ss_pred             C
Confidence            5

>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=99.63  E-value=8.8e-17  Score=148.51  Aligned_cols=123  Identities=13%  Similarity=0.174  Sum_probs=73.9

Q ss_pred             ccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEeccccCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHH
Q 045516          457 KGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQV  535 (675)
Q Consensus       457 kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i  535 (675)
                      .|+||..|..++.+-.++. +... +.|..+--....                ..........++|||+|||+.+++++ 
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~-~gg~~~g~~~g~----------------~~~~~~~~~~~~lfV~nLp~~~te~d-   62 (139)
T 2hgn_A            1 MGSSHHHHHHSSGLVPRGSHMASM-TGGQQMGRGSGD----------------SEFTVQSTTGHCVHMRGLPYKATEND-   62 (139)
T ss_dssp             -------------------------------------------------------------CCCCEECCSCCTTCCHHH-
T ss_pred             CCcccccccCccccchhcccchhc-cCCCCCCCCCCC----------------cccCCCCCCCCEEEEeCCCCCCCHHH-
Confidence            3789999998887776664 3222 222222100000                00011223368999999999999998 


Q ss_pred             HHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEeccccCC
Q 045516          536 RASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDEAKQRG  602 (675)
Q Consensus       536 ~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~~a~~r~  602 (675)
                         |+++|..|| |..|+|+++.. |+++|||||+|.+.++|.+||.+|+..|+||.|.|.++.++.
T Consensus        63 ---L~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al~~~g~~l~gR~i~V~~a~~~~  124 (139)
T 2hgn_A           63 ---IYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAMSKDRANMQHRYIELFLNSTTG  124 (139)
T ss_dssp             ---HHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHTTCCSCSSSSCCCCCEECCCSC
T ss_pred             ---HHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHHhhCCCEECCEEEEEEECCCCC
Confidence               789999999 77999999976 999999999999999999999999999999999999887654

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

Probab=99.63  E-value=8.6e-16  Score=132.92  Aligned_cols=78  Identities=24%  Similarity=0.439  Sum_probs=70.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ....++|||+|||+++++++|+.+|..||.|. +.|+.   ++++|||||+|.+.++|.+||. |||..|.|+.|+|.++
T Consensus        16 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~---~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   91 (97)
T 2e5j_A           16 APLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTW---QGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALA   91 (97)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEE---ETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEEC
T ss_pred             CCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEc---CCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            44578999999999999999999999999997 66664   4789999999999999999997 9999999999999999


Q ss_pred             ccc
Q 045516          492 RER  494 (675)
Q Consensus       492 ~~~  494 (675)
                      ..+
T Consensus        92 ~~~   94 (97)
T 2e5j_A           92 RQQ   94 (97)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            765

>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=99.63  E-value=9.1e-17  Score=148.40  Aligned_cols=82  Identities=30%  Similarity=0.479  Sum_probs=75.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEecc
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a~  492 (675)
                      ....++|||+|||+++|+++|++||++|| |+.|+|+++.+|+++|||||+|.+.++|.+||.+|+..|.||.|.|.++.
T Consensus        43 ~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al~~~g~~l~gR~i~V~~a~  121 (139)
T 2hgn_A           43 STTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAMSKDRANMQHRYIELFLNS  121 (139)
T ss_dssp             --CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHTTCCSCSSSSCCCCCEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHHhhCCCEECCEEEEEEECC
Confidence            34568999999999999999999999999 77999999989999999999999999999999999999999999999887


Q ss_pred             ccC
Q 045516          493 ERG  495 (675)
Q Consensus       493 ~~~  495 (675)
                      ...
T Consensus       122 ~~~  124 (139)
T 2hgn_A          122 TTG  124 (139)
T ss_dssp             CSC
T ss_pred             CCC
Confidence            543

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=9.8e-16  Score=133.69  Aligned_cols=86  Identities=27%  Similarity=0.470  Sum_probs=79.9

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      ...++|||+|||+.+++++    |+++|..||.|..|.|+++..++.++|||||+|.+.++|.+||. ||+..|+|+.|+
T Consensus        10 ~~~~~l~V~nLp~~~t~~~----l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   85 (102)
T 2cqb_A           10 TTKRVLYVGGLAEEVDDKV----LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIR   85 (102)
T ss_dssp             CCCSCEEEESCCSSCCHHH----HHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEE
Confidence            3479999999999999998    78899999999999999999999999999999999999999997 999999999999


Q ss_pred             EeccccCCCCC
Q 045516          595 VDEAKQRGDFG  605 (675)
Q Consensus       595 V~~a~~r~~~~  605 (675)
                      |.++.++....
T Consensus        86 V~~a~~~~~~~   96 (102)
T 2cqb_A           86 VNLAKPMRIKE   96 (102)
T ss_dssp             EEECCCCCCCC
T ss_pred             EEeCCCCCCCC
Confidence            99998776554

>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=99.63  E-value=8.5e-16  Score=133.43  Aligned_cols=78  Identities=26%  Similarity=0.448  Sum_probs=72.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ....++|||+|||+.+++++|+++|.+||.|..|+|+++     +|||||+|.+.++|.+||. ||+..|.|+.|+|.++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~-----kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a   86 (99)
T 2cpj_A           12 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFA   86 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT-----TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEc
Confidence            456789999999999999999999999999999999854     8999999999999999997 9999999999999999


Q ss_pred             cccC
Q 045516          492 RERG  495 (675)
Q Consensus       492 ~~~~  495 (675)
                      ....
T Consensus        87 ~~~~   90 (99)
T 2cpj_A           87 CHSA   90 (99)
T ss_dssp             SCCS
T ss_pred             CCCC
Confidence            7654

>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=99.63  E-value=1.9e-15  Score=132.30  Aligned_cols=77  Identities=30%  Similarity=0.442  Sum_probs=71.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecc
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~  492 (675)
                      ...++|||+|||+++++++|++||.+||.|..|+|+       +|||||+|.+.++|.+||. ||+..|.|+.|+|.++.
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~-------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   81 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL-------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAK   81 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC-------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE-------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcC
Confidence            456899999999999999999999999999999997       6799999999999999998 99999999999999998


Q ss_pred             ccCCC
Q 045516          493 ERGAY  497 (675)
Q Consensus       493 ~~~~~  497 (675)
                      .....
T Consensus        82 ~~~~~   86 (103)
T 2dgu_A           82 PPDQK   86 (103)
T ss_dssp             CCCCC
T ss_pred             CCccc
Confidence            76543

>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=99.63  E-value=1e-15  Score=132.34  Aligned_cols=78  Identities=22%  Similarity=0.419  Sum_probs=71.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccC--CeeEEEE
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLG--NRAIRLD  489 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~--gr~i~V~  489 (675)
                      ....++|||+|||+++++++|+++|.+||.|..|+|+.+     +|||||+|.+.++|.+||. ||+..|.  |+.|+|.
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~   88 (97)
T 1why_A           14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD   88 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-----SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC-----CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEE
Confidence            345689999999999999999999999999999999854     7899999999999999998 9999999  9999999


Q ss_pred             eccccC
Q 045516          490 FARERG  495 (675)
Q Consensus       490 ~a~~~~  495 (675)
                      ++..+.
T Consensus        89 ~a~~~~   94 (97)
T 1why_A           89 FAKSGP   94 (97)
T ss_dssp             ECCCCC
T ss_pred             ECCCCC
Confidence            997653

>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=99.63  E-value=9.6e-16  Score=129.00  Aligned_cols=75  Identities=23%  Similarity=0.423  Sum_probs=70.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-h-CCcccCCeeEEEEe
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-L-NGQMLGNRAIRLDF  490 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l-~g~~~~gr~i~V~~  490 (675)
                      ....++|||+|||+++++++|+++|.+||.|..|+|+++     +|||||+|.+.++|.+||. | |+..|.|+.|+|.+
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~-----kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~   83 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR-----QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKW   83 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG-----GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEE
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC-----CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEe
Confidence            456789999999999999999999999999999999963     8999999999999999998 8 99999999999998


Q ss_pred             cc
Q 045516          491 AR  492 (675)
Q Consensus       491 a~  492 (675)
                      ++
T Consensus        84 ak   85 (85)
T 2ytc_A           84 GR   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            73

>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=99.62  E-value=1.8e-15  Score=135.11  Aligned_cols=86  Identities=22%  Similarity=0.337  Sum_probs=79.8

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      ...++|||+|||+.+++++    |+++|..||.|..|+|+++..++.++|||||+|.+.++|.+||. ||+..|+|+.|+
T Consensus        23 ~~~~~l~V~nLp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   98 (115)
T 2cpz_A           23 PEGANLFIYHLPQEFGDQD----LLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLK   98 (115)
T ss_dssp             STTCCEEEESCCSSCCHHH----HHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCcEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            4478999999999999998    77899999999999999999899999999999999999999997 999999999999


Q ss_pred             EeccccCCCCC
Q 045516          595 VDEAKQRGDFG  605 (675)
Q Consensus       595 V~~a~~r~~~~  605 (675)
                      |.|++++....
T Consensus        99 V~~a~~~~~~~  109 (115)
T 2cpz_A           99 VQLKRSKNDSK  109 (115)
T ss_dssp             EECCCCSCCCC
T ss_pred             EEEcCCCCcCC
Confidence            99998876544

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.62  E-value=1.5e-15  Score=132.85  Aligned_cols=85  Identities=22%  Similarity=0.374  Sum_probs=79.0

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      ...++|||+|||..+++++    |+.+|..||.|..|.|+++..++.++|||||+|.+.++|.+||. ||+..|+|+.|+
T Consensus        11 ~~~~~l~V~nLp~~~t~~~----l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   86 (103)
T 2dnm_A           11 DGMITLKVDNLTYRTSPDS----LRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELR   86 (103)
T ss_dssp             SCCCEEEEESCCTTCCHHH----HHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCE
T ss_pred             CCCeEEEEeCCCCCCCHHH----HHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEE
Confidence            3479999999999999998    77899999999999999999999999999999999999999998 999999999999


Q ss_pred             EeccccCCCC
Q 045516          595 VDEAKQRGDF  604 (675)
Q Consensus       595 V~~a~~r~~~  604 (675)
                      |.++.+....
T Consensus        87 V~~a~~~~~~   96 (103)
T 2dnm_A           87 VQVARYGRRD   96 (103)
T ss_dssp             EEECSSCCSC
T ss_pred             EEECCcCCCC
Confidence            9999875544

>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=99.62  E-value=1.1e-15  Score=135.12  Aligned_cols=77  Identities=22%  Similarity=0.464  Sum_probs=72.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEeccc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~  493 (675)
                      ..++|||+|||+.+++++|+.+|..||.|..|+|+++     +|||||+|.+.++|.+||. |||..|.|+.|+|.++..
T Consensus        24 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   98 (109)
T 1x4g_A           24 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKE   98 (109)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-----CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecCC
Confidence            4689999999999999999999999999999999976     8999999999999999997 999999999999999987


Q ss_pred             cCC
Q 045516          494 RGA  496 (675)
Q Consensus       494 ~~~  496 (675)
                      +..
T Consensus        99 ~~~  101 (109)
T 1x4g_A           99 SPD  101 (109)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            653

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.62  E-value=5e-16  Score=137.78  Aligned_cols=78  Identities=23%  Similarity=0.292  Sum_probs=70.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCC-CeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVA-EVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G-~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ...++|||+|||+++++++|++||..|| .|..|+|+.   +.++|||||+|.+.++|.+||. |||..|.|+.|+|.++
T Consensus        26 ~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~---~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a  102 (111)
T 2jvr_A           26 AKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT---RDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERD  102 (111)
T ss_dssp             CCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS---CSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc---CCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            4568999999999999999999999999 899999863   3579999999999999999997 9999999999999998


Q ss_pred             ccc
Q 045516          492 RER  494 (675)
Q Consensus       492 ~~~  494 (675)
                      ...
T Consensus       103 ~~~  105 (111)
T 2jvr_A          103 DNP  105 (111)
T ss_dssp             CC-
T ss_pred             CCC
Confidence            654

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=1.3e-15  Score=136.35  Aligned_cols=84  Identities=20%  Similarity=0.369  Sum_probs=78.9

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEec
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDE  597 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~~  597 (675)
                      .++|||+|||+.+++++    |+.+|..||.|..|+|+++..+|.++|||||+|.+.+.|.+||.+|+..|+|+.|+|.+
T Consensus        27 ~~~l~V~nLp~~~te~~----l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~V~~  102 (116)
T 1x4b_A           27 FRKLFIGGLSFETTEES----LRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKR  102 (116)
T ss_dssp             HTEEEEECCTTCCCHHH----HHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEEC
T ss_pred             CCEEEEeCCCCCCCHHH----HHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHhCCcEECCEEEEEEE
Confidence            68999999999999998    77899999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCCC
Q 045516          598 AKQRGDFG  605 (675)
Q Consensus       598 a~~r~~~~  605 (675)
                      +.++....
T Consensus       103 a~~~~~~~  110 (116)
T 1x4b_A          103 AVAREESG  110 (116)
T ss_dssp             CSSCCCCC
T ss_pred             CCCCccCC
Confidence            98876543

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.62  E-value=6.8e-16  Score=134.51  Aligned_cols=74  Identities=23%  Similarity=0.399  Sum_probs=69.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEeccc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~  493 (675)
                      ..++|||+|||+++++++|+++|..||.|..|+|+     +++|||||+|.+.++|.+||. |||..|.|+.|+|.++..
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~-----~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  100 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY-----PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKE  100 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE-----TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCC
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe-----cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccC
Confidence            46899999999999999999999999999999998     458999999999999999997 999999999999999864

>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=99.62  E-value=1.3e-15  Score=131.83  Aligned_cols=75  Identities=24%  Similarity=0.490  Sum_probs=70.5

Q ss_pred             CCCCceEEEcCCCC-CCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          413 SGGSKTLFVGNLPF-SVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       413 ~~~~~tlfV~nLp~-~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      ....++|||+|||+ ++++++|+++|..||.|..|+|.       +|||||+|.+.++|.+||. |||..|.|+.|+|.+
T Consensus        19 ~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~-------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   91 (97)
T 2xnq_A           19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEV   91 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC-------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            45789999999999 99999999999999999999994       8999999999999999998 999999999999999


Q ss_pred             cccc
Q 045516          491 ARER  494 (675)
Q Consensus       491 a~~~  494 (675)
                      +..+
T Consensus        92 a~~~   95 (97)
T 2xnq_A           92 SSSN   95 (97)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            8654

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.62  E-value=2.4e-15  Score=132.28  Aligned_cols=86  Identities=23%  Similarity=0.461  Sum_probs=79.6

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEeccc-CCCCCeeeEEEEEeCCHHHHHHHHH-h-CCceeCCee
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKD-YDTGSVKGIAYLDFTDADSFNKALE-M-SGTEIGGYS  592 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d-~~tG~~rG~afV~F~~~e~A~~Al~-l-ng~~~~Gr~  592 (675)
                      ...++|||+|||..+++++    |+.+|..||.|..|+|+++ ..+|.++|||||+|.+.++|.+||. | |+..|+|+.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~   88 (107)
T 2cph_A           13 QTTSKILVRNIPFQANQRE----IRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRR   88 (107)
T ss_dssp             SCCCCEEEESCCTTCCHHH----HHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCB
T ss_pred             CCCCEEEEeCCCCcCCHHH----HHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCE
Confidence            4479999999999999998    7788999999999999999 7899999999999999999999998 8 999999999


Q ss_pred             eEEeccccCCCCC
Q 045516          593 LVVDEAKQRGDFG  605 (675)
Q Consensus       593 l~V~~a~~r~~~~  605 (675)
                      |+|.|+.++....
T Consensus        89 l~v~~a~~~~~~~  101 (107)
T 2cph_A           89 LVLEWADSEVTVQ  101 (107)
T ss_dssp             CEEEECCCCCCCC
T ss_pred             EEEEeCCCCCCCC
Confidence            9999998876654

>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=99.62  E-value=3.6e-16  Score=135.06  Aligned_cols=81  Identities=20%  Similarity=0.469  Sum_probs=74.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHH----HHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEE
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQ----NFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIR  487 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~----~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~  487 (675)
                      ...+++|||+|||+++++++|+    ++|.+||.|..|+|+.  +|.++|||||+|.+.++|..||. |||..|.|+.|+
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~--~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   82 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   82 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH--HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc--CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEE
Confidence            4567999999999999999999    9999999999999874  57789999999999999999997 999999999999


Q ss_pred             EEeccccC
Q 045516          488 LDFARERG  495 (675)
Q Consensus       488 V~~a~~~~  495 (675)
                      |.++....
T Consensus        83 v~~a~~~~   90 (97)
T 1nu4_A           83 IQYAKTDS   90 (97)
T ss_dssp             EEECSSCC
T ss_pred             EEEccCCC
Confidence            99997653

>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=99.62  E-value=2.3e-15  Score=134.92  Aligned_cols=82  Identities=27%  Similarity=0.501  Sum_probs=76.5

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEE
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVV  595 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V  595 (675)
                      ..++|||+|||..+++++    |+.+|..||.|..|.|+.+. +|.++|||||+|.+.++|.+||. |||..|+|+.|+|
T Consensus         6 ~~~~l~V~nLp~~~t~~~----l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V   80 (116)
T 2fy1_A            6 HPGKLFIGGLNRETNEKM----LKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKV   80 (116)
T ss_dssp             SCCEEEEECCTTTCCHHH----HHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEE
T ss_pred             CCCEEEEeCCCCCCCHHH----HHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            368999999999999998    77889999999999999997 89999999999999999999998 9999999999999


Q ss_pred             eccccCCC
Q 045516          596 DEAKQRGD  603 (675)
Q Consensus       596 ~~a~~r~~  603 (675)
                      .++.++..
T Consensus        81 ~~a~~~~~   88 (116)
T 2fy1_A           81 EQAKKPSF   88 (116)
T ss_dssp             EECCCSSC
T ss_pred             EECCCCCC
Confidence            99986554

>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=99.62  E-value=1.4e-15  Score=135.71  Aligned_cols=80  Identities=25%  Similarity=0.491  Sum_probs=72.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCe----EEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEE
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEV----VDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRL  488 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I----~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V  488 (675)
                      ...++|||+|||+++++++|++||..||.|    ..+++.   +++++|||||+|.+.++|.+||. ||+..|.|+.|+|
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~---~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v   99 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM---TGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVI   99 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEE---CSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcC---CCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            457899999999999999999999999998    555555   78899999999999999999997 9999999999999


Q ss_pred             EeccccCC
Q 045516          489 DFARERGA  496 (675)
Q Consensus       489 ~~a~~~~~  496 (675)
                      .++..+..
T Consensus       100 ~~a~~~~~  107 (115)
T 2cpx_A          100 EFGKNKKQ  107 (115)
T ss_dssp             EECCCCSC
T ss_pred             EEccCCCC
Confidence            99987654

>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=99.62  E-value=2e-15  Score=127.54  Aligned_cols=81  Identities=22%  Similarity=0.438  Sum_probs=75.2

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEE
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVV  595 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V  595 (675)
                      ..++|||+|||..+++++    |+.+|..||.|..|.|+++..+|.++|||||+|.+.++|..||. |||..|+|+.|+|
T Consensus         5 ~~~~l~v~nlp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   80 (87)
T 3bs9_A            5 SHFHVFVGDLSPEITTAA----IAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRT   80 (87)
T ss_dssp             -CEEEEEESCCTTCCHHH----HHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CceEEEEeCCCCCCCHHH----HHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            478999999999999998    77889999999999999999899999999999999999999998 9999999999999


Q ss_pred             eccccC
Q 045516          596 DEAKQR  601 (675)
Q Consensus       596 ~~a~~r  601 (675)
                      .|+.++
T Consensus        81 ~~a~~k   86 (87)
T 3bs9_A           81 NWATRK   86 (87)
T ss_dssp             EEEC--
T ss_pred             EecCCC
Confidence            999865

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=3.4e-15  Score=129.60  Aligned_cols=76  Identities=29%  Similarity=0.480  Sum_probs=70.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhC--CCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEE
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEV--AEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLD  489 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~--G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~  489 (675)
                      ....++|||+|||+++++++|+++|.+|  |.|..|+++       +|||||+|.+.++|.+||. ||+..|.|+.|+|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   84 (99)
T 2cpd_A           12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI-------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVT   84 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC-------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEE
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe-------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            3457899999999999999999999999  999999886       7899999999999999998 99999999999999


Q ss_pred             eccccC
Q 045516          490 FARERG  495 (675)
Q Consensus       490 ~a~~~~  495 (675)
                      ++..+.
T Consensus        85 ~a~~~~   90 (99)
T 2cpd_A           85 LAKPVD   90 (99)
T ss_dssp             CCCCCC
T ss_pred             ECCCCC
Confidence            998654

>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=99.62  E-value=3.1e-15  Score=132.51  Aligned_cols=86  Identities=28%  Similarity=0.419  Sum_probs=79.8

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hC------Ccee
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MS------GTEI  588 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-ln------g~~~  588 (675)
                      ...++|||+|||+.+++++    |+.+|..||.|..|+|+++..+|.++|||||+|.+.++|.+||. ||      +..|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~   88 (111)
T 1x4h_A           13 TEGKTVFIRNLSFDSEEEA----LGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKL   88 (111)
T ss_dssp             CCCCCEEEESCCTTCCHHH----HHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEES
T ss_pred             CCCCEEEEECCCCCCCHHH----HHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEE
Confidence            3478999999999999998    77889999999999999999999999999999999999999998 99      9999


Q ss_pred             CCeeeEEeccccCCCCC
Q 045516          589 GGYSLVVDEAKQRGDFG  605 (675)
Q Consensus       589 ~Gr~l~V~~a~~r~~~~  605 (675)
                      +|+.|+|.|+.++....
T Consensus        89 ~g~~l~v~~a~~~~~~~  105 (111)
T 1x4h_A           89 DGRQLKVDLAVTRDEAA  105 (111)
T ss_dssp             SSCEEEEECCCCCCCCC
T ss_pred             cCEEEEEEECCCCccCC
Confidence            99999999998876554

>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=99.62  E-value=4.6e-16  Score=137.81  Aligned_cols=77  Identities=17%  Similarity=0.288  Sum_probs=69.5

Q ss_pred             CCCceEEEcCCCCC-CCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hC--CcccCCeeEEEE
Q 045516          414 GGSKTLFVGNLPFS-VEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LN--GQMLGNRAIRLD  489 (675)
Q Consensus       414 ~~~~tlfV~nLp~~-~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~--g~~~~gr~i~V~  489 (675)
                      ..+++|||+|||++ +++++|+++|.+||.|.+|+|++     ++|||||+|.+.++|..||. ||  +..|.||.|+|.
T Consensus        23 ~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~-----~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~   97 (112)
T 1x4f_A           23 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR-----MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVD   97 (112)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET-----TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEE
T ss_pred             CCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec-----CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            34789999999998 99999999999999999999984     48999999999999999997 75  567999999999


Q ss_pred             eccccC
Q 045516          490 FARERG  495 (675)
Q Consensus       490 ~a~~~~  495 (675)
                      ++..+.
T Consensus        98 ~a~~~~  103 (112)
T 1x4f_A           98 LSEKYK  103 (112)
T ss_dssp             EECSCS
T ss_pred             ECcccc
Confidence            997654

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.62  E-value=1.9e-15  Score=130.87  Aligned_cols=85  Identities=21%  Similarity=0.394  Sum_probs=77.8

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCC---CCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCee
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYD---TGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYS  592 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~---tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~  592 (675)
                      +.++|||+|||+.+++++    |+++|..||.|..|.|+++..   ++.++|||||+|.+.++|..||. ||+..|+|+.
T Consensus         4 ~~~~l~V~nLp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   79 (98)
T 2cpf_A            4 GSSGLFIKNLNFSTTEET----LKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHK   79 (98)
T ss_dssp             CCCCEEEESCCTTCCHHH----HHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEE
T ss_pred             CCCEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeE
Confidence            478999999999999998    778899999999999999876   67999999999999999999998 9999999999


Q ss_pred             eEEeccccCCCCC
Q 045516          593 LVVDEAKQRGDFG  605 (675)
Q Consensus       593 l~V~~a~~r~~~~  605 (675)
                      |+|.++.++....
T Consensus        80 l~V~~a~~~~~~~   92 (98)
T 2cpf_A           80 LEVRISERATKPA   92 (98)
T ss_dssp             CEEECSSCSSCCC
T ss_pred             EEEEEccCCCCCC
Confidence            9999998765543

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.62  E-value=1.7e-16  Score=138.41  Aligned_cols=82  Identities=32%  Similarity=0.414  Sum_probs=73.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a  491 (675)
                      ....++|||+|||+++++++|+++|..||.|.. .++.+. +++++|||||+|.+.++|.+||+||+..|.|+.|+|.++
T Consensus        14 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a   92 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKP   92 (101)
T ss_dssp             CSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGCCBTTBCCEEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHhcCCcEECCcEEEEEEc
Confidence            346789999999999999999999999999888 455554 789999999999999999999999999999999999999


Q ss_pred             cccC
Q 045516          492 RERG  495 (675)
Q Consensus       492 ~~~~  495 (675)
                      ..+.
T Consensus        93 ~~~~   96 (101)
T 1fj7_A           93 KGRD   96 (101)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            7653

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.61  E-value=2.2e-15  Score=134.07  Aligned_cols=86  Identities=28%  Similarity=0.510  Sum_probs=79.4

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEE--------EEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCc
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEIT--------RISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGT  586 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~--------~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~  586 (675)
                      ...++|||+|||+.+++++    |+++|..||.|.        .|+|+++..+|+++|||||+|.+.++|.+||. ||+.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~----l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~   88 (113)
T 2cpe_A           13 SDNSAIYVQGLNDSVTLDD----LADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGK   88 (113)
T ss_dssp             CCCCEEEEECCCTTCCHHH----HHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             CCCCEEEEcCCCCCCCHHH----HHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCC
Confidence            3479999999999999998    778999999999        69999999999999999999999999999998 9999


Q ss_pred             eeCCeeeEEeccccCCCCC
Q 045516          587 EIGGYSLVVDEAKQRGDFG  605 (675)
Q Consensus       587 ~~~Gr~l~V~~a~~r~~~~  605 (675)
                      .|+|+.|+|.++.++....
T Consensus        89 ~~~g~~l~V~~a~~~~~~~  107 (113)
T 2cpe_A           89 DFQGSKLKVSLARKKPPMN  107 (113)
T ss_dssp             EETTEECEEECSSCCCCST
T ss_pred             ccCCCEEEEEECCCCCCCC
Confidence            9999999999998766543

>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=99.61  E-value=3.1e-15  Score=125.21  Aligned_cols=81  Identities=23%  Similarity=0.434  Sum_probs=76.5

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~  596 (675)
                      +.+|||+|||..+++++    |+.+|..||.|..|.|+++..+|.++|||||+|.+.++|..|+. |||..|+|+.|+|.
T Consensus         1 t~~l~V~nlp~~~t~~~----l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~   76 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDET----LRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRIN   76 (83)
T ss_dssp             CEEEEEECCCTTCCHHH----HHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CeEEEEeCCCCCCCHHH----HHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEE
Confidence            36899999999999998    77899999999999999999999999999999999999999998 99999999999999


Q ss_pred             ccccCC
Q 045516          597 EAKQRG  602 (675)
Q Consensus       597 ~a~~r~  602 (675)
                      ++.++.
T Consensus        77 ~a~~~~   82 (83)
T 3md1_A           77 WAAKLE   82 (83)
T ss_dssp             ECCCCC
T ss_pred             ecCcCC
Confidence            998764

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.61  E-value=4.5e-16  Score=135.90  Aligned_cols=81  Identities=26%  Similarity=0.497  Sum_probs=76.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEecccc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARER  494 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a~~~  494 (675)
                      ..++|||+|||+++++++|+++|..||.|..|+|+++.+|+++|||||+|.+.++|.+||. |+..|.|+.|.|.++..+
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~-~~~~~~g~~l~v~~a~~~   86 (102)
T 2xs2_A            8 MPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE-SQINFHGKKLKLGPAIRK   86 (102)
T ss_dssp             EEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT-CCCEETTEECEEEEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh-CCCeECCEEEEEEECCcC
Confidence            4689999999999999999999999999999999999999999999999999999999999 999999999999998765


Q ss_pred             CC
Q 045516          495 GA  496 (675)
Q Consensus       495 ~~  496 (675)
                      ..
T Consensus        87 ~~   88 (102)
T 2xs2_A           87 QN   88 (102)
T ss_dssp             C-
T ss_pred             cc
Confidence            43

>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=99.61  E-value=7.9e-16  Score=136.79  Aligned_cols=75  Identities=24%  Similarity=0.239  Sum_probs=70.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEeccc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~  493 (675)
                      ..++|||+|||+.+++++|+++|.+||.|..|+|+.     ++|||||+|.+.++|.+||. |||..|.|+.|+|.|+..
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   83 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-----GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPI   83 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS-----SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEET
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC-----CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCC
Confidence            468999999999999999999999999999999874     58999999999999999997 999999999999999875


Q ss_pred             c
Q 045516          494 R  494 (675)
Q Consensus       494 ~  494 (675)
                      .
T Consensus        84 ~   84 (111)
T 1whx_A           84 G   84 (111)
T ss_dssp             T
T ss_pred             C
Confidence            4

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.61  E-value=4.1e-15  Score=129.28  Aligned_cols=84  Identities=23%  Similarity=0.400  Sum_probs=78.0

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      ...++|||+|||..+++++    |+.+|..||.|..|+|+.+. +|.++|||||+|.+.++|.+||. ||+..|+|+.|+
T Consensus        15 ~~~~~l~v~nlp~~~t~~~----l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   89 (100)
T 2do4_A           15 LEKHKLFISGLPFSCTKEE----LEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIK   89 (100)
T ss_dssp             CCCSCEEEESCCTTCCHHH----HHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            4478999999999999998    78899999999999999998 89999999999999999999997 999999999999


Q ss_pred             EeccccCCCC
Q 045516          595 VDEAKQRGDF  604 (675)
Q Consensus       595 V~~a~~r~~~  604 (675)
                      |.++.++...
T Consensus        90 v~~a~~~~~~   99 (100)
T 2do4_A           90 VAISNSGPSS   99 (100)
T ss_dssp             EEECCCCSCC
T ss_pred             EEECCCCCCC
Confidence            9999876653

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.61  E-value=2.2e-15  Score=131.38  Aligned_cols=81  Identities=33%  Similarity=0.531  Sum_probs=73.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      ....++|||+|||+++++++|++||..|+   .|+|+++. +++++|||||+|.+.++|.+||. ||+..|.|+.|+|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2fc8_A           12 SQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDW   88 (102)
T ss_dssp             SCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            45679999999999999999999999873   67788886 89999999999999999999998 999999999999999


Q ss_pred             ccccCC
Q 045516          491 ARERGA  496 (675)
Q Consensus       491 a~~~~~  496 (675)
                      +..+..
T Consensus        89 a~~~~~   94 (102)
T 2fc8_A           89 AKPKGE   94 (102)
T ss_dssp             CCCCCS
T ss_pred             ecCCCC
Confidence            987643

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.61  E-value=2.5e-15  Score=131.85  Aligned_cols=86  Identities=21%  Similarity=0.389  Sum_probs=79.8

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVV  595 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V  595 (675)
                      ...++|||+|||+.+++++    |+.+|..||.|..|.|+++..++.++|||||+|.+.++|.+||.+|+..|+|+.|+|
T Consensus        14 ~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~V   89 (105)
T 2dh8_A           14 DEIGKLFVGGLDWSTTQET----LRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLDGRNIDP   89 (105)
T ss_dssp             SSSSEECCBSCCTTCCHHH----HHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHHCSEEETTEEEBC
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHhCCCeECCEEEEE
Confidence            4479999999999999998    778899999999999999999999999999999999999999988999999999999


Q ss_pred             eccccCCCCC
Q 045516          596 DEAKQRGDFG  605 (675)
Q Consensus       596 ~~a~~r~~~~  605 (675)
                      .++.++....
T Consensus        90 ~~a~~~~~~~   99 (105)
T 2dh8_A           90 KPCTPRGMQP   99 (105)
T ss_dssp             CCSCCSSCCT
T ss_pred             EEccCCCCCC
Confidence            9998876544

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.61  E-value=4e-15  Score=130.04  Aligned_cols=83  Identities=23%  Similarity=0.453  Sum_probs=77.6

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEE
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVV  595 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V  595 (675)
                      ..++|||+|||+.+++++    |+.+|..||.|..|.|+.+  +|.++|||||+|.+.++|..||. ||+..|+|+.|+|
T Consensus        14 ~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   87 (103)
T 2d9p_A           14 QVVNLYVKNLDDGIDDER----LRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYV   87 (103)
T ss_dssp             SCCCEEEECCCTTCCHHH----HHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEE
T ss_pred             CCCEEEEeCCCCCCCHHH----HHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            479999999999999998    7899999999999999998  89999999999999999999998 9999999999999


Q ss_pred             eccccCCCCC
Q 045516          596 DEAKQRGDFG  605 (675)
Q Consensus       596 ~~a~~r~~~~  605 (675)
                      .|+.++....
T Consensus        88 ~~a~~~~~~~   97 (103)
T 2d9p_A           88 ALAQRKEERQ   97 (103)
T ss_dssp             EECSSCCCCC
T ss_pred             EEecccccCC
Confidence            9998876544

>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=99.61  E-value=1.5e-15  Score=132.86  Aligned_cols=81  Identities=15%  Similarity=0.258  Sum_probs=74.1

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVV  595 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V  595 (675)
                      ...++|||+|||+.+++++    |+++|..||. ..|+|+++. +|+++|||||+|.+.++|.+||.+|+..|+||.|+|
T Consensus        13 ~~~~~l~V~nLp~~~te~~----l~~~F~~~G~-~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V   86 (102)
T 1wez_A           13 TTGHCVHMRGLPYRATEND----IYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVEL   86 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHH----HHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHHHcCc-eEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHhCCCeECCcEEEE
Confidence            3478999999999999998    7899999995 599999997 899999999999999999999999999999999999


Q ss_pred             eccccCC
Q 045516          596 DEAKQRG  602 (675)
Q Consensus       596 ~~a~~r~  602 (675)
                      .++.+..
T Consensus        87 ~~~~~~~   93 (102)
T 1wez_A           87 FLNSTAG   93 (102)
T ss_dssp             EEECCCC
T ss_pred             EECCCCC
Confidence            9887544

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.61  E-value=1e-15  Score=132.21  Aligned_cols=76  Identities=22%  Similarity=0.476  Sum_probs=70.1

Q ss_pred             CCCCceEEEcCCCC-CCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          413 SGGSKTLFVGNLPF-SVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       413 ~~~~~tlfV~nLp~-~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      ....++|||+|||+ .+++++|+.+|.+||.|..|+|.       +|||||+|.+.++|..||. ||+..|.|+.|+|.+
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   79 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEV   79 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE-------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            34578999999999 99999999999999999999995       7999999999999999998 999999999999999


Q ss_pred             ccccC
Q 045516          491 ARERG  495 (675)
Q Consensus       491 a~~~~  495 (675)
                      +....
T Consensus        80 a~~~~   84 (96)
T 2kvi_A           80 SSSNA   84 (96)
T ss_dssp             EECCC
T ss_pred             cCcCC
Confidence            97654

>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=99.60  E-value=7e-15  Score=129.95  Aligned_cols=83  Identities=19%  Similarity=0.367  Sum_probs=74.1

Q ss_pred             CCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeee
Q 045516          515 GQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSL  593 (675)
Q Consensus       515 ~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l  593 (675)
                      ....++|||+|||..+++++    |+++|..||.|..|.|+.+   +.++|||||+|.+.++|.+||. ||+..|+|+.|
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~----l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   91 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKD----IEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRL   91 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHH----HHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEE
Confidence            34579999999999999998    7789999999999999665   5689999999999999999997 99999999999


Q ss_pred             EEeccccCCCC
Q 045516          594 VVDEAKQRGDF  604 (675)
Q Consensus       594 ~V~~a~~r~~~  604 (675)
                      +|.|++++...
T Consensus        92 ~V~~a~~~~~~  102 (109)
T 1x4a_A           92 RVEFPRSGRGT  102 (109)
T ss_dssp             EEECCCCCCCC
T ss_pred             EEEEcccCCCC
Confidence            99999875543

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.60  E-value=3.6e-15  Score=130.57  Aligned_cols=84  Identities=23%  Similarity=0.296  Sum_probs=77.6

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcc-cCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCce-eCCeee
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGS-CGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTE-IGGYSL  593 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~-~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~-~~Gr~l  593 (675)
                      +.++|||+|||..+++++    |+.+|.. ||.|..|+|+++. +|.++|||||+|.+.++|.+||. ||+.. |+|+.|
T Consensus         8 ~~~~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            8 PEYSLFVGDLTPDVDDGM----LYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPV   82 (104)
T ss_dssp             CCCCEEEECCCTTCCHHH----HHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCC
T ss_pred             CCcEEEEeCCCCCCCHHH----HHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeE
Confidence            478999999999999998    7788888 9999999999998 89999999999999999999998 99999 999999


Q ss_pred             EEeccccCCCCC
Q 045516          594 VVDEAKQRGDFG  605 (675)
Q Consensus       594 ~V~~a~~r~~~~  605 (675)
                      +|.++.++....
T Consensus        83 ~v~~a~~~~~~~   94 (104)
T 2dhg_A           83 RLSVAIPKASRV   94 (104)
T ss_dssp             CCCBCCCCCSCC
T ss_pred             EEEEccCCCcCC
Confidence            999998766544

>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=99.60  E-value=3.5e-15  Score=125.41  Aligned_cols=80  Identities=29%  Similarity=0.550  Sum_probs=75.3

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      .+.++|||+|||..+++++    |+++|..||.|..|.|+++..+|.++|||||+|.+.++|..|+. |||..|+|+.|+
T Consensus         5 ~~~~~l~V~nl~~~~~~~~----l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   80 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKV----LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIR   80 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHH----HHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEECCCCCCCHHH----HHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEE
Confidence            3479999999999999988    77889999999999999999999999999999999999999997 999999999999


Q ss_pred             Eeccc
Q 045516          595 VDEAK  599 (675)
Q Consensus       595 V~~a~  599 (675)
                      |.|++
T Consensus        81 v~~ak   85 (85)
T 3mdf_A           81 VNLAK   85 (85)
T ss_dssp             EEECC
T ss_pred             EEEcC
Confidence            99874

>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=99.60  E-value=3.7e-15  Score=128.58  Aligned_cols=82  Identities=20%  Similarity=0.361  Sum_probs=77.4

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~  596 (675)
                      .++|||+|||..+++++    |+.+|..||.|..|+|+++..+|.++|||||+|.+.++|..||. |||..|+|+.|+|.
T Consensus         2 ~~~l~V~nLp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   77 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQ----ILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCG   77 (96)
T ss_dssp             CSEEEEESCCTTCCHHH----HHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CcEEEEECCCCCCCHHH----HHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            68999999999999998    77889999999999999999999999999999999999999997 99999999999999


Q ss_pred             ccccCCC
Q 045516          597 EAKQRGD  603 (675)
Q Consensus       597 ~a~~r~~  603 (675)
                      ++.++..
T Consensus        78 ~a~~~~~   84 (96)
T 2x1f_A           78 YSSNSDI   84 (96)
T ss_dssp             ECSCSSG
T ss_pred             EcCCCCC
Confidence            9987654

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.60  E-value=1.3e-15  Score=131.25  Aligned_cols=79  Identities=22%  Similarity=0.346  Sum_probs=73.5

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCc--EEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCc----eeCC
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGE--ITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGT----EIGG  590 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~--I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~----~~~G  590 (675)
                      .++|||+|||+.+++++    |+++|+.||.  |..|+|++|+.+|+++|||||+|.+.++|.+||+ |||.    .|+|
T Consensus         9 m~tlfV~nL~~~~tee~----L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~G   84 (95)
T 2lkz_A            9 MDTIILRNIAPHTVVDS----IMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDG   84 (95)
T ss_dssp             CCEEEEESCCTTCCHHH----HHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETT
T ss_pred             cCEEEEeCCCCcCCHHH----HHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECC
Confidence            68999999999999998    7889999995  6799999999999999999999999999999998 9886    5999


Q ss_pred             eeeEEecccc
Q 045516          591 YSLVVDEAKQ  600 (675)
Q Consensus       591 r~l~V~~a~~  600 (675)
                      |.|.|.|++.
T Consensus        85 r~i~V~~Aks   94 (95)
T 2lkz_A           85 KTIGVDFAKS   94 (95)
T ss_dssp             EEEEEEECCC
T ss_pred             EEEEEEEccC
Confidence            9999999874

>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=99.60  E-value=2.9e-15  Score=131.62  Aligned_cols=85  Identities=26%  Similarity=0.330  Sum_probs=78.3

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCcee---CCe
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEI---GGY  591 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~---~Gr  591 (675)
                      ...++|||+|||..+++++    |+.+|..||.|..|+|+++..+|.++|||||+|.+.++|.+||. ||+..|   .|+
T Consensus        11 ~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~   86 (106)
T 2dgp_A           11 HDAIKLFIGQIPRNLDEKD----LKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNR   86 (106)
T ss_dssp             TTCEEEEEESCCTTCCHHH----HHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSS
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCc
Confidence            3479999999999999998    77888899999999999999999999999999999999999998 999988   899


Q ss_pred             eeEEeccccCCCC
Q 045516          592 SLVVDEAKQRGDF  604 (675)
Q Consensus       592 ~l~V~~a~~r~~~  604 (675)
                      .|+|.++.++...
T Consensus        87 ~l~v~~a~~~~~~   99 (106)
T 2dgp_A           87 PIQVKPADSESRG   99 (106)
T ss_dssp             CCEEEECCCCSCC
T ss_pred             eEEEEECCccccc
Confidence            9999999876544

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.60  E-value=1e-15  Score=133.29  Aligned_cols=82  Identities=20%  Similarity=0.342  Sum_probs=75.9

Q ss_pred             ceEEEEecCCC------CcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCC
Q 045516          518 AHTIFIKGFDS------SVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGG  590 (675)
Q Consensus       518 ~~~lfV~nLp~------~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~G  590 (675)
                      .++|||+|||+      .+++++    |+++|++||.|..|+|+++..||+++|||||+|.+.++|.+||. |||..|.|
T Consensus         6 ~~~vfV~nLp~v~~~~~~~~~~~----L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g   81 (100)
T 3ns6_A            6 DQYIVVNGAPVIPSAKVPVLKKA----LTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDL   81 (100)
T ss_dssp             GGEEEEESCCCCBGGGHHHHHHH----HHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSS
T ss_pred             CcEEEEeCCCcCChHHHHHHHHH----HHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCC
Confidence            68999999999      666666    88999999999999999999999999999999999999999998 99999999


Q ss_pred             -eeeEEeccccCCC
Q 045516          591 -YSLVVDEAKQRGD  603 (675)
Q Consensus       591 -r~l~V~~a~~r~~  603 (675)
                       +.|+|.++.++..
T Consensus        82 ~r~l~V~~a~~~~~   95 (100)
T 3ns6_A           82 KHRLFLYTMKDVER   95 (100)
T ss_dssp             SCBCEEEESHHHHH
T ss_pred             CeEEEEEECchhhh
Confidence             9999999987543

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

Probab=99.59  E-value=2.4e-15  Score=132.93  Aligned_cols=76  Identities=25%  Similarity=0.548  Sum_probs=71.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ....++|||+|||+++++++|+.+|.+||.|..|+|+       +|||||+|.+.++|.+||. |||..|.|+.|.|.++
T Consensus        28 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~-------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  100 (108)
T 2jvo_A           28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYS  100 (108)
T ss_dssp             CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE-------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEe
Confidence            4567999999999999999999999999999999998       7999999999999999997 9999999999999998


Q ss_pred             cccC
Q 045516          492 RERG  495 (675)
Q Consensus       492 ~~~~  495 (675)
                      ....
T Consensus       101 ~~~~  104 (108)
T 2jvo_A          101 KLPA  104 (108)
T ss_dssp             SCCC
T ss_pred             cCCC
Confidence            7643

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.59  E-value=2.2e-15  Score=145.34  Aligned_cols=83  Identities=29%  Similarity=0.450  Sum_probs=78.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ....++|||+|||+.+++++|++||..||.|..|.|+.+.++.++|||||+|.+.++|.+||. ||+..|.|+.|+|.++
T Consensus        85 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a  164 (177)
T 2f3j_A           85 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV  164 (177)
T ss_dssp             CTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            345789999999999999999999999999999999999899999999999999999999998 9999999999999998


Q ss_pred             cccC
Q 045516          492 RERG  495 (675)
Q Consensus       492 ~~~~  495 (675)
                      ....
T Consensus       165 ~~~~  168 (177)
T 2f3j_A          165 ASQI  168 (177)
T ss_dssp             SSGG
T ss_pred             cCCC
Confidence            7543

>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=99.59  E-value=2.4e-15  Score=128.95  Aligned_cols=77  Identities=27%  Similarity=0.481  Sum_probs=69.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCC-eEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCC-cccCCeeEEEE
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAE-VVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNG-QMLGNRAIRLD  489 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~-I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g-~~~~gr~i~V~  489 (675)
                      ....++|||+|||+++++++|+++|.+||. |..+.|.      ++|||||+|.+.++|.+||. ||| ..|.|+.|+|.
T Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~   78 (93)
T 2cqh_A            5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVD   78 (93)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEE
Confidence            345789999999999999999999999999 6666664      48999999999999999997 999 99999999999


Q ss_pred             eccccC
Q 045516          490 FARERG  495 (675)
Q Consensus       490 ~a~~~~  495 (675)
                      ++..+.
T Consensus        79 ~a~~~~   84 (93)
T 2cqh_A           79 YSVSKK   84 (93)
T ss_dssp             ECCCCC
T ss_pred             EccCcc
Confidence            998654

>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=99.59  E-value=7.7e-15  Score=128.65  Aligned_cols=85  Identities=24%  Similarity=0.361  Sum_probs=78.2

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCC---e
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGG---Y  591 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~G---r  591 (675)
                      ...++|||+|||+.+++++    |+.+|..||.|..|+|+++. +|.++|||||+|.+.++|.+||. ||+..|.|   +
T Consensus        13 ~~~~~l~v~nLp~~~t~~~----l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~   87 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEED----VLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASS   87 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHH----HHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSS
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCc
Confidence            4479999999999999998    78899999999999999997 79999999999999999999998 99999998   9


Q ss_pred             eeEEeccccCCCCC
Q 045516          592 SLVVDEAKQRGDFG  605 (675)
Q Consensus       592 ~l~V~~a~~r~~~~  605 (675)
                      .|+|.|+.++..+.
T Consensus        88 ~l~V~~a~~~~~~~  101 (105)
T 2dnh_A           88 SLVVKFADTDKESG  101 (105)
T ss_dssp             CCEEEESCSSCCCS
T ss_pred             cEEEEECccCcccC
Confidence            99999998876554

>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=99.59  E-value=4.2e-15  Score=131.65  Aligned_cols=75  Identities=28%  Similarity=0.530  Sum_probs=69.7

Q ss_pred             CCCceEEEcCCCCC-CCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          414 GGSKTLFVGNLPFS-VEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       414 ~~~~tlfV~nLp~~-~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ...++|||+|||++ +++++|+++|.+||.|..|+|       ++|||||+|.+.++|.+||. ||+..|.|+.|+|.++
T Consensus        25 ~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i-------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   97 (110)
T 1wf1_A           25 SINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMA   97 (110)
T ss_dssp             TCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE-------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEES
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE-------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            34689999999999 999999999999999999999       48999999999999999996 9999999999999999


Q ss_pred             cccC
Q 045516          492 RERG  495 (675)
Q Consensus       492 ~~~~  495 (675)
                      ....
T Consensus        98 ~~~~  101 (110)
T 1wf1_A           98 GEPK  101 (110)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7543

>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=99.59  E-value=2.3e-15  Score=133.42  Aligned_cols=78  Identities=19%  Similarity=0.307  Sum_probs=70.0

Q ss_pred             CCCceEEE--cCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCccc-----CCee
Q 045516          414 GGSKTLFV--GNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQML-----GNRA  485 (675)
Q Consensus       414 ~~~~tlfV--~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~-----~gr~  485 (675)
                      ..+++|||  +||++++++++|+++|++||.|..|+|+.     .+|||||+|.+.++|.+||. |||..|     .|++
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~-----~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~   97 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-----NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKIT   97 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT-----TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEE
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcE
Confidence            45789999  77999999999999999999999999874     37999999999999999997 999988     7899


Q ss_pred             EEEEeccccCC
Q 045516          486 IRLDFARERGA  496 (675)
Q Consensus       486 i~V~~a~~~~~  496 (675)
                      |+|.|+.....
T Consensus        98 l~v~~a~~~p~  108 (114)
T 2cq2_A           98 LYLNFVEKVQW  108 (114)
T ss_dssp             CEEEEESCCCC
T ss_pred             EEEEecccCcc
Confidence            99999875543

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.59  E-value=9.9e-16  Score=132.09  Aligned_cols=79  Identities=30%  Similarity=0.563  Sum_probs=71.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ....++|||+|||+.+++++|+++|..||.|..|    ..+++++|||||+|.+.++|.+||. |||..|.|+.|+|.++
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   88 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT   88 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEc
Confidence            3457899999999999999999999999988766    3378899999999999999999998 9999999999999999


Q ss_pred             cccC
Q 045516          492 RERG  495 (675)
Q Consensus       492 ~~~~  495 (675)
                      ..+.
T Consensus        89 ~~~~   92 (96)
T 1fjc_A           89 GEKG   92 (96)
T ss_dssp             SSSC
T ss_pred             CCCC
Confidence            7654

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

Probab=99.59  E-value=2.9e-15  Score=136.23  Aligned_cols=85  Identities=22%  Similarity=0.347  Sum_probs=78.4

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      .+.++|||+||++.+++++|+..|..+|++||.|..|.|..   +++++|||||+|.+.++|..||. |||..|.|+.|+
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~  103 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLV  103 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEE
Confidence            34789999999999999999999999999999999998864   57899999999999999999998 999999999999


Q ss_pred             EeccccCCC
Q 045516          595 VDEAKQRGD  603 (675)
Q Consensus       595 V~~a~~r~~  603 (675)
                      |.|++.+..
T Consensus       104 V~~a~~~~~  112 (127)
T 2a3j_A          104 ITFSETPQS  112 (127)
T ss_dssp             EEECCCCCH
T ss_pred             EEEccCcch
Confidence            999987654

>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=99.58  E-value=1.4e-14  Score=126.58  Aligned_cols=85  Identities=24%  Similarity=0.371  Sum_probs=78.0

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVV  595 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V  595 (675)
                      ...++|||+|||+.+++++    |+.+|..||.|..|+|+++..+|.++|||||+|.+.+.|.+||. +++.|+|+.|+|
T Consensus        13 ~~~~~l~v~nlp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~g~~l~v   87 (103)
T 2cqg_A           13 QKTSDLIVLGLPWKTTEQD----LKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS-QRHMIDGRWCDC   87 (103)
T ss_dssp             CCCCCEEEESCCSSCCHHH----HHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH-SCEEETTEEEEE
T ss_pred             CCCCEEEEEcCCCcCCHHH----HHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH-cCCeeCCeEEEE
Confidence            3478999999999999998    77899999999999999999999999999999999999999999 578999999999


Q ss_pred             eccccCCCCC
Q 045516          596 DEAKQRGDFG  605 (675)
Q Consensus       596 ~~a~~r~~~~  605 (675)
                      .++.++....
T Consensus        88 ~~a~~~~~~~   97 (103)
T 2cqg_A           88 KLPNSKQSQD   97 (103)
T ss_dssp             ECCCTTCCCC
T ss_pred             EecCCCCcCC
Confidence            9998876654

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.58  E-value=7.9e-15  Score=125.99  Aligned_cols=82  Identities=23%  Similarity=0.370  Sum_probs=76.9

Q ss_pred             CCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeee
Q 045516          515 GQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSL  593 (675)
Q Consensus       515 ~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l  593 (675)
                      ..+.++|||+|||..+++++    |+++|..||.|..|.|+++..++.++|||||+|.+.++|.+||. |||..|+|+.|
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~----l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   87 (95)
T 2cqc_A           12 PDPNCCLGVFGLSLYTTERD----LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI   87 (95)
T ss_dssp             CCGGGCEEEESCCSSCCHHH----HHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCCCEEEEECCCCCCCHHH----HHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            34579999999999999998    77889999999999999999999999999999999999999998 99999999999


Q ss_pred             EEecccc
Q 045516          594 VVDEAKQ  600 (675)
Q Consensus       594 ~V~~a~~  600 (675)
                      +|.|++.
T Consensus        88 ~v~~a~~   94 (95)
T 2cqc_A           88 RVSGPSS   94 (95)
T ss_dssp             EEECCSC
T ss_pred             EEEecCC
Confidence            9999864

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.37  E-value=1.1e-16  Score=143.26  Aligned_cols=83  Identities=27%  Similarity=0.514  Sum_probs=77.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEE--------EEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCC
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVD--------VRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGN  483 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~--------v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~g  483 (675)
                      ...++|||+|||+.+++++|++||..||.|..        |+|++++ +++++|||||+|.+.++|.+||. ||+..|.|
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   84 (116)
T 2lcw_A            5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSG   84 (116)
Confidence            35689999999999999999999999999999        9999986 79999999999999999999998 99999999


Q ss_pred             eeEEEEeccccCC
Q 045516          484 RAIRLDFARERGA  496 (675)
Q Consensus       484 r~i~V~~a~~~~~  496 (675)
                      +.|+|.++..+..
T Consensus        85 ~~l~V~~a~~~~~   97 (116)
T 2lcw_A           85 NPIKVSFATRRAD   97 (116)
Confidence            9999999987643

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.58  E-value=5.6e-15  Score=126.99  Aligned_cols=77  Identities=22%  Similarity=0.440  Sum_probs=68.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEecc
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a~  492 (675)
                      ...++|||+|||+++++++|+.+|..||.|..|  +.+. +++   ||||+|.+.++|.+||.||+..|.|+.|+|.++.
T Consensus         6 ~~~~~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            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLSQSQHSLGGHRLRVRPRE   80 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHTCSCCEETTEECCCBCSC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHhcCCeEECCEEEEEEECC
Confidence            356899999999999999999999999999998  3443 554   9999999999999999999999999999999886


Q ss_pred             ccC
Q 045516          493 ERG  495 (675)
Q Consensus       493 ~~~  495 (675)
                      .+.
T Consensus        81 ~~~   83 (94)
T 2e5g_A           81 QKE   83 (94)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            554

>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=99.58  E-value=7.4e-15  Score=129.99  Aligned_cols=84  Identities=29%  Similarity=0.440  Sum_probs=78.8

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      ...++|||+|||..+++++    |+.+|..||.|..|.|+.+..+|.++|||||+|.+.+.|..||. |||..|+|+.|+
T Consensus        24 ~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~   99 (110)
T 1oo0_B           24 VEGWILFVTSIHEEAQEDE----IQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQ   99 (110)
T ss_dssp             TTBEEEEEESCCTTCCHHH----HHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEE
Confidence            4479999999999999998    77899999999999999999999999999999999999999998 999999999999


Q ss_pred             EeccccCCC
Q 045516          595 VDEAKQRGD  603 (675)
Q Consensus       595 V~~a~~r~~  603 (675)
                      |.|+.++..
T Consensus       100 V~~a~~~~~  108 (110)
T 1oo0_B          100 VDWCFVKGP  108 (110)
T ss_dssp             EEESEESSC
T ss_pred             EEEcccCCC
Confidence            999987654

>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=99.58  E-value=3.5e-15  Score=139.86  Aligned_cols=78  Identities=22%  Similarity=0.383  Sum_probs=73.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ....++|||+|||+.+++++|+++|++||.|..|+|+++    ++|||||+|.+.++|.+||. |||..|.|+.|+|.++
T Consensus        70 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  145 (150)
T 2i2y_A           70 CPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELS  145 (150)
T ss_dssp             STTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEc
Confidence            456799999999999999999999999999999999976    58999999999999999998 9999999999999998


Q ss_pred             ccc
Q 045516          492 RER  494 (675)
Q Consensus       492 ~~~  494 (675)
                      .++
T Consensus       146 ~~~  148 (150)
T 2i2y_A          146 NGE  148 (150)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            754

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.58  E-value=8.1e-15  Score=125.75  Aligned_cols=80  Identities=23%  Similarity=0.408  Sum_probs=75.7

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      ...++|||+|||..+++++    |+++|..||.|..|.|+++..++.++|||||+|.+.++|.+||. ||+..|+|+.|+
T Consensus        14 ~~~~~l~V~nlp~~~t~~~----l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   89 (94)
T 2e5h_A           14 PSKSTVYVSNLPFSLTNND----LYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIK   89 (94)
T ss_dssp             CCTTSEEEESCCTTSCHHH----HHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEE
T ss_pred             CCCCEEEEECCCCCCCHHH----HHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEE
Confidence            4478999999999999998    78999999999999999999999999999999999999999997 999999999999


Q ss_pred             Eeccc
Q 045516          595 VDEAK  599 (675)
Q Consensus       595 V~~a~  599 (675)
                      |.|++
T Consensus        90 v~~ak   94 (94)
T 2e5h_A           90 ASIAI   94 (94)
T ss_dssp             EEECC
T ss_pred             EEecC
Confidence            99974

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.58  E-value=1e-14  Score=126.12  Aligned_cols=77  Identities=19%  Similarity=0.379  Sum_probs=70.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ....++|||+||  ++++++|++||.+||.|..|+|.     +++|||||+|.+.++|.+||. ||+..|.|+.|+|.++
T Consensus        12 ~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~-----~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a   84 (97)
T 1x5p_A           12 PRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD-----PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA   84 (97)
T ss_dssp             CCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE-----TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECC
T ss_pred             CCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec-----CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEC
Confidence            456789999996  99999999999999999999995     568999999999999999997 9999999999999999


Q ss_pred             cccCC
Q 045516          492 RERGA  496 (675)
Q Consensus       492 ~~~~~  496 (675)
                      ..+..
T Consensus        85 ~~~~~   89 (97)
T 1x5p_A           85 RKQPM   89 (97)
T ss_dssp             SSCCC
T ss_pred             CCCCC
Confidence            76643

>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=99.58  E-value=2e-15  Score=134.64  Aligned_cols=83  Identities=23%  Similarity=0.490  Sum_probs=78.3

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEec
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDE  597 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~~  597 (675)
                      .++|||+|||+.+++++    |+.+|..||.|..|.|+.+..+|.++|||||+|.+.+.|.+||.||+..|+|+.|+|.+
T Consensus        25 ~~~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           25 ARTVFCMQLAARIRPRD----LEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQA  100 (114)
T ss_dssp             HTEEEEESCCTTCCHHH----HHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCEEEEeCCCCCCCHHH----HHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHHHcCCCEeCCeEEEEEe
Confidence            68999999999999998    78899999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCC
Q 045516          598 AKQRGDF  604 (675)
Q Consensus       598 a~~r~~~  604 (675)
                      +.++..+
T Consensus       101 a~~~~~~  107 (114)
T 2cq4_A          101 SQAEKNR  107 (114)
T ss_dssp             HHHHHHH
T ss_pred             cCCCccC
Confidence            9876554

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.58  E-value=6.5e-15  Score=129.36  Aligned_cols=84  Identities=25%  Similarity=0.480  Sum_probs=78.6

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      ...++|||+|||..+++++    |+.+|..||.|..|.|+++..+|.++|||||+|.+.++|..||. |||..|+|+.|+
T Consensus        21 ~~~~~l~V~nlp~~~t~~~----l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   96 (106)
T 1p27_B           21 VEGWILFVTGVHEEATEED----IHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPIS   96 (106)
T ss_dssp             TTBEEEEEECCCTTCCHHH----HHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCE
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEE
Confidence            3478999999999999998    77899999999999999999999999999999999999999998 999999999999


Q ss_pred             EeccccCCC
Q 045516          595 VDEAKQRGD  603 (675)
Q Consensus       595 V~~a~~r~~  603 (675)
                      |.++.++..
T Consensus        97 V~~a~~~~~  105 (106)
T 1p27_B           97 VDWCFVRGP  105 (106)
T ss_dssp             EEESEESSC
T ss_pred             EEeecCCCC
Confidence            999987653

>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=99.58  E-value=8.1e-15  Score=129.54  Aligned_cols=83  Identities=28%  Similarity=0.522  Sum_probs=78.3

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      ...++|||+|||..+++++    |+.+|..||.|..|.|+++..+|.++|||||+|.+.+.|..||. |||..|+|+.|+
T Consensus        24 ~~~~~l~V~nLp~~~te~~----l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~   99 (108)
T 2jrs_A           24 AGPMRLYVGSLHFNITEDM----LRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMK   99 (108)
T ss_dssp             SSCEEEEEECCCSSCCHHH----HHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            4479999999999999998    77899999999999999999999999999999999999999998 999999999999


Q ss_pred             EeccccCC
Q 045516          595 VDEAKQRG  602 (675)
Q Consensus       595 V~~a~~r~  602 (675)
                      |.++.++.
T Consensus       100 V~~a~~k~  107 (108)
T 2jrs_A          100 VGHVTERT  107 (108)
T ss_dssp             EECSCSSC
T ss_pred             EEEcccCC
Confidence            99998764

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.58  E-value=6.2e-15  Score=133.39  Aligned_cols=82  Identities=29%  Similarity=0.521  Sum_probs=76.8

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEec
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDE  597 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~~  597 (675)
                      .++|||+|||+.+++++    |+++|..||.|..|+|+++..+|.++|||||+|.+.++|..||.|||..|+|+.|+|.+
T Consensus        36 ~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~  111 (124)
T 2jwn_A           36 KRSVYVGNVDYGSTAQD----LEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMDETVFRGRTIKVLP  111 (124)
T ss_dssp             HTEEEEEEECTTCCHHH----HHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCEEEEeCCCCCCCHHH----HHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHHhcCCCeECCeEEEEEE
Confidence            68999999999999998    77899999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCCC
Q 045516          598 AKQRGD  603 (675)
Q Consensus       598 a~~r~~  603 (675)
                      +++...
T Consensus       112 a~~~~~  117 (124)
T 2jwn_A          112 KRTNMP  117 (124)
T ss_dssp             SSCCCS
T ss_pred             CCCCCC
Confidence            875433

>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=99.58  E-value=8.4e-15  Score=123.79  Aligned_cols=78  Identities=24%  Similarity=0.462  Sum_probs=74.0

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEe
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVD  596 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~  596 (675)
                      ..++|||+|||+.+++++    |+++|..||.|..|+|+++..+|+++|||||+|.+.++|.+||.+++..|+|+.|+|.
T Consensus        10 ~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~i~v~   85 (87)
T 3s7r_A           10 DAGKMFVGGLSWDTSKKD----LKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKEHRLDGRVIDPK   85 (87)
T ss_dssp             CTTEEEEECCCTTCCHHH----HHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHSSCEEETTEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHH----HHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHhCCCEECCEEEEEE
Confidence            478999999999999998    7789999999999999999999999999999999999999999999999999999998


Q ss_pred             cc
Q 045516          597 EA  598 (675)
Q Consensus       597 ~a  598 (675)
                      ++
T Consensus        86 ~A   87 (87)
T 3s7r_A           86 KA   87 (87)
T ss_dssp             EC
T ss_pred             eC
Confidence            75

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.57  E-value=7.3e-15  Score=127.37  Aligned_cols=84  Identities=19%  Similarity=0.419  Sum_probs=77.6

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEE-EEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCee-
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEIT-RISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYS-  592 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~-~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~-  592 (675)
                      ...++|||+|||..+++++    |+.+|..||.|. .|+|+++..+|.++|||||+|.+.++|.+||. |||..|.|+. 
T Consensus         7 ~~~~~l~V~nLp~~~t~~~----l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~   82 (99)
T 2div_A            7 GMAASLWMGDLEPYMDENF----ISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATP   82 (99)
T ss_dssp             SSSSEEEECSCCTTCCHHH----HHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSS
T ss_pred             CCccEEEEeCCCCCCCHHH----HHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCc
Confidence            3479999999999999998    778888999999 99999999999999999999999999999999 9999999999 


Q ss_pred             ---eEEeccccCCC
Q 045516          593 ---LVVDEAKQRGD  603 (675)
Q Consensus       593 ---l~V~~a~~r~~  603 (675)
                         |+|.|+.+...
T Consensus        83 ~~~l~v~~a~~~~~   96 (99)
T 2div_A           83 AKRFKLNYATYSGP   96 (99)
T ss_dssp             CEECCEEETTCCSS
T ss_pred             ceeEEEeecCCCCC
Confidence               99999976543

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.57  E-value=3.4e-14  Score=126.46  Aligned_cols=83  Identities=22%  Similarity=0.355  Sum_probs=76.2

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      ...++|||+|||+.+++++    |+++|..||.|..|.|+.+. +|.++|||||+|.+.++|..||. ||+..|+|+.|+
T Consensus        13 ~~~~~l~V~nlp~~~~~~~----l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   87 (114)
T 2do0_A           13 RLGSTVFVANLDYKVGWKK----LKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMH   87 (114)
T ss_dssp             CCCSCEEEESCCTTCCHHH----HHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEE
Confidence            3478999999999999998    77899999999999999987 59999999999999999999998 999999999999


Q ss_pred             EeccccCCC
Q 045516          595 VDEAKQRGD  603 (675)
Q Consensus       595 V~~a~~r~~  603 (675)
                      |.++.....
T Consensus        88 v~~a~~~~~   96 (114)
T 2do0_A           88 VKMDERALP   96 (114)
T ss_dssp             EEECSCCCC
T ss_pred             EEEcccCCC
Confidence            999875443

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.57  E-value=6.5e-15  Score=124.37  Aligned_cols=73  Identities=19%  Similarity=0.352  Sum_probs=65.4

Q ss_pred             CCce-EEEcCCCCCCCHHH----HHHHhhhC-CCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEE
Q 045516          415 GSKT-LFVGNLPFSVEQAD----VQNFFSEV-AEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIR  487 (675)
Q Consensus       415 ~~~t-lfV~nLp~~~te~~----L~~~F~~~-G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~  487 (675)
                      ++.| |||+|||+.+++++    |+++|.+| |.|++|      ++   |||||.|.+.++|.+||+ |||..|.||+|+
T Consensus         7 p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~   77 (96)
T 2diu_A            7 GCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI------TG---CSAILRFINQDSAERAQKRMENEDVFGNRII   77 (96)
T ss_dssp             CSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             CcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE------ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEE
Confidence            4566 99999999999988    56899999 599999      23   999999999999999997 999999999999


Q ss_pred             EEeccccCC
Q 045516          488 LDFARERGA  496 (675)
Q Consensus       488 V~~a~~~~~  496 (675)
                      |.|+..+..
T Consensus        78 v~~A~~~sd   86 (96)
T 2diu_A           78 VSFTPKNRE   86 (96)
T ss_dssp             EESSCCSCC
T ss_pred             EEecCCCcc
Confidence            999987654

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.57  E-value=1.3e-14  Score=126.48  Aligned_cols=82  Identities=34%  Similarity=0.574  Sum_probs=73.3

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      ...++|||+|||..+++++    |+++|..|+   .|.|+.+..++.++|||||+|.+.++|.+||. ||+..|+|+.|+
T Consensus        13 ~~~~~l~V~nLp~~~t~~~----l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   85 (102)
T 2fc8_A           13 QPSKTLFVKGLSEDTTEET----LKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVT   85 (102)
T ss_dssp             CCCSSEEEECCCTTCCHHH----HHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEeCCCCccCHHH----HHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEE
Confidence            4579999999999999998    778888774   57777888889999999999999999999998 999999999999


Q ss_pred             EeccccCCCC
Q 045516          595 VDEAKQRGDF  604 (675)
Q Consensus       595 V~~a~~r~~~  604 (675)
                      |.|++++...
T Consensus        86 V~~a~~~~~~   95 (102)
T 2fc8_A           86 LDWAKPKGEG   95 (102)
T ss_dssp             EEECCCCCSS
T ss_pred             EEEecCCCCC
Confidence            9999886654

>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=99.57  E-value=1.5e-14  Score=128.43  Aligned_cols=87  Identities=15%  Similarity=0.318  Sum_probs=76.4

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCC---CeeeEEEEEeCCHHHHHHHHH-hCCceeCCe
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTG---SVKGIAYLDFTDADSFNKALE-MSGTEIGGY  591 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG---~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr  591 (675)
                      ...++|||+|||+.+++++|+. |+++|.+||.|..|.|+++..++   +++|||||+|.+.++|.+||. |||..|+|+
T Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~-~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr   91 (111)
T 2cpi_A           13 VQKNLVFVVGLSQRLADPEVLK-RPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGR   91 (111)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHH-STTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             cCCCEEEEECCCCCCCHHHHHH-HHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCE
Confidence            3478999999999999998322 23999999999999999987654   566999999999999999998 999999999


Q ss_pred             eeEEeccccCCC
Q 045516          592 SLVVDEAKQRGD  603 (675)
Q Consensus       592 ~l~V~~a~~r~~  603 (675)
                      .|+|.|+.++..
T Consensus        92 ~l~V~~a~~k~~  103 (111)
T 2cpi_A           92 TLKASLGTTKYC  103 (111)
T ss_dssp             EEEEESCCCCSC
T ss_pred             EEEEEecccccc
Confidence            999999988764

>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=99.57  E-value=1.9e-14  Score=125.76  Aligned_cols=84  Identities=17%  Similarity=0.248  Sum_probs=75.4

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      ...++|||+|||..+++++    |+.+|..||.|..|.|+++..+  .+|||||+|.+.++|.+||. ||+..|.|+.|+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   86 (103)
T 2cqi_A           13 GQPRTLYVGNLSRDVTEVL----ILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVK   86 (103)
T ss_dssp             CCCCEEEEESCCTTCCHHH----HHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCEEEEeCCCccCCHHH----HHHHHHhcCCEeEEEEEecCCC--CCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEE
Confidence            3479999999999999998    7788889999999999998543  68999999999999999998 999999999999


Q ss_pred             EeccccCCCCC
Q 045516          595 VDEAKQRGDFG  605 (675)
Q Consensus       595 V~~a~~r~~~~  605 (675)
                      |.|+.++....
T Consensus        87 V~~a~~~~~~~   97 (103)
T 2cqi_A           87 VNWATTPSSQK   97 (103)
T ss_dssp             EEECCCTTCCC
T ss_pred             EEECCCCcccc
Confidence            99998865543

>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=99.57  E-value=4e-15  Score=126.32  Aligned_cols=75  Identities=19%  Similarity=0.309  Sum_probs=69.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecc
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~  492 (675)
                      ...++|||+|||+.+++++|+++|.+| .|..|+|.     +++|||||+|.+.++|.+||. |||..|.|+.|+|.++.
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~-----~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   76 (88)
T 1wg1_A            3 SGSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD-----RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE-----GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe-----CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcC
Confidence            356899999999999999999999999 99999985     679999999999999999998 99999999999999986


Q ss_pred             cc
Q 045516          493 ER  494 (675)
Q Consensus       493 ~~  494 (675)
                      ..
T Consensus        77 ~~   78 (88)
T 1wg1_A           77 TD   78 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.57  E-value=2.5e-14  Score=124.95  Aligned_cols=84  Identities=19%  Similarity=0.368  Sum_probs=76.4

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      ...++|||+|||..+++++    |+++|..||.|..|.|+++..  .++|||||+|.+.++|.+||. ||+..|+|+.|+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~----l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   86 (103)
T 2cq3_A           13 STPKRLHVSNIPFRFRDPD----LRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIE   86 (103)
T ss_dssp             CCCCEEEEESCCTTCCHHH----HHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            4479999999999999998    788999999999999999864  389999999999999999998 999999999999


Q ss_pred             EeccccCCCCC
Q 045516          595 VDEAKQRGDFG  605 (675)
Q Consensus       595 V~~a~~r~~~~  605 (675)
                      |.++.++....
T Consensus        87 v~~a~~~~~~~   97 (103)
T 2cq3_A           87 VNNATARVMTN   97 (103)
T ss_dssp             EEECCSSCCCC
T ss_pred             EEEcccCCCCC
Confidence            99998876554

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.35  E-value=1.9e-16  Score=141.76  Aligned_cols=84  Identities=32%  Similarity=0.545  Sum_probs=78.4

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEE--------EEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCce
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITR--------ISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTE  587 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~--------v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~  587 (675)
                      +.++|||+|||..+++++    |+.+|..||.|..        |+|+++..+|.++|||||+|.+.++|.+||. ||+..
T Consensus         6 ~~~~l~V~nLp~~~t~~~----l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~   81 (116)
T 2lcw_A            6 DNNTIFVQGLGENVTIES----VADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKE   81 (116)
Confidence            478999999999999998    7899999999999        9999998999999999999999999999998 99999


Q ss_pred             eCCeeeEEeccccCCCC
Q 045516          588 IGGYSLVVDEAKQRGDF  604 (675)
Q Consensus       588 ~~Gr~l~V~~a~~r~~~  604 (675)
                      |.|+.|+|.++.++..+
T Consensus        82 ~~g~~l~V~~a~~~~~~   98 (116)
T 2lcw_A           82 FSGNPIKVSFATRRADF   98 (116)
Confidence            99999999999877654

>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=99.57  E-value=8.1e-15  Score=131.03  Aligned_cols=81  Identities=27%  Similarity=0.457  Sum_probs=73.6

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~  596 (675)
                      ..+|||+|||+.+++++    |+++|..||.|..|+|+++.  +.++|||||+|.+.++|.+||. |||..|+|+.|+|.
T Consensus         5 ~~~lfV~nLp~~~te~~----L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~   78 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKA----LYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVG   78 (115)
T ss_dssp             CCEEEEESCCTTCCHHH----HHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCEEEECCCCCCCCHHH----HHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            57899999999999998    78899999999999999985  5589999999999999999998 99999999999999


Q ss_pred             ccccCCCC
Q 045516          597 EAKQRGDF  604 (675)
Q Consensus       597 ~a~~r~~~  604 (675)
                      ++.++..+
T Consensus        79 ~a~~~~~~   86 (115)
T 4f25_A           79 RFKSRKER   86 (115)
T ss_dssp             ESSCCCC-
T ss_pred             ECCCcccc
Confidence            99876543

>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=99.56  E-value=1e-14  Score=123.69  Aligned_cols=80  Identities=28%  Similarity=0.561  Sum_probs=75.9

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEec
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDE  597 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~~  597 (675)
                      .++|||+|||..+++++    |+++|..||.|..|.|+++..+|.++|||||+|.+.++|.+||.||+..|+|+.|+|.+
T Consensus         6 ~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~g~~~~g~~l~V~~   81 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEE----LEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALDESLFRGRQIKVIP   81 (89)
T ss_dssp             HTEEEEESCCTTCCHHH----HHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHGGGTTCEETTEECEEEE
T ss_pred             CCEEEEeCCCCCCCHHH----HHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHhcCCCEECCcEEEEEE
Confidence            58999999999999998    77889999999999999999999999999999999999999999999999999999999


Q ss_pred             cccC
Q 045516          598 AKQR  601 (675)
Q Consensus       598 a~~r  601 (675)
                      +++.
T Consensus        82 a~~~   85 (89)
T 3ucg_A           82 KRTN   85 (89)
T ss_dssp             TTTT
T ss_pred             ccCC
Confidence            9764

>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=99.56  E-value=2.1e-15  Score=140.10  Aligned_cols=81  Identities=26%  Similarity=0.436  Sum_probs=72.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEE--------EEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCC
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDV--------RLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGN  483 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v--------~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~g  483 (675)
                      ...+++|||+|||+++++++|+.||..||.|..|        ++.  .+|+++|||||+|.+.++|.+||. |||..|.|
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~--~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g  119 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLM--KEGRMKGQAFIGLPNEKAAAKALKEANGYVLFG  119 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEE--EETTTEEEEEEECSSHHHHHHHHHHHTTBEETT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEec--cCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCC
Confidence            3456899999999999999999999999998764        333  378999999999999999999998 99999999


Q ss_pred             eeEEEEeccccC
Q 045516          484 RAIRLDFARERG  495 (675)
Q Consensus       484 r~i~V~~a~~~~  495 (675)
                      +.|+|.++....
T Consensus       120 ~~l~V~~a~~~~  131 (143)
T 3egn_A          120 KPMVVQFARSAR  131 (143)
T ss_dssp             EECEEEECCCSC
T ss_pred             cEEEEEECCCCC
Confidence            999999997643

>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=99.56  E-value=2e-14  Score=125.63  Aligned_cols=78  Identities=26%  Similarity=0.475  Sum_probs=70.2

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      .+.++|||+|||..+++++    |+++|..||.|..|.|+        ++||||+|.+.++|.+||. ||+..|.|+.|+
T Consensus         9 ~~~~~l~V~nl~~~~t~~~----l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   76 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEI----LEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIE   76 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHH----HHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEE
Confidence            3478999999999999998    77888889999999987        4599999999999999998 999999999999


Q ss_pred             EeccccCCCCC
Q 045516          595 VDEAKQRGDFG  605 (675)
Q Consensus       595 V~~a~~r~~~~  605 (675)
                      |.|+.++....
T Consensus        77 v~~a~~~~~~~   87 (103)
T 2dgu_A           77 IVFAKPPDQKR   87 (103)
T ss_dssp             EEECCCCCCCC
T ss_pred             EEEcCCCcccc
Confidence            99998766543

>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=99.56  E-value=2.3e-15  Score=128.41  Aligned_cols=81  Identities=21%  Similarity=0.315  Sum_probs=70.6

Q ss_pred             eEEEEecCCCCcCHHHHHHHHHhhhcccC--cEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEE
Q 045516          519 HTIFIKGFDSSVGEDQVRASLEEHFGSCG--EITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVV  595 (675)
Q Consensus       519 ~~lfV~nLp~~~te~~i~~~L~~~F~~~G--~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V  595 (675)
                      .+|||+|||+.+++++    |+++|..||  .|..|+|+++..+|+++|||||+|.+.++|.+||. |||..|+|+.|+|
T Consensus         2 ~~l~V~nL~~~~t~~~----l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V   77 (90)
T 3p5t_L            2 IALYIGNLTWWTTDED----LTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVV   77 (90)
T ss_dssp             --CEEESCCTTCCHHH----HHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEE
T ss_pred             eEEEEeCCCCCCCHHH----HHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEE
Confidence            5799999999999998    778899999  99999999999999999999999999999999997 9999999999999


Q ss_pred             eccccCCC
Q 045516          596 DEAKQRGD  603 (675)
Q Consensus       596 ~~a~~r~~  603 (675)
                      .++.+...
T Consensus        78 ~~~~~~~~   85 (90)
T 3p5t_L           78 TPSNKLEH   85 (90)
T ss_dssp             CCC-----
T ss_pred             EECCCCcc
Confidence            99987654

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.56  E-value=1.4e-14  Score=123.78  Aligned_cols=83  Identities=19%  Similarity=0.399  Sum_probs=75.8

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      ...++|||+|||..+++++    |+.+|..||.|..|.|++  .+|.++|||||+|.+.++|..||. ||+..|+|+.|+
T Consensus         6 ~~~~~l~V~nlp~~~t~~~----l~~~f~~~G~v~~~~i~~--~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~   79 (92)
T 2dgv_A            6 SGACQIFVRNLPFDFTWKM----LKDKFNECGHVLYADIKM--ENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREID   79 (92)
T ss_dssp             SSCCEEEECSCCTTCCHHH----HHHHHHTTSCEEEEEEEE--SSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCC
T ss_pred             CCCcEEEEeCCCCCCCHHH----HHHHHHhcCCEEEEEEEc--cCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEE
Confidence            3479999999999999998    778899999999999998  478999999999999999999998 999999999999


Q ss_pred             EeccccCCCC
Q 045516          595 VDEAKQRGDF  604 (675)
Q Consensus       595 V~~a~~r~~~  604 (675)
                      |.+++++...
T Consensus        80 v~~a~~~~~~   89 (92)
T 2dgv_A           80 VRIDRNASGP   89 (92)
T ss_dssp             CEECSCCSSC
T ss_pred             EEEcCCCCCC
Confidence            9999876554

>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=99.56  E-value=1.1e-14  Score=123.22  Aligned_cols=81  Identities=27%  Similarity=0.450  Sum_probs=75.4

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCC-eeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEE
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGS-VKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVV  595 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~-~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V  595 (675)
                      .++|||+|||..+++++    |+.+|..||.|..|.|+.+..++. ++|||||+|.+.++|.+|+. |||..|+|+.|+|
T Consensus         4 ~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   79 (88)
T 4a8x_A            4 PTKVHIGRLTRNVTKDH----IMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITA   79 (88)
T ss_dssp             CCEEEEECCCTTCCHHH----HHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCEEEEeCCCCCCCHHH----HHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEE
Confidence            68999999999999998    778899999999999999988766 99999999999999999998 9999999999999


Q ss_pred             eccccCC
Q 045516          596 DEAKQRG  602 (675)
Q Consensus       596 ~~a~~r~  602 (675)
                      .++.+..
T Consensus        80 ~~a~~~~   86 (88)
T 4a8x_A           80 TAVLAPW   86 (88)
T ss_dssp             EEECCCC
T ss_pred             EECCCCC
Confidence            9997654

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

Probab=99.56  E-value=6.9e-15  Score=126.78  Aligned_cols=79  Identities=18%  Similarity=0.326  Sum_probs=70.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEE-EeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVR-LSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~-i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      ....++|||+|||+++++++|+.+|..||.|..|+ |+.++   ..|+|||+|.+.++|.+||. |||..|.|+.|+|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~---~~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   88 (96)
T 2e44_A           12 RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDS---ETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAY   88 (96)
T ss_dssp             CCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSS---SSEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            44578999999999999999999999999999994 77664   23449999999999999997 999999999999999


Q ss_pred             cccc
Q 045516          491 ARER  494 (675)
Q Consensus       491 a~~~  494 (675)
                      +.++
T Consensus        89 a~~~   92 (96)
T 2e44_A           89 IPDE   92 (96)
T ss_dssp             CCCC
T ss_pred             cCcc
Confidence            9765

>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=99.56  E-value=5.2e-15  Score=132.29  Aligned_cols=75  Identities=27%  Similarity=0.391  Sum_probs=65.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCee-----EE
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRA-----IR  487 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~-----i~  487 (675)
                      ...++|||+|||+++++++|++||.+||.|..|.|+.+      |||||+|.+.++|.+||. ||+..|+|+.     |.
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~   87 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR   87 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEE
Confidence            45789999999999999999999999999999999865      999999999999999998 9999999998     67


Q ss_pred             EEecccc
Q 045516          488 LDFARER  494 (675)
Q Consensus       488 V~~a~~~  494 (675)
                      |.....+
T Consensus        88 v~~~~~~   94 (115)
T 3beg_B           88 VKVDGPR   94 (115)
T ss_dssp             EEECC--
T ss_pred             eccCCCC
Confidence            7666554

>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=99.55  E-value=9.1e-15  Score=130.46  Aligned_cols=82  Identities=16%  Similarity=0.167  Sum_probs=76.5

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcE-EEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEI-TRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I-~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~  594 (675)
                      ...++|||+|||+.+++++    |+++|..||.| ..|+|+++. +|+++|||||+|.+.++|.+||.+|+..|+|+.|+
T Consensus        13 ~~~~~l~V~nLp~~~t~~~----l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~   87 (114)
T 2cpy_A           13 SAKVCAHITNIPFSITKMD----VLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERLHRKKLNGREAF   87 (114)
T ss_dssp             SCCCEEEEESCCTTSCHHH----HHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEE
T ss_pred             CCccEEEEeCcCCcCCHHH----HHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHhCCCccCCeEEE
Confidence            3478999999999999998    78999999999 899999998 89999999999999999999999999999999999


Q ss_pred             EeccccCC
Q 045516          595 VDEAKQRG  602 (675)
Q Consensus       595 V~~a~~r~  602 (675)
                      |.++.++.
T Consensus        88 v~~a~~~~   95 (114)
T 2cpy_A           88 VHVVTLED   95 (114)
T ss_dssp             EEEECHHH
T ss_pred             EEECCHHH
Confidence            99998754

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.55  E-value=1.7e-14  Score=125.16  Aligned_cols=80  Identities=30%  Similarity=0.497  Sum_probs=75.5

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEE--------EEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCc
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITR--------ISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGT  586 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~--------v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~  586 (675)
                      .+.++|||+|||..+++++    |+++|..||.|..        |+|+++..+|+++|||||+|.+.++|..||. |||.
T Consensus        11 ~~~~~l~V~nLp~~~t~~~----l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~   86 (99)
T 2la6_A           11 SDNNTIFVQGLGENVTIES----VADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGK   86 (99)
T ss_dssp             CCCSEEEEECCCSSCCHHH----HHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCC
Confidence            4479999999999999998    7889999999999        9999999999999999999999999999998 9999


Q ss_pred             eeCCeeeEEeccc
Q 045516          587 EIGGYSLVVDEAK  599 (675)
Q Consensus       587 ~~~Gr~l~V~~a~  599 (675)
                      .|+|+.|+|.+++
T Consensus        87 ~~~g~~l~V~~A~   99 (99)
T 2la6_A           87 EFSGNPIKVSFAT   99 (99)
T ss_dssp             BSSSSBCEEEECC
T ss_pred             EeCCcEEEEEecC
Confidence            9999999999874

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.55  E-value=3e-14  Score=124.02  Aligned_cols=80  Identities=26%  Similarity=0.479  Sum_probs=71.9

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      ...++|||+|||..+++++    |+++|..||.|   +|+.+ .++.++|||||+|.+.++|.+||. ||+..|+|+.|+
T Consensus        13 ~~~~~l~V~nLp~~~t~~~----l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   84 (101)
T 2fc9_A           13 GESKTLVLSNLSYSATEET----LQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIR   84 (101)
T ss_dssp             CCCSEEEEESCCTTCCHHH----HHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEE
Confidence            4479999999999999998    77899999987   56666 679999999999999999999998 999999999999


Q ss_pred             EeccccCCC
Q 045516          595 VDEAKQRGD  603 (675)
Q Consensus       595 V~~a~~r~~  603 (675)
                      |.|+.++..
T Consensus        85 v~~a~~~~~   93 (101)
T 2fc9_A           85 LELQGPRGS   93 (101)
T ss_dssp             EEECSSCCC
T ss_pred             EEEcCCCCC
Confidence            999987644

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.55  E-value=5.2e-15  Score=131.97  Aligned_cols=76  Identities=14%  Similarity=0.226  Sum_probs=68.7

Q ss_pred             ceEEEcCC----CCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecC----HHH----HHHHHH---hCCcc
Q 045516          417 KTLFVGNL----PFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFAS----VED----AHKAIE---LNGQM  480 (675)
Q Consensus       417 ~tlfV~nL----p~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~----~e~----A~~Al~---l~g~~  480 (675)
                      +.|||+||    ||.+++..|++||+.||.|..|.+++|+ +|+++|||||+|.+    +..    |.+||.   |||..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            68999999    9999999999999999999999999999 99999999999996    333    778875   79999


Q ss_pred             cCCeeEEEEecc
Q 045516          481 LGNRAIRLDFAR  492 (675)
Q Consensus       481 ~~gr~i~V~~a~  492 (675)
                      |+||.|+|.+..
T Consensus        83 I~Gr~irV~ln~   94 (136)
T 2j8a_A           83 IMGFKFEVILNK   94 (136)
T ss_dssp             ETTEEEEEEECC
T ss_pred             ecCcEEEEEECc
Confidence            999999999864

>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=99.55  E-value=3.7e-14  Score=125.19  Aligned_cols=77  Identities=17%  Similarity=0.353  Sum_probs=70.9

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCC----
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGG----  590 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~G----  590 (675)
                      ...++|||+|||+.+++++    |+++|..||.|..|.|+.+       |||||+|.+.++|..||. ||+..|.|    
T Consensus        13 ~~~~~l~V~nLp~~~t~~~----l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~   81 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQD----LKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGE   81 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHH----HHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSC
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCc
Confidence            3478999999999999998    7789999999999999886       899999999999999998 99999999    


Q ss_pred             -eeeEEeccccCCC
Q 045516          591 -YSLVVDEAKQRGD  603 (675)
Q Consensus       591 -r~l~V~~a~~r~~  603 (675)
                       +.|+|.++.++..
T Consensus        82 ~~~i~V~~a~~~~~   95 (108)
T 1x4c_A           82 TAYIRVKVDGPRSP   95 (108)
T ss_dssp             EEEEEEEESSCCSC
T ss_pred             ceEEEEEeCCCCCC
Confidence             9999999987543

>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=99.55  E-value=1.1e-14  Score=133.09  Aligned_cols=85  Identities=24%  Similarity=0.359  Sum_probs=79.3

Q ss_pred             CCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeee
Q 045516          515 GQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSL  593 (675)
Q Consensus       515 ~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l  593 (675)
                      ..+.++|||+|||+.+++++    |+++|..||.|..|.|+++..+|.++|||||+|.+.++|.+||. |||..|+|+.|
T Consensus        43 ~~~~~~l~V~nLp~~~te~~----L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l  118 (129)
T 2kxn_B           43 PDPNCCLGVFGLSLYTTERD----LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI  118 (129)
T ss_dssp             CCCSSCBCEETCTTSCCHHH----HHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCC
T ss_pred             CCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            34578999999999999998    78899999999999999999999999999999999999999998 99999999999


Q ss_pred             EEeccccCCC
Q 045516          594 VVDEAKQRGD  603 (675)
Q Consensus       594 ~V~~a~~r~~  603 (675)
                      +|.|+.++..
T Consensus       119 ~V~~a~~~~p  128 (129)
T 2kxn_B          119 RVDFSITKRP  128 (129)
T ss_dssp             EESCCSSSSC
T ss_pred             EEEEecCCCC
Confidence            9999987653

>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=99.55  E-value=1.2e-14  Score=125.78  Aligned_cols=83  Identities=17%  Similarity=0.181  Sum_probs=76.8

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      ...++|||+|||+.+++++    |+.+|..||.|..+.++.+..+|+++|||||+|.+.++|.+||. ||+..|+|+.|+
T Consensus        13 ~~~~~l~v~nLp~~~t~~~----l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~   88 (98)
T 2cqp_A           13 PGPTIIKVQNMPFTVSIDE----ILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVK   88 (98)
T ss_dssp             CSSEEEEEESCCTTCCHHH----HHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEE
Confidence            3479999999999999998    77899999999999999998999999999999999999999997 999999999999


Q ss_pred             EeccccCC
Q 045516          595 VDEAKQRG  602 (675)
Q Consensus       595 V~~a~~r~  602 (675)
                      |.++..+.
T Consensus        89 V~~a~~~~   96 (98)
T 2cqp_A           89 LVLGSGPS   96 (98)
T ss_dssp             EEESSCSS
T ss_pred             EEEcCCCC
Confidence            99987543

>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=99.55  E-value=2.1e-14  Score=135.15  Aligned_cols=80  Identities=21%  Similarity=0.284  Sum_probs=71.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCC--eeEEEE
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGN--RAIRLD  489 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~g--r~i~V~  489 (675)
                      .....+|||+||++.+++++|+++|++||.|..|+|+..   ..+|||||+|.+.++|..||. |||..|.|  +.|+|.
T Consensus        43 ps~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k---~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~  119 (164)
T 1sjr_A           43 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK---NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID  119 (164)
T ss_dssp             CCCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES---SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEE
T ss_pred             CCceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC---CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEE
Confidence            344578999999999999999999999999999999754   357999999999999999998 99999966  999999


Q ss_pred             eccccC
Q 045516          490 FARERG  495 (675)
Q Consensus       490 ~a~~~~  495 (675)
                      |++.+.
T Consensus       120 ~Ak~~~  125 (164)
T 1sjr_A          120 FSKLTS  125 (164)
T ss_dssp             ECSSSS
T ss_pred             EecCCc
Confidence            998764

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

Probab=99.55  E-value=1.5e-14  Score=129.66  Aligned_cols=81  Identities=25%  Similarity=0.374  Sum_probs=75.7

Q ss_pred             CCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeee
Q 045516          515 GQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSL  593 (675)
Q Consensus       515 ~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l  593 (675)
                      ....++|||+|||+.+++++    |+++|..||.|..|+|+++..+|.++|||||+|.+.++|.+||. |||..|+|+.|
T Consensus        37 ~~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l  112 (118)
T 2khc_A           37 GPEGCNLFIYHLPQEFTDTD----LASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRL  112 (118)
T ss_dssp             CCCSEEEEEECSCTTCCHHH----HHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            34579999999999999998    78899999999999999999999999999999999999999998 99999999999


Q ss_pred             EEeccc
Q 045516          594 VVDEAK  599 (675)
Q Consensus       594 ~V~~a~  599 (675)
                      +|.|++
T Consensus       113 ~V~~ak  118 (118)
T 2khc_A          113 KVQLKK  118 (118)
T ss_dssp             CEEEC-
T ss_pred             EEEecC
Confidence            999874

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.55  E-value=1.5e-14  Score=128.00  Aligned_cols=84  Identities=25%  Similarity=0.370  Sum_probs=76.7

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEe
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVD  596 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~  596 (675)
                      ..++|||+|||..+++++    |+.+|..||.|..|+|+++..+|.++|||||+|.+.++|.+||.+++..|+|+.|+|.
T Consensus        24 ~~~~lfV~nLp~~~te~~----L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~g~~l~V~   99 (109)
T 2rs2_A           24 SGCKMFIGGLSWQTTQEG----LREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPK   99 (109)
T ss_dssp             --CCEEEESCCTTCCHHH----HHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSCEEETTEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHH----HHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCCCcCCCEEEEEE
Confidence            478999999999999998    7889999999999999999999999999999999999999999955699999999999


Q ss_pred             ccccCCCC
Q 045516          597 EAKQRGDF  604 (675)
Q Consensus       597 ~a~~r~~~  604 (675)
                      ++.++...
T Consensus       100 ~a~~~~~~  107 (109)
T 2rs2_A          100 VAFPRRAQ  107 (109)
T ss_dssp             ECCCCCCC
T ss_pred             EccCCCCC
Confidence            99877654

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.55  E-value=8e-15  Score=128.39  Aligned_cols=79  Identities=20%  Similarity=0.385  Sum_probs=74.2

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEe
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVD  596 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~  596 (675)
                      ..++|||+|||+.+++++    |+++|+.||.|..|+|+++.. |.++|||||+|.+.++|..||.+|++.|+|+.|+|.
T Consensus        10 ~~~~lfV~~Lp~~~te~~----L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~~~~~~~~gr~l~V~   84 (103)
T 1s79_A           10 KNRSVYIKGFPTDATLDD----IKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLIL   84 (103)
T ss_dssp             GGGCEEEECCCTTCCHHH----HHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHTSSCCCCTTTTCEEE
T ss_pred             CCCEEEEECCCCCCCHHH----HHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHHcCCCEECCEEEEEE
Confidence            368999999999999998    778999999999999999987 999999999999999999999999999999999999


Q ss_pred             cccc
Q 045516          597 EAKQ  600 (675)
Q Consensus       597 ~a~~  600 (675)
                      ++..
T Consensus        85 ~~~~   88 (103)
T 1s79_A           85 FKDD   88 (103)
T ss_dssp             EHHH
T ss_pred             EchH
Confidence            8754

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.54  E-value=2.4e-14  Score=135.24  Aligned_cols=80  Identities=33%  Similarity=0.610  Sum_probs=76.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      ....++|||+|||+.+++++|+++|+.||.|..|+|+++. +|.++|||||+|.+.++|.+||. |||..|.|+.|+|.|
T Consensus        84 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  163 (166)
T 3md3_A           84 SDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINW  163 (166)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEe
Confidence            4567899999999999999999999999999999999996 89999999999999999999998 999999999999999


Q ss_pred             cc
Q 045516          491 AR  492 (675)
Q Consensus       491 a~  492 (675)
                      +.
T Consensus       164 a~  165 (166)
T 3md3_A          164 AA  165 (166)
T ss_dssp             SC
T ss_pred             cC
Confidence            85

>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=99.54  E-value=2.7e-14  Score=125.64  Aligned_cols=80  Identities=19%  Similarity=0.363  Sum_probs=75.0

Q ss_pred             CCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeee
Q 045516          515 GQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSL  593 (675)
Q Consensus       515 ~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l  593 (675)
                      ..+.++|||+|||+.+++++    |+++|..||.|..|.|+++. +|.++|||||+|.+.++|.+||. ||+..|+|+.|
T Consensus        26 ~~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l  100 (107)
T 3ulh_A           26 VETGGKLLVSNLDFGVSDAD----IQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPM  100 (107)
T ss_dssp             CCCSEEEEEESCCTTCCHHH----HHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEE
Confidence            34589999999999999998    77889999999999999998 89999999999999999999998 99999999999


Q ss_pred             EEeccc
Q 045516          594 VVDEAK  599 (675)
Q Consensus       594 ~V~~a~  599 (675)
                      +|.++.
T Consensus       101 ~V~~a~  106 (107)
T 3ulh_A          101 NIQLVT  106 (107)
T ss_dssp             EEEEEC
T ss_pred             EEEEeC
Confidence            999875

>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=99.54  E-value=2.7e-14  Score=122.70  Aligned_cols=80  Identities=25%  Similarity=0.478  Sum_probs=74.7

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      ...++|||+|||..+++++    |+++|..||.|..|.|+++.. |.++|||||+|.+.++|.+||. ||+..|+|+.|+
T Consensus        14 ~~~~~l~v~nlp~~~~~~~----l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   88 (95)
T 2ywk_A           14 EADRTVFVGNLEARVREEI----LYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPIN   88 (95)
T ss_dssp             TGGGEEEEECCCTTCCHHH----HHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEECCCCCCCHHH----HHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEE
Confidence            3479999999999999998    788999999999999999976 9999999999999999999998 999999999999


Q ss_pred             Eecccc
Q 045516          595 VDEAKQ  600 (675)
Q Consensus       595 V~~a~~  600 (675)
                      |.+++.
T Consensus        89 V~~a~~   94 (95)
T 2ywk_A           89 VSGPSS   94 (95)
T ss_dssp             EECCCC
T ss_pred             EEEcCC
Confidence            999864

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.54  E-value=2.3e-14  Score=141.72  Aligned_cols=83  Identities=20%  Similarity=0.436  Sum_probs=78.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ...++|||+|||+.+++++|+++|+.||.|..|+|+++. +|+++|||||+|.+.++|.+||. |||..|+|+.|+|.++
T Consensus       123 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a  202 (216)
T 2qfj_A          123 RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA  202 (216)
T ss_dssp             TTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEEC
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEe
Confidence            346899999999999999999999999999999999997 89999999999999999999998 9999999999999999


Q ss_pred             cccCC
Q 045516          492 RERGA  496 (675)
Q Consensus       492 ~~~~~  496 (675)
                      .....
T Consensus       203 ~~~~~  207 (216)
T 2qfj_A          203 VTPPM  207 (216)
T ss_dssp             SSCSS
T ss_pred             cCCCC
Confidence            87643

>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=99.54  E-value=8.1e-15  Score=127.56  Aligned_cols=82  Identities=27%  Similarity=0.484  Sum_probs=75.2

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccC-CCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDY-DTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~-~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~  594 (675)
                      ...++|||+|||+.+++++    |+.+|..|| |..|+|+++. .+|+++|||||+|.+.++|.+||.|||..|+|+.|+
T Consensus        17 ~~~~~l~V~nLp~~~t~~~----l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai~l~g~~~~g~~l~   91 (100)
T 2j76_E           17 SPPYTAFLGNLPYDVTEES----IKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNRRIR   91 (100)
T ss_dssp             ---CEEEESCCSSCCSSSH----HHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHHHTTTCCBTTBCCC
T ss_pred             CCCcEEEEeCCCCCCCHHH----HHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHHhcCCCEECCeEEE
Confidence            3479999999999999998    789999999 9999999998 689999999999999999999999999999999999


Q ss_pred             EeccccCC
Q 045516          595 VDEAKQRG  602 (675)
Q Consensus       595 V~~a~~r~  602 (675)
                      |.++.++.
T Consensus        92 V~~a~~~~   99 (100)
T 2j76_E           92 VDVADQAQ   99 (100)
T ss_dssp             CEECCCSC
T ss_pred             EEeccCCC
Confidence            99998764

>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=99.54  E-value=1.5e-14  Score=141.42  Aligned_cols=79  Identities=20%  Similarity=0.433  Sum_probs=73.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEeccc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a~~  493 (675)
                      ..++|||+|||+.+++++|++||++||.|..|+|+++.+++++|||||+|.+.++|.+||.+.+..|.|+.|.|.+...
T Consensus       108 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~~~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKDD  186 (193)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCTTCEETTEECEEEETTT
T ss_pred             ccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEhHH
Confidence            3589999999999999999999999999999999999899999999999999999999999656799999999998754

>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=99.54  E-value=3.8e-14  Score=124.27  Aligned_cols=82  Identities=16%  Similarity=0.300  Sum_probs=75.5

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEE-EEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEE
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITR-ISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVV  595 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~-v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V  595 (675)
                      ..++|||+|||+.+++++    |+++|..||.|.. |+|+.+ .+|+++|||||+|.+.++|.+||.+|+..|+||.|+|
T Consensus        14 ~~~~l~V~nLp~~~te~~----l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~~~~~~~gr~i~v   88 (104)
T 1wg5_A           14 NDGFVRLRGLPFGCSKEE----IVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEI   88 (104)
T ss_dssp             CCCEEEEESCCTTCCHHH----HHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEE
T ss_pred             CCCEEEEeCCCCCCCHHH----HHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHhCcchhCCcEEEE
Confidence            378999999999999998    7899999999998 889888 7899999999999999999999999999999999999


Q ss_pred             eccccCCC
Q 045516          596 DEAKQRGD  603 (675)
Q Consensus       596 ~~a~~r~~  603 (675)
                      .++.++..
T Consensus        89 ~~~~~~~~   96 (104)
T 1wg5_A           89 FKSSRAEV   96 (104)
T ss_dssp             EEECTTTS
T ss_pred             EECCHHHH
Confidence            99876543

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.54  E-value=3e-14  Score=121.48  Aligned_cols=81  Identities=21%  Similarity=0.379  Sum_probs=75.8

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEe
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVD  596 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~  596 (675)
                      ..++|||+|||+.+++++    |+++|..| .|..|+|+++ .+|+++|||||+|.+.++|.+||.||+..|+|+.|+|.
T Consensus         9 ~~~~l~v~nLp~~~t~~~----l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~~~g~~~~gr~i~v~   82 (91)
T 2dgw_A            9 TCHTVKLRGAPFNVTEKN----VMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALKCNREYMGGRYIEVF   82 (91)
T ss_dssp             CCCEEEEECCCSSCCHHH----HHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHHSCSEEETTEEEEEE
T ss_pred             CccEEEEECCCCCCCHHH----HHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHHhCCceeCCcEEEEE
Confidence            378999999999999998    78899999 9999999999 78999999999999999999999999999999999999


Q ss_pred             ccccCCC
Q 045516          597 EAKQRGD  603 (675)
Q Consensus       597 ~a~~r~~  603 (675)
                      ++.++..
T Consensus        83 ~a~~~~~   89 (91)
T 2dgw_A           83 REKSGPS   89 (91)
T ss_dssp             EESSCCC
T ss_pred             ECCcCCC
Confidence            9987754

>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=99.54  E-value=1.4e-14  Score=123.43  Aligned_cols=75  Identities=25%  Similarity=0.437  Sum_probs=62.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcc--cCCeeEEEEec
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQM--LGNRAIRLDFA  491 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~--~~gr~i~V~~a  491 (675)
                      ...++|||+|||+++++++|+++|++||.|..|+|+++    ++|||||+|.+.++|.+   |++..  +.|+.|.|.++
T Consensus         9 ~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~----srGfaFV~F~~~~~A~~---~~~~~~~~~g~~v~v~~a   81 (89)
T 3d2w_A            9 HHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP----FRAFAFVTFADDKVAQS---LCGEDLIIKGISVHISNA   81 (89)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS----CCSEEEEEESCHHHHHH---HTTCEEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC----CCCEEEEEECCHHHHHH---HcCCCcccCCEEEEEEEc
Confidence            35689999999999999999999999999999999874    79999999999999884   44444  56999999998


Q ss_pred             cccC
Q 045516          492 RERG  495 (675)
Q Consensus       492 ~~~~  495 (675)
                      .++.
T Consensus        82 ~~k~   85 (89)
T 3d2w_A           82 EPKH   85 (89)
T ss_dssp             C---
T ss_pred             CCCC
Confidence            7653

>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=99.54  E-value=6.9e-15  Score=139.47  Aligned_cols=80  Identities=24%  Similarity=0.454  Sum_probs=76.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEeccc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a~~  493 (675)
                      ..++|||+|||+.+++++|+++|+.||.|..|+|+.+. +|.++|||||+|.+.++|.+||++|+..|.|+.|.|.++.+
T Consensus        86 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~i~V~~a~p  165 (167)
T 2cjk_A           86 KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRAEP  165 (167)
T ss_dssp             HCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHHCSEECSSSSCEEEEECCC
T ss_pred             CCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHhCCCEEeCCeEEEEeecCC
Confidence            35799999999999999999999999999999999997 89999999999999999999999999999999999999876


Q ss_pred             c
Q 045516          494 R  494 (675)
Q Consensus       494 ~  494 (675)
                      +
T Consensus       166 k  166 (167)
T 2cjk_A          166 R  166 (167)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.54  E-value=9e-15  Score=123.47  Aligned_cols=72  Identities=26%  Similarity=0.690  Sum_probs=67.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhC----C-------CeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccC
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEV----A-------EVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLG  482 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~----G-------~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~  482 (675)
                      ...++|||+|||+++++++|+++|.+|    |       .|..|+|.++     +|||||+|.+.++|.+||.|||..|.
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~-----kg~afV~f~~~~~a~~A~~l~g~~~~   78 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-----KNFAFLEFRSVDETTQAMAFDGIIFQ   78 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS-----SSEEEEEESSHHHHHHHGGGTTCEET
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC-----CcEEEEEcCCHHHHHHHHhcCCCEEC
Confidence            356899999999999999999999999    8       9999999864     89999999999999999999999999


Q ss_pred             CeeEEEEe
Q 045516          483 NRAIRLDF  490 (675)
Q Consensus       483 gr~i~V~~  490 (675)
                      |+.|+|..
T Consensus        79 g~~l~V~r   86 (87)
T 2hzc_A           79 GQSLKIRR   86 (87)
T ss_dssp             TEECEEEC
T ss_pred             CeEEEEeC
Confidence            99999964

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.54  E-value=2.5e-14  Score=129.74  Aligned_cols=78  Identities=22%  Similarity=0.333  Sum_probs=70.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccE-EEEEecCHHHHHHHHH-hCCcccCC--eeEEEE
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGY-GHVEFASVEDAHKAIE-LNGQMLGN--RAIRLD  489 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~-afV~F~~~e~A~~Al~-l~g~~~~g--r~i~V~  489 (675)
                      +.--+|||+||++.+|+++|+++|++||.|..|+|+..    .+|| |||+|.+.++|..||. |||..|.|  +.|+|.
T Consensus        26 s~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~  101 (130)
T 3zzy_A           26 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID  101 (130)
T ss_dssp             CSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE----TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEE
T ss_pred             CceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC----CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEE
Confidence            34467889999999999999999999999999999864    3688 9999999999999998 99999988  999999


Q ss_pred             eccccC
Q 045516          490 FARERG  495 (675)
Q Consensus       490 ~a~~~~  495 (675)
                      |++...
T Consensus       102 ~ak~~~  107 (130)
T 3zzy_A          102 FSKLTS  107 (130)
T ss_dssp             ECSCSS
T ss_pred             ecCCCc
Confidence            998764

>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=99.54  E-value=1.4e-14  Score=124.96  Aligned_cols=85  Identities=27%  Similarity=0.467  Sum_probs=78.3

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      .+.++|||+|||..+++++|+..|..+|..||.|..|.|+.   +|.++|||||+|.+.++|..|+. |||..|+|+.|+
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   82 (97)
T 1nu4_A            6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   82 (97)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEE
Confidence            34799999999999999999989999999999999999974   47889999999999999999998 999999999999


Q ss_pred             EeccccCCC
Q 045516          595 VDEAKQRGD  603 (675)
Q Consensus       595 V~~a~~r~~  603 (675)
                      |.|+.++..
T Consensus        83 v~~a~~~~~   91 (97)
T 1nu4_A           83 IQYAKTDSD   91 (97)
T ss_dssp             EEECSSCCT
T ss_pred             EEEccCCCc
Confidence            999987643

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.53  E-value=8e-15  Score=120.29  Aligned_cols=75  Identities=20%  Similarity=0.345  Sum_probs=71.3

Q ss_pred             EEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEecc
Q 045516          520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDEA  598 (675)
Q Consensus       520 ~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~~a  598 (675)
                      +|||+|||..+++++    |+++|..||.|..|.|+++..+|.++|||||+|.+.+.|.+|+.||+..|+|+.|+|.++
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 KIFVGGLSVNTTVED----VKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHH----HHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHSSSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHH----HHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHCCCCEECCEEEEEEeC
Confidence            489999999999998    778899999999999999998999999999999999999999999999999999999875

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.53  E-value=1.6e-14  Score=136.34  Aligned_cols=81  Identities=21%  Similarity=0.361  Sum_probs=75.3

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccC--cEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeee
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCG--EITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSL  593 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G--~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l  593 (675)
                      ..++|||+||++.+++++    |+++|..||  .|..|+|+++..+|+++|||||+|.+.++|.+||. |||..|+|+.|
T Consensus        54 ~~~~lfVgnLp~~~te~~----L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l  129 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQ----LIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKV  129 (156)
T ss_dssp             --CEEEEECCCTTCCHHH----HHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEEC
T ss_pred             CCCEEEEeCCCCCCCHHH----HHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEe
Confidence            368999999999999998    778899999  99999999999999999999999999999999998 99999999999


Q ss_pred             EEeccccC
Q 045516          594 VVDEAKQR  601 (675)
Q Consensus       594 ~V~~a~~r  601 (675)
                      +|.++.++
T Consensus       130 ~V~~a~~~  137 (156)
T 3n9u_C          130 DVRPATRQ  137 (156)
T ss_dssp             EEEECCHH
T ss_pred             EEEEcCCC
Confidence            99999754

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.53  E-value=3.7e-14  Score=120.72  Aligned_cols=78  Identities=14%  Similarity=0.336  Sum_probs=71.0

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      ...++|||+|||..+++++    |+.+|..||.|..|.|+        +|||||+|.+.++|..||. ||+..|+|+.|+
T Consensus         6 ~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   73 (90)
T 2dnq_A            6 SGMVKLFIGNLPREATEQE----IRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNIN   73 (90)
T ss_dssp             SCCEEEEEESCCSSCCHHH----HHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCE
T ss_pred             CCCeEEEEeCCCCCCCHHH----HHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEE
Confidence            3479999999999999998    77899999999999997        5799999999999999997 999999999999


Q ss_pred             EeccccCCCCC
Q 045516          595 VDEAKQRGDFG  605 (675)
Q Consensus       595 V~~a~~r~~~~  605 (675)
                      |.++.++....
T Consensus        74 v~~a~~~~~~~   84 (90)
T 2dnq_A           74 VEASKNKSKAS   84 (90)
T ss_dssp             EECSSCCCCCC
T ss_pred             EEECCCCCCCC
Confidence            99998766543

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.53  E-value=1e-14  Score=133.54  Aligned_cols=83  Identities=19%  Similarity=0.318  Sum_probs=76.5

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEE--EEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCc----ee
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITR--ISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGT----EI  588 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~--v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~----~~  588 (675)
                      ...++|||+|||+.+++++    |+++|..||.|..  |+|+++..+|+++|||||+|.+. +|.+||. |||.    .|
T Consensus        21 ~~~~~lfV~nL~~~~te~~----L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~   95 (131)
T 2m2b_A           21 NANDTIILRNLNPHSTMDS----ILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTI   95 (131)
T ss_dssp             CCCCEEEECSCCTTCCSHH----HHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCG
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccC
Confidence            4478999999999999998    7789999999977  99999999999999999999999 9999998 9999    99


Q ss_pred             CCeeeEEeccccCCC
Q 045516          589 GGYSLVVDEAKQRGD  603 (675)
Q Consensus       589 ~Gr~l~V~~a~~r~~  603 (675)
                      +|+.|+|.++.++..
T Consensus        96 ~gr~l~V~~a~~~~~  110 (131)
T 2m2b_A           96 DGKTINVEFAKGSKR  110 (131)
T ss_dssp             GGCCCCCEECCCSCC
T ss_pred             CCEEEEEEECCCCCC
Confidence            999999999987543

>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=99.53  E-value=2.1e-14  Score=139.83  Aligned_cols=84  Identities=15%  Similarity=0.335  Sum_probs=75.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEecc
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a~  492 (675)
                      ...++|||+|||+.+++++|+++|+.||.|..|+|+++. +|.++|||||+|.+.++|.+||.+++..|.|+.|.|.++.
T Consensus       102 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~~~~~~~G~~i~v~~a~  181 (196)
T 1l3k_A          102 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKAL  181 (196)
T ss_dssp             -CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHCSCCEETTEECEEEECC
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHhCCcEECCEEEEEEecC
Confidence            356899999999999999999999999999999999997 8999999999999999999999988999999999999998


Q ss_pred             ccCCC
Q 045516          493 ERGAY  497 (675)
Q Consensus       493 ~~~~~  497 (675)
                      ++...
T Consensus       182 ~k~~~  186 (196)
T 1l3k_A          182 SKQEM  186 (196)
T ss_dssp             -----
T ss_pred             ChhHh
Confidence            76543

>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=99.52  E-value=1.3e-14  Score=126.86  Aligned_cols=83  Identities=24%  Similarity=0.469  Sum_probs=77.8

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~  596 (675)
                      .++|||+|||..+++++    |+.+|..||.|..|.|+++..+|.++|||||+|.+.++|.+||. |||..|+|+.|+|.
T Consensus         8 ~~~l~V~nlp~~~~~~~----l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   83 (104)
T 1p1t_A            8 LRSVFVGNIPYEATEEQ----LKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVD   83 (104)
T ss_dssp             HSCEEEESCCTTSCHHH----HHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEE
T ss_pred             ccEEEEeCCCCcCCHHH----HHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Confidence            68999999999999998    77889999999999999999999999999999999999999998 99999999999999


Q ss_pred             ccccCCCC
Q 045516          597 EAKQRGDF  604 (675)
Q Consensus       597 ~a~~r~~~  604 (675)
                      ++.++...
T Consensus        84 ~a~~~~~~   91 (104)
T 1p1t_A           84 NAASEKNK   91 (104)
T ss_dssp             ETTCTTHH
T ss_pred             eCCCccch
Confidence            99876543

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.52  E-value=2.8e-14  Score=120.50  Aligned_cols=79  Identities=23%  Similarity=0.415  Sum_probs=72.0

Q ss_pred             CceE-EEEecCCCCcCHHHHHHHHHhhhccc-CcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeee
Q 045516          517 AAHT-IFIKGFDSSVGEDQVRASLEEHFGSC-GEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSL  593 (675)
Q Consensus       517 ~~~~-lfV~nLp~~~te~~i~~~L~~~F~~~-G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l  593 (675)
                      +..+ |||+|||+.++.++|+..|+++|+.| |.|..|       +|   |||||.|.+.++|.+|+. |||..|.||.|
T Consensus         7 p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i   76 (96)
T 2diu_A            7 GCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGNRI   76 (96)
T ss_dssp             CSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCC
T ss_pred             CcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCceE
Confidence            3555 99999999999999999999999999 599998       33   999999999999999998 99999999999


Q ss_pred             EEeccccCCCCC
Q 045516          594 VVDEAKQRGDFG  605 (675)
Q Consensus       594 ~V~~a~~r~~~~  605 (675)
                      +|.|++.+.+.-
T Consensus        77 ~v~~A~~~sd~~   88 (96)
T 2diu_A           77 IVSFTPKNRELC   88 (96)
T ss_dssp             EEESSCCSCCCC
T ss_pred             EEEecCCCccee
Confidence            999999877653

>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=99.52  E-value=5.5e-14  Score=124.06  Aligned_cols=84  Identities=18%  Similarity=0.268  Sum_probs=76.6

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCc-EEEEEec-ccCCCCCeeeEEEEEeCCHHHHHHHHH-hC--CceeCCe
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGE-ITRISVP-KDYDTGSVKGIAYLDFTDADSFNKALE-MS--GTEIGGY  591 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~-I~~v~i~-~d~~tG~~rG~afV~F~~~e~A~~Al~-ln--g~~~~Gr  591 (675)
                      ..++|||+|||..+++++    |+.+|..||. |..|.|+ .+..+|.++|||||+|.+.++|..||. ||  +..|+|+
T Consensus         7 ~~~~l~V~nLp~~~t~~~----l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~   82 (109)
T 2dis_A            7 GNCRLFIGGIPKMKKREE----ILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGH   82 (109)
T ss_dssp             CSEEEEEECCCTTSCHHH----HHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTB
T ss_pred             CCCEEEEeCCCCcCCHHH----HHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCC
Confidence            479999999999999998    6788888898 9999999 888899999999999999999999998 86  5899999


Q ss_pred             eeEEeccccCCCC
Q 045516          592 SLVVDEAKQRGDF  604 (675)
Q Consensus       592 ~l~V~~a~~r~~~  604 (675)
                      .|+|.|+.++...
T Consensus        83 ~l~V~~a~~~~~~   95 (109)
T 2dis_A           83 QIAVDWAEPEIDV   95 (109)
T ss_dssp             CCEEEESCSSCST
T ss_pred             eEEEEEcCCCCCc
Confidence            9999999876653

>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=99.52  E-value=9.7e-15  Score=130.23  Aligned_cols=87  Identities=22%  Similarity=0.371  Sum_probs=74.1

Q ss_pred             CCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeee
Q 045516          515 GQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSL  593 (675)
Q Consensus       515 ~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l  593 (675)
                      ..+.++|||+|||..+++++    |+.+|..||.|..|.+..+..+|.++|||||+|.+.++|..||. ||+..|+|+.|
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~----l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l   97 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERD----LVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKIL   97 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHH----HHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBC
T ss_pred             CCCCCEEEEeCCCCCCCHHH----HHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEE
Confidence            34579999999999999998    77889999999544443333478999999999999999999998 99999999999


Q ss_pred             EEeccccCCCCC
Q 045516          594 VVDEAKQRGDFG  605 (675)
Q Consensus       594 ~V~~a~~r~~~~  605 (675)
                      +|.|+.++....
T Consensus        98 ~v~~a~~~~~~~  109 (115)
T 2cpx_A           98 VIEFGKNKKQRS  109 (115)
T ss_dssp             EEEECCCCSCCC
T ss_pred             EEEEccCCCCCC
Confidence            999998866543

>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=99.52  E-value=1.5e-14  Score=124.30  Aligned_cols=80  Identities=18%  Similarity=0.220  Sum_probs=74.4

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEE
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVV  595 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V  595 (675)
                      +.++|||+|||+.+++++    |+++|..||.|..|.++.+..+|+++|||||+|.+.++|.+||. ||+..|+|+.|+|
T Consensus        14 ~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v   89 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDE----ILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKL   89 (95)
T ss_dssp             -CEEEEEECCCTTCCHHH----HHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHH----HHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEE
Confidence            469999999999999998    77899999999999999999999999999999999999999998 9999999999999


Q ss_pred             ecccc
Q 045516          596 DEAKQ  600 (675)
Q Consensus       596 ~~a~~  600 (675)
                      .++..
T Consensus        90 ~~a~s   94 (95)
T 2ek1_A           90 SGPSS   94 (95)
T ss_dssp             ECCC-
T ss_pred             EeccC
Confidence            98764

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.52  E-value=1e-14  Score=122.64  Aligned_cols=79  Identities=16%  Similarity=0.321  Sum_probs=74.6

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEE
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVV  595 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V  595 (675)
                      +.++|||+|||..+++++    |+.+|..||.|..|.|+++..+|.++|||||+|.+.++|..||. |||..|.|+.|++
T Consensus         4 ~~~~l~v~nlp~~~t~~~----l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~   79 (85)
T 1x4e_A            4 GSSGLYIRGLQPGTTDQD----LVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQ   79 (85)
T ss_dssp             CCCEEEEESCCTTCCHHH----HHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCS
T ss_pred             CCcEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEee
Confidence            478999999999999998    78999999999999999999999999999999999999999998 9999999999988


Q ss_pred             eccc
Q 045516          596 DEAK  599 (675)
Q Consensus       596 ~~a~  599 (675)
                      .+.+
T Consensus        80 ~~~~   83 (85)
T 1x4e_A           80 SGPS   83 (85)
T ss_dssp             SCCC
T ss_pred             cCCC
Confidence            8754

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.52  E-value=3.1e-14  Score=126.99  Aligned_cols=76  Identities=22%  Similarity=0.322  Sum_probs=66.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-C---CCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEE
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-D---GRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIR  487 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~---g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~  487 (675)
                      ....++|||+|||+++++++|+++|.+||.|. +.++.+. +   |+++|||||+|.+.++|.+||. |+  .|+|+.|.
T Consensus         5 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~   81 (114)
T 2dnl_A            5 SSGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYL   81 (114)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEE
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEE
Confidence            34679999999999999999999999999999 8888776 4   7999999999999999999997 74  36777777


Q ss_pred             EEec
Q 045516          488 LDFA  491 (675)
Q Consensus       488 V~~a  491 (675)
                      +...
T Consensus        82 ~~~~   85 (114)
T 2dnl_A           82 CVSS   85 (114)
T ss_dssp             EECC
T ss_pred             eccC
Confidence            6654

>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=99.52  E-value=3.8e-14  Score=123.56  Aligned_cols=79  Identities=13%  Similarity=0.174  Sum_probs=70.3

Q ss_pred             CCceEEEEecCCC-CcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCC--ceeCCe
Q 045516          516 QAAHTIFIKGFDS-SVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSG--TEIGGY  591 (675)
Q Consensus       516 ~~~~~lfV~nLp~-~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng--~~~~Gr  591 (675)
                      .+.++|||+|||+ .+++++    |+.+|..||.|..|+|+++      +|||||+|.+.++|..||. ||+  ..|.|+
T Consensus        13 ~p~~~l~V~nLp~~~~te~d----L~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr   82 (102)
T 1x4d_A           13 ETRRVVHIMDFQRGKNLRYQ----LLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGK   82 (102)
T ss_dssp             CCCCEEEEESCCCSSSHHHH----HHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTE
T ss_pred             CCCCEEEEeCCCCCcCCHHH----HHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCc
Confidence            3589999999999 999998    8899999999999999876      6899999999999999998 775  569999


Q ss_pred             eeEEeccccCCCC
Q 045516          592 SLVVDEAKQRGDF  604 (675)
Q Consensus       592 ~l~V~~a~~r~~~  604 (675)
                      .|+|.|++.....
T Consensus        83 ~l~V~~a~~~~~~   95 (102)
T 1x4d_A           83 PVRVHLSQKYKRI   95 (102)
T ss_dssp             ECEEEEECCCTTS
T ss_pred             EEEEEECCCCCCC
Confidence            9999999865443

>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=99.52  E-value=2.3e-14  Score=136.45  Aligned_cols=78  Identities=28%  Similarity=0.549  Sum_probs=74.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ...++|||+|||+.+++++|+++|++||.|..|+|+++. +|.++|||||+|.+.++|.+||. |||..|.|+.|.|.++
T Consensus        92 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A           92 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             TTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            347899999999999999999999999999999999997 89999999999999999999998 9999999999999987

>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=99.51  E-value=1.1e-14  Score=123.37  Aligned_cols=77  Identities=22%  Similarity=0.410  Sum_probs=66.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEeccc
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a~~  493 (675)
                      ...++|||+|||+++++++|+++|..||.|..|+|+++    ++|||||+|.+.++|++|+.. ...+.|+.|.|.++.+
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~~~~~-~~~~~g~~l~v~~a~~   77 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQSLCGE-DLIIKGISVHISNAEP   77 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS----CCSCCEEECSCHHHHHHTTTC-EEEETTEEEEEECCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC----CCCEEEEEECCHHHHHHHhcC-CceeCCEEEEEEecCC
Confidence            35689999999999999999999999999999999864    689999999999999765433 3456899999999876


Q ss_pred             cC
Q 045516          494 RG  495 (675)
Q Consensus       494 ~~  495 (675)
                      +.
T Consensus        78 ~~   79 (88)
T 1wf0_A           78 KH   79 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.51  E-value=5.3e-14  Score=126.96  Aligned_cols=76  Identities=24%  Similarity=0.286  Sum_probs=68.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccE-EEEEecCHHHHHHHHH-hCCcccCC--eeEEEEe
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGY-GHVEFASVEDAHKAIE-LNGQMLGN--RAIRLDF  490 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~-afV~F~~~e~A~~Al~-l~g~~~~g--r~i~V~~  490 (675)
                      ....|||+||++.+++++|+.+|++||.|..|+|+..     .|| |||+|.+.++|..||. |||..|.|  +.|+|.+
T Consensus        24 ~vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~-----~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~   98 (124)
T 2e5i_A           24 KVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR-----NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEY   98 (124)
T ss_dssp             SEEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES-----SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEEC
T ss_pred             cEEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEE
Confidence            3445789999999999999999999999999999763     386 9999999999999998 99999987  6999999


Q ss_pred             ccccC
Q 045516          491 ARERG  495 (675)
Q Consensus       491 a~~~~  495 (675)
                      +..+.
T Consensus        99 Ak~~~  103 (124)
T 2e5i_A           99 ARPTR  103 (124)
T ss_dssp             CSCSC
T ss_pred             ecCCc
Confidence            98764

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.51  E-value=2.2e-14  Score=142.43  Aligned_cols=79  Identities=30%  Similarity=0.563  Sum_probs=73.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEeccc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~  493 (675)
                      ..++|||+|||+.+++++|+++|..||.|..|+|+++. +.++|||||+|.+.++|.+||. |||..|.|+.|+|.++..
T Consensus       102 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~-~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~  180 (213)
T 4f02_A          102 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE-NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS  180 (213)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET-TEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             ccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC-CCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            45799999999999999999999999999999999885 4479999999999999999997 999999999999999875


Q ss_pred             c
Q 045516          494 R  494 (675)
Q Consensus       494 ~  494 (675)
                      +
T Consensus       181 ~  181 (213)
T 4f02_A          181 R  181 (213)
T ss_dssp             H
T ss_pred             C
Confidence            4

>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=99.51  E-value=3.6e-14  Score=125.64  Aligned_cols=75  Identities=21%  Similarity=0.403  Sum_probs=68.5

Q ss_pred             CceEEEEecCCCC-cCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          517 AAHTIFIKGFDSS-VGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       517 ~~~~lfV~nLp~~-~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      ..++|||+|||.. +++++    |+.+|..||.|..|.|        ++|||||+|.+.++|..||. ||+..|+|+.|+
T Consensus        26 ~~~~l~V~nl~~~~~t~~~----l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   93 (110)
T 1wf1_A           26 INSRVFIGNLNTALVKKSD----VETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLD   93 (110)
T ss_dssp             CSSEEEECSCCCSSCCHHH----HHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECC
T ss_pred             CCcEEEEeCCCcccCCHHH----HHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEE
Confidence            3689999999999 99998    7889999999999998        47999999999999999997 999999999999


Q ss_pred             EeccccCCC
Q 045516          595 VDEAKQRGD  603 (675)
Q Consensus       595 V~~a~~r~~  603 (675)
                      |.++.++..
T Consensus        94 V~~a~~~~~  102 (110)
T 1wf1_A           94 INMAGEPKP  102 (110)
T ss_dssp             EEESCCCCS
T ss_pred             EEECCCCCC
Confidence            999975444

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=3.7e-14  Score=123.86  Aligned_cols=80  Identities=15%  Similarity=0.243  Sum_probs=71.5

Q ss_pred             CCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hC--CceeCCe
Q 045516          515 GQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MS--GTEIGGY  591 (675)
Q Consensus       515 ~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-ln--g~~~~Gr  591 (675)
                      ..+.++|||+|||+.+++++    |+++|..||.|..|+|+++      +|||||+|.+.++|..||. |+  +..|+|+
T Consensus        13 ~~~~~~LfV~nLp~~vte~d----L~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr   82 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGE----VISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQ   82 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHH----HHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTE
T ss_pred             CCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCE
Confidence            34579999999999999998    7788999999999999986      7999999999999999998 76  4789999


Q ss_pred             eeEEeccccCCCC
Q 045516          592 SLVVDEAKQRGDF  604 (675)
Q Consensus       592 ~l~V~~a~~r~~~  604 (675)
                      .|+|.|+.++.-.
T Consensus        83 ~l~V~~A~~~~~~   95 (105)
T 1sjq_A           83 PIYIQFSNHKELK   95 (105)
T ss_dssp             ECCBCCCSSSSCC
T ss_pred             EEEEEEcCCCCCC
Confidence            9999999876554

>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=99.51  E-value=1.9e-14  Score=132.39  Aligned_cols=80  Identities=14%  Similarity=0.286  Sum_probs=75.0

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCc---EEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeee
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGE---ITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSL  593 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~---I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l  593 (675)
                      ..++|||+|||+.+++++    |+++|..||.   |..|+|+++.. |+++|||||+|.+.++|.+||.||+..|+||.|
T Consensus        43 ~~~~lfVgnLp~~~te~d----L~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~~~g~~l~gr~i  117 (136)
T 2hgl_A           43 EGFVVKLRGLPWSCSVED----VQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALKKDRESMGHRYI  117 (136)
T ss_dssp             TTCEEEEESCCTTCCHHH----HHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHTTTEEESSSSEE
T ss_pred             CCCEEEEeCCCCCCCHHH----HHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCEECCEEE
Confidence            368999999999999998    7899999999   89999999987 999999999999999999999999999999999


Q ss_pred             EEeccccC
Q 045516          594 VVDEAKQR  601 (675)
Q Consensus       594 ~V~~a~~r  601 (675)
                      +|.++.++
T Consensus       118 ~V~~a~~~  125 (136)
T 2hgl_A          118 EVFKSHRT  125 (136)
T ss_dssp             EEEECCHH
T ss_pred             EEEECChH
Confidence            99998654

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.50  E-value=1.1e-13  Score=118.26  Aligned_cols=78  Identities=17%  Similarity=0.317  Sum_probs=70.5

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      ...++|||+|||..+++++    |+.+|..||.|..|.|++        +||||+|.+.++|.+||. ||+..|.|+.|+
T Consensus         8 ~~~~~l~V~nLp~~~t~~~----l~~~F~~~G~v~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   75 (92)
T 2dgt_A            8 KASTKLHVGNISPTCTNQE----LRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMH   75 (92)
T ss_dssp             CSSEEEEEESCCSSCCHHH----HHHHHHTTSCCCEEEECS--------SEEEEEESCHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCeeCCcEEE
Confidence            3479999999999999998    778999999999999974        399999999999999998 999999999999


Q ss_pred             EeccccCCCCC
Q 045516          595 VDEAKQRGDFG  605 (675)
Q Consensus       595 V~~a~~r~~~~  605 (675)
                      |.++.++....
T Consensus        76 V~~a~~~~~~~   86 (92)
T 2dgt_A           76 VQLSTSRLRTA   86 (92)
T ss_dssp             EEESSCCCSCC
T ss_pred             EEEccCCCCCC
Confidence            99998766543

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.50  E-value=5.7e-14  Score=136.98  Aligned_cols=82  Identities=26%  Similarity=0.494  Sum_probs=77.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ...++|||+|||+.+++++|+++|..||.|..|+|+++. +|.++|||||+|.+.++|.+||. |||..|.|+.|.|.++
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  191 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  191 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            467999999999999999999999999999999999997 89999999999999999999998 9999999999999999


Q ss_pred             cccC
Q 045516          492 RERG  495 (675)
Q Consensus       492 ~~~~  495 (675)
                      .++.
T Consensus       192 ~~~~  195 (198)
T 2yh0_A          192 SVGA  195 (198)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>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=99.50  E-value=1.5e-14  Score=123.10  Aligned_cols=80  Identities=20%  Similarity=0.424  Sum_probs=72.2

Q ss_pred             eEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEec
Q 045516          519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVDE  597 (675)
Q Consensus       519 ~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~~  597 (675)
                      ++|||+|||..+++++    |+++|..||.|..|.|+++..+|.++|||||+|.+.+ |..|+. |||..|+|+.|+|.+
T Consensus         2 ~~l~V~nLp~~~t~~~----l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~   76 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQ----VKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTE   76 (90)
T ss_dssp             EEEEEEEECTTSSHHH----HTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEE
T ss_pred             cEEEECCCCCCCCHHH----HHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEE
Confidence            6899999999999998    7889999999999999999999999999999999999 999998 999999999999999


Q ss_pred             cccCCC
Q 045516          598 AKQRGD  603 (675)
Q Consensus       598 a~~r~~  603 (675)
                      +.+...
T Consensus        77 a~~~~~   82 (90)
T 2ki2_A           77 ANPKKS   82 (90)
T ss_dssp             C-----
T ss_pred             cCCCCC
Confidence            987544

>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=99.50  E-value=1.6e-13  Score=119.53  Aligned_cols=80  Identities=13%  Similarity=0.181  Sum_probs=71.7

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-h--CCceeCCee
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-M--SGTEIGGYS  592 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-l--ng~~~~Gr~  592 (675)
                      .+.++|||+|||+.+++++    |+.+|..||.|..|.|+++      +|||||+|.+.++|..||. |  ++..|.|+.
T Consensus        13 ~p~~~l~V~nLp~~~te~~----L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~   82 (101)
T 2cq1_A           13 APSRVLHIRKLPGEVTETE----VIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQP   82 (101)
T ss_dssp             SCCSEEEEESCCTTCCHHH----HHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEE
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcE
Confidence            4579999999999999998    7899999999999999875      8999999999999999997 5  578899999


Q ss_pred             eEEeccccCCCCC
Q 045516          593 LVVDEAKQRGDFG  605 (675)
Q Consensus       593 l~V~~a~~r~~~~  605 (675)
                      |+|.|+..+....
T Consensus        83 l~V~~a~~~~~~~   95 (101)
T 2cq1_A           83 IYIQYSNHKELKT   95 (101)
T ss_dssp             CEEEECSCSSCCC
T ss_pred             EEEEEcCcccCcC
Confidence            9999998765543

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.50  E-value=4.4e-14  Score=126.86  Aligned_cols=81  Identities=14%  Similarity=0.285  Sum_probs=75.2

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCc---EEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeee
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGE---ITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSL  593 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~---I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l  593 (675)
                      ..++|||+|||+.+++++    |+++|..||.   |..|+|+++.. |+++|||||+|.+.++|.+||.||+..|+||.|
T Consensus        16 ~~~~l~V~nLp~~~te~~----l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i   90 (118)
T 2db1_A           16 EGYVVKLRGLPWSCSIED----VQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALKKDRESMGHRYI   90 (118)
T ss_dssp             CCCEEEEESCCTTCCHHH----HHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGGGTTEEETTEEE
T ss_pred             CCcEEEEeCCCCCCCHHH----HHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCeECCeEE
Confidence            378999999999999998    7899999999   89999999977 999999999999999999999999999999999


Q ss_pred             EEeccccCC
Q 045516          594 VVDEAKQRG  602 (675)
Q Consensus       594 ~V~~a~~r~  602 (675)
                      +|.++..+.
T Consensus        91 ~V~~a~~~~   99 (118)
T 2db1_A           91 EVFKSHRTE   99 (118)
T ss_dssp             EEEEECHHH
T ss_pred             EEEECCHHH
Confidence            999986543

>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=99.50  E-value=5.1e-14  Score=134.27  Aligned_cols=78  Identities=22%  Similarity=0.400  Sum_probs=73.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccC---CeeEEEE
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLG---NRAIRLD  489 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~---gr~i~V~  489 (675)
                      ...++|||+|||+.+++++|+++|+.||.|..|+|+++.+|+++|||||+|.+.++|.+||. |||..|.   |++|+|.
T Consensus        93 ~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~  172 (175)
T 3nmr_A           93 VEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVK  172 (175)
T ss_dssp             GGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEE
T ss_pred             CCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEE
Confidence            35789999999999999999999999999999999999999999999999999999999997 9998776   4999999


Q ss_pred             ec
Q 045516          490 FA  491 (675)
Q Consensus       490 ~a  491 (675)
                      |+
T Consensus       173 ~a  174 (175)
T 3nmr_A          173 FA  174 (175)
T ss_dssp             EC
T ss_pred             ec
Confidence            86

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.50  E-value=1.3e-13  Score=127.20  Aligned_cols=81  Identities=27%  Similarity=0.532  Sum_probs=75.1

Q ss_pred             CCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCee
Q 045516          514 RGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYS  592 (675)
Q Consensus       514 ~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~  592 (675)
                      .....++|||+|||..+++++    |+.+|..||.|..|+|+++..+|+++|||||+|.+.++|.+||. |||..|+|+.
T Consensus        59 ~~~~~~~l~v~nlp~~~~~~~----l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~  134 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDDKV----LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRT  134 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCHHH----HHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEE
T ss_pred             CCCCCcEEEEEeCCCCCCHHH----HHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            344589999999999999988    77899999999999999999999999999999999999999997 9999999999


Q ss_pred             eEEecc
Q 045516          593 LVVDEA  598 (675)
Q Consensus       593 l~V~~a  598 (675)
                      |+|.++
T Consensus       135 l~v~~A  140 (140)
T 2ku7_A          135 IRVNLA  140 (140)
T ss_dssp             EEEEC-
T ss_pred             EEEEeC
Confidence            999985

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.50  E-value=5e-14  Score=121.83  Aligned_cols=78  Identities=23%  Similarity=0.324  Sum_probs=70.1

Q ss_pred             CCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCce--eCC
Q 045516          514 RGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTE--IGG  590 (675)
Q Consensus       514 ~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~--~~G  590 (675)
                      ...++++|||+|||+.+++++    |+.+|.+||.|..|+|++.      ||||||+|.+.++|..|+. |++..  |+|
T Consensus        17 ~~~ps~~l~V~NLp~~~te~~----L~~lF~~fG~V~~v~i~~~------kg~AFVef~~~~~A~~Av~~ln~~~~~i~G   86 (100)
T 3r27_A           17 KTPASPVVHIRGLIDGVVEAD----LVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYAADNQIYIAG   86 (100)
T ss_dssp             CCCCCSEEEEESCCTTCCHHH----HHHHHGGGSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCEEETT
T ss_pred             cCCCCcEEEEeCCCCCCCHHH----HHHHHhccCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhcCCCceeCC
Confidence            345689999999999999998    7899999999999999864      7999999999999999998 88765  889


Q ss_pred             eeeEEeccccC
Q 045516          591 YSLVVDEAKQR  601 (675)
Q Consensus       591 r~l~V~~a~~r  601 (675)
                      +.|+|.|++.+
T Consensus        87 r~i~V~~S~~k   97 (100)
T 3r27_A           87 HPAFVNYSTSQ   97 (100)
T ss_dssp             EEEEEEECSCS
T ss_pred             cEEEEEecccc
Confidence            99999999765

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.50  E-value=2.1e-14  Score=127.01  Aligned_cols=79  Identities=18%  Similarity=0.212  Sum_probs=73.6

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEec
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDE  597 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~~  597 (675)
                      ..+|||+|||+.+++++    |+++|..| .|..|+|+++.. |+++|||||+|.+.++|.+||.||+..|+||.|.|..
T Consensus        16 ~~~v~V~nLp~~~te~d----l~~~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~   89 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMEND----VRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEALKRNRMLMIQRYVEVSP   89 (109)
T ss_dssp             HHEEEEECCCSSCCHHH----HHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCEEEEeCCCCCCCHHH----HHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEEEE
Confidence            57999999999999999    78899999 899999999976 9999999999999999999999999999999999998


Q ss_pred             cccCC
Q 045516          598 AKQRG  602 (675)
Q Consensus       598 a~~r~  602 (675)
                      +.++.
T Consensus        90 a~~~~   94 (109)
T 2dnn_A           90 ATERQ   94 (109)
T ss_dssp             CCHHH
T ss_pred             CCccc
Confidence            87653

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.49  E-value=8e-14  Score=122.37  Aligned_cols=79  Identities=20%  Similarity=0.197  Sum_probs=71.1

Q ss_pred             CCceEEEcCCCC-----CCCHHHHHHHhhhCCCeEEEEEeeCC--CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeE
Q 045516          415 GSKTLFVGNLPF-----SVEQADVQNFFSEVAEVVDVRLSSDA--DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAI  486 (675)
Q Consensus       415 ~~~tlfV~nLp~-----~~te~~L~~~F~~~G~I~~v~i~~~~--~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i  486 (675)
                      .+++|+|+||..     ..++++|+++|++||.|.+|+|++++  +++++|||||+|.+.++|.+|+. |||..|.||.|
T Consensus         7 ~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~i   86 (105)
T 2pe8_A            7 PTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVV   86 (105)
T ss_dssp             CCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcEE
Confidence            578999999963     23789999999999999999999986  36899999999999999999997 99999999999


Q ss_pred             EEEeccc
Q 045516          487 RLDFARE  493 (675)
Q Consensus       487 ~V~~a~~  493 (675)
                      +|.++..
T Consensus        87 ~v~~a~~   93 (105)
T 2pe8_A           87 KACFYNL   93 (105)
T ss_dssp             EEEECCH
T ss_pred             EEEEcCH
Confidence            9999864

>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=99.49  E-value=1.1e-13  Score=122.32  Aligned_cols=80  Identities=24%  Similarity=0.412  Sum_probs=73.0

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      ...++|||+|||..+++++    |+.+|..||.|..|+|+++      +|||||+|.+.++|..||. |||..|+|+.|+
T Consensus        23 ~~~~~l~V~nl~~~~t~~~----l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   92 (109)
T 1x4g_A           23 PKNCTVYCGGIASGLTDQL----MRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVK   92 (109)
T ss_dssp             SSCCEEEEECCSSCCCHHH----HHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCcEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEE
Confidence            3478999999999999998    7788889999999999987      7999999999999999997 999999999999


Q ss_pred             EeccccCCCCC
Q 045516          595 VDEAKQRGDFG  605 (675)
Q Consensus       595 V~~a~~r~~~~  605 (675)
                      |.|++++....
T Consensus        93 v~~a~~~~~~~  103 (109)
T 1x4g_A           93 CYWGKESPDMT  103 (109)
T ss_dssp             EECCCCCCSSC
T ss_pred             EEecCCCCCCC
Confidence            99998876543

>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=99.49  E-value=1.1e-13  Score=119.41  Aligned_cols=79  Identities=24%  Similarity=0.392  Sum_probs=72.0

Q ss_pred             CCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeC--Ce
Q 045516          515 GQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIG--GY  591 (675)
Q Consensus       515 ~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~--Gr  591 (675)
                      ..+.++|||+|||..+++++    |+++|..||.|..|.|+++      +|||||+|.+.++|.+||. ||+..|.  |+
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~   83 (97)
T 1why_A           14 ANPTTRLWVGGLGPNTSLAA----LAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDR   83 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHH----HHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSC
T ss_pred             CCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCc
Confidence            34579999999999999998    7789999999999999865      7899999999999999998 9999999  99


Q ss_pred             eeEEeccccCCC
Q 045516          592 SLVVDEAKQRGD  603 (675)
Q Consensus       592 ~l~V~~a~~r~~  603 (675)
                      .|+|.|++++..
T Consensus        84 ~l~V~~a~~~~~   95 (97)
T 1why_A           84 RLRVDFAKSGPS   95 (97)
T ss_dssp             BCEEEECCCCCC
T ss_pred             EEEEEECCCCCC
Confidence            999999988654

>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=99.49  E-value=9.4e-14  Score=120.40  Aligned_cols=80  Identities=16%  Similarity=0.309  Sum_probs=72.9

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      ...++|||+|||..+++++    |+.+|..||.|..|+|+++      +|||||+|.+.+.|.+||. ||+..|+|+.|+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~   82 (99)
T 2cpj_A           13 TQRSRLFVGNLPPDITEEE----MRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLR   82 (99)
T ss_dssp             CCTTEEEEESCCTTCCHHH----HHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCE
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEE
Confidence            3478999999999999998    7899999999999999875      7999999999999999997 999999999999


Q ss_pred             EeccccCCCCC
Q 045516          595 VDEAKQRGDFG  605 (675)
Q Consensus       595 V~~a~~r~~~~  605 (675)
                      |.|+.++....
T Consensus        83 v~~a~~~~~~~   93 (99)
T 2cpj_A           83 VRFACHSASLT   93 (99)
T ss_dssp             EEESSCCSCCC
T ss_pred             EEEcCCCCCCC
Confidence            99998766543

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.49  E-value=1.4e-13  Score=124.58  Aligned_cols=85  Identities=19%  Similarity=0.352  Sum_probs=78.1

Q ss_pred             CCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeee
Q 045516          515 GQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSL  593 (675)
Q Consensus       515 ~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l  593 (675)
                      ....++|||+|||..+++++    |+.+|..||.|..|.|+++. +|.++|||||+|.+.++|..||. |||..|+|+.|
T Consensus        32 ~~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l  106 (124)
T 2kt5_A           32 VETGAKLLVSNLDFGVSDAD----IQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPM  106 (124)
T ss_dssp             CSSCEEEEEESCCSSCCHHH----HHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEE
Confidence            34579999999999999998    77889999999999999998 89999999999999999999998 99999999999


Q ss_pred             EEeccccCCCC
Q 045516          594 VVDEAKQRGDF  604 (675)
Q Consensus       594 ~V~~a~~r~~~  604 (675)
                      +|.++.+....
T Consensus       107 ~V~~a~~~~~~  117 (124)
T 2kt5_A          107 DIQLVASQIDL  117 (124)
T ss_dssp             EEEEECCTTCC
T ss_pred             EEEEeCCCCCC
Confidence            99999875543

>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=99.49  E-value=4.7e-14  Score=126.04  Aligned_cols=73  Identities=16%  Similarity=0.354  Sum_probs=63.7

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCee---
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYS---  592 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~---  592 (675)
                      ..++|||+|||+.+++++    |+++|..||.|..|.|+.+       |||||+|.+.++|..||. ||+..|+|+.   
T Consensus        15 ~~~~l~V~nLp~~~t~~~----l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~   83 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQD----LKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGET   83 (115)
T ss_dssp             --CCEEEEECCSSCCTTH----HHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCC
T ss_pred             CCcEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeee
Confidence            368999999999999998    7788999999999999876       899999999999999998 9999999998   


Q ss_pred             --eEEecccc
Q 045516          593 --LVVDEAKQ  600 (675)
Q Consensus       593 --l~V~~a~~  600 (675)
                        |+|.+..+
T Consensus        84 ~~i~v~~~~~   93 (115)
T 3beg_B           84 AYIRVKVDGP   93 (115)
T ss_dssp             CBCEEEECC-
T ss_pred             EEEEeccCCC
Confidence              55555444

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.49  E-value=7.9e-14  Score=122.42  Aligned_cols=84  Identities=15%  Similarity=0.276  Sum_probs=72.8

Q ss_pred             ceEEEEecCCCCcCHHH--HHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCe-ee
Q 045516          518 AHTIFIKGFDSSVGEDQ--VRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGY-SL  593 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~--i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr-~l  593 (675)
                      .++|||+|||+.+.+..  +.+.|+.+|+.||.|..|.|+  ..+|.++|||||+|.+.++|..||. |||..|+|+ .|
T Consensus        15 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~l   92 (105)
T 2nlw_A           15 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF   92 (105)
T ss_dssp             CSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCEE
T ss_pred             CCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCceE
Confidence            68999999999884311  233488999999999999998  4689999999999999999999998 999999998 99


Q ss_pred             EEeccccCCC
Q 045516          594 VVDEAKQRGD  603 (675)
Q Consensus       594 ~V~~a~~r~~  603 (675)
                      +|.++.....
T Consensus        93 ~V~~a~~~~k  102 (105)
T 2nlw_A           93 RVNLFTDFDK  102 (105)
T ss_dssp             EEECSCCCCC
T ss_pred             EEEEcchHhh
Confidence            9999976544

>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=99.48  E-value=1.9e-14  Score=117.92  Aligned_cols=75  Identities=25%  Similarity=0.525  Sum_probs=70.9

Q ss_pred             EEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEecc
Q 045516          520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDEA  598 (675)
Q Consensus       520 ~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~~a  598 (675)
                      +|||+|||..+++++    |+.+|..||.|..|.|+++..+|.++|||||+|.+.+.|.+||.+++..|+|+.|+|.++
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 KIFVGGLSPDTPEEK----IREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHH----HHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTTSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEC
Confidence            589999999999998    778888899999999999999999999999999999999999999999999999999875

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.48  E-value=6.5e-14  Score=121.85  Aligned_cols=76  Identities=18%  Similarity=0.436  Sum_probs=70.3

Q ss_pred             eEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEec
Q 045516          519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVDE  597 (675)
Q Consensus       519 ~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~~  597 (675)
                      ++|||+|||..+++++    |+++|..||.|..|.|+++     ++|||||+|.+.++|..||. ||+..|+|+.|+|.+
T Consensus         1 ~~l~V~nLp~~~t~~~----l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   71 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGE----LERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVEL   71 (101)
T ss_dssp             CEEEEECCCSSCSHHH----HHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEE
T ss_pred             CEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEE
Confidence            4799999999999998    7788889999999999987     68999999999999999998 999999999999999


Q ss_pred             cccCCC
Q 045516          598 AKQRGD  603 (675)
Q Consensus       598 a~~r~~  603 (675)
                      +.++..
T Consensus        72 a~~~~~   77 (101)
T 2hvz_A           72 STGMPR   77 (101)
T ss_dssp             SSSCCC
T ss_pred             ccCCCC
Confidence            987653

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.48  E-value=2.1e-13  Score=118.16  Aligned_cols=76  Identities=18%  Similarity=0.435  Sum_probs=69.1

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhccc--CcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCee
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSC--GEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYS  592 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~--G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~  592 (675)
                      ...++|||+|||+.+++++    |+.+|..|  |.|..|.++        +|||||+|.+.++|..||. ||+..|+|+.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~----l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   80 (99)
T 2cpd_A           13 SSVKILYVRNLMLSTSEEM----IEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSP   80 (99)
T ss_dssp             SCCCEEEEESCCTTCCHHH----HHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEE
T ss_pred             CCcCEEEEeCCCCCCCHHH----HHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcE
Confidence            4479999999999999998    77889999  999999875        5799999999999999998 9999999999


Q ss_pred             eEEeccccCCC
Q 045516          593 LVVDEAKQRGD  603 (675)
Q Consensus       593 l~V~~a~~r~~  603 (675)
                      |+|.|++++..
T Consensus        81 l~v~~a~~~~~   91 (99)
T 2cpd_A           81 IEVTLAKPVDK   91 (99)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEEECCCCCC
Confidence            99999987654

>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=99.48  E-value=1.6e-13  Score=120.31  Aligned_cols=80  Identities=19%  Similarity=0.229  Sum_probs=70.7

Q ss_pred             CCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCC--ceeCCe
Q 045516          515 GQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSG--TEIGGY  591 (675)
Q Consensus       515 ~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng--~~~~Gr  591 (675)
                      ..+.++|||+|||+.+++++    |+.+|.+||.|..|.|+++      +|||||+|.+.++|..||. |++  ..|+|+
T Consensus        12 ~~p~~~l~V~nLp~~~te~~----L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr   81 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEAD----LVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQ   81 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHH----HHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSS
T ss_pred             CCCCCEEEEeCCCCCCCHHH----HHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCE
Confidence            34579999999999999998    7899999999999999875      7999999999999999998 765  459999


Q ss_pred             eeEEeccccCCCC
Q 045516          592 SLVVDEAKQRGDF  604 (675)
Q Consensus       592 ~l~V~~a~~r~~~  604 (675)
                      .|+|.|+..+...
T Consensus        82 ~l~V~~a~~~~~~   94 (104)
T 1wex_A           82 QAFFNYSTSKRIT   94 (104)
T ss_dssp             BCEEEECSSSSCC
T ss_pred             EEEEEEccCcccc
Confidence            9999999876544

>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=99.48  E-value=1.2e-13  Score=122.87  Aligned_cols=81  Identities=16%  Similarity=0.359  Sum_probs=74.8

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCcee------
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEI------  588 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~------  588 (675)
                      ...++|||+|||..+++++    |+.+|..||.|..|+|+++. +|.++|||||+|.+.+.|..||. |||..|      
T Consensus        23 ~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~   97 (114)
T 1x5o_A           23 QDPTNLYISNLPLSMDEQE----LENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGV   97 (114)
T ss_dssp             CCTTEEEEESCCTTCCHHH----HHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTS
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccc
Confidence            3478999999999999998    78999999999999999998 89999999999999999999998 999999      


Q ss_pred             --CCeeeEEeccccC
Q 045516          589 --GGYSLVVDEAKQR  601 (675)
Q Consensus       589 --~Gr~l~V~~a~~r  601 (675)
                        .++.|+|.|+.++
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              5788999998754

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.48  E-value=1.9e-14  Score=125.27  Aligned_cols=83  Identities=22%  Similarity=0.372  Sum_probs=75.2

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEe
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVD  596 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~  596 (675)
                      ..++|||+|||+.+++++    |+.+|..||.|.. .++.+..+|.++|||||+|.+.++|.+||.||+..|.|+.|+|.
T Consensus        16 ~~~~l~V~nLp~~~t~~~----l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~   90 (101)
T 1fj7_A           16 TPFNLFIGNLNPNKSVAE----LKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLE   90 (101)
T ss_dssp             CSEEEEEECCCTTSCHHH----HHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGCCBTTBCCEEE
T ss_pred             CCCEEEEeCCCCCCCHHH----HHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHhcCCcEECCcEEEEE
Confidence            478999999999999998    7788888899888 77777788999999999999999999999999999999999999


Q ss_pred             ccccCCCC
Q 045516          597 EAKQRGDF  604 (675)
Q Consensus       597 ~a~~r~~~  604 (675)
                      ++.++...
T Consensus        91 ~a~~~~~~   98 (101)
T 1fj7_A           91 KPKGRDGT   98 (101)
T ss_dssp             CCSCCCCS
T ss_pred             EcCCCCCC
Confidence            99876554

>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=99.48  E-value=1e-13  Score=131.37  Aligned_cols=78  Identities=24%  Similarity=0.452  Sum_probs=74.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCC--eeEEEE
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGN--RAIRLD  489 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~g--r~i~V~  489 (675)
                      ...++|||+|||+.+++++|+++|+.||.|..|+|+++. +|+++|||||+|.+.++|.+||. |||..|.|  ++|+|.
T Consensus        87 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~  166 (168)
T 1b7f_A           87 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR  166 (168)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEE
Confidence            456899999999999999999999999999999999998 89999999999999999999998 99999988  999998


Q ss_pred             ec
Q 045516          490 FA  491 (675)
Q Consensus       490 ~a  491 (675)
                      |+
T Consensus       167 ~A  168 (168)
T 1b7f_A          167 LA  168 (168)
T ss_dssp             EC
T ss_pred             eC
Confidence            85

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.48  E-value=2.9e-14  Score=117.37  Aligned_cols=75  Identities=25%  Similarity=0.411  Sum_probs=71.0

Q ss_pred             eEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEec
Q 045516          519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVDE  597 (675)
Q Consensus       519 ~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~~  597 (675)
                      ++|||+|||..+++++    |+.+|+.||.|..|.|+++..+|.++|||||+|.+.++|.+|+. ++ ..|+|+.|+|.+
T Consensus         1 ~~l~v~nlp~~~t~~~----l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~   75 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEG----LREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKV   75 (77)
T ss_dssp             CCEEEESCCSSCCSHH----HHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEE
T ss_pred             CEEEEeCCCCCCCHHH----HHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEe
Confidence            4799999999999998    77899999999999999999999999999999999999999999 77 999999999998


Q ss_pred             c
Q 045516          598 A  598 (675)
Q Consensus       598 a  598 (675)
                      +
T Consensus        76 a   76 (77)
T 1uaw_A           76 A   76 (77)
T ss_dssp             C
T ss_pred             c
Confidence            6

>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=99.47  E-value=2.5e-14  Score=129.57  Aligned_cols=82  Identities=15%  Similarity=0.279  Sum_probs=75.4

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEe
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVD  596 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~  596 (675)
                      ..++|||+|||+.+++++    |+.+|..||.|..+.++.+..+|+++|||||+|.+.++|.+||.||+..|+|+.|.|.
T Consensus        24 ~~~~l~V~nLp~~~te~~----l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V~   99 (124)
T 1wel_A           24 AGFCVYLKGLPFEAENKH----VIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVH   99 (124)
T ss_dssp             CCCEEEEECCCTTCCHHH----HHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEE
T ss_pred             CCcEEEEeCCCCCCCHHH----HHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHHhCCCeECCcEEEEE
Confidence            468999999999999998    7899999999998777777789999999999999999999999999999999999999


Q ss_pred             ccccCC
Q 045516          597 EAKQRG  602 (675)
Q Consensus       597 ~a~~r~  602 (675)
                      ++.++.
T Consensus       100 ~a~~~~  105 (124)
T 1wel_A          100 PITKKG  105 (124)
T ss_dssp             EECHHH
T ss_pred             ECCHHH
Confidence            987643

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.47  E-value=6.4e-14  Score=120.86  Aligned_cols=76  Identities=20%  Similarity=0.375  Sum_probs=69.2

Q ss_pred             CCceEEEEecCCC-CcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeee
Q 045516          516 QAAHTIFIKGFDS-SVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSL  593 (675)
Q Consensus       516 ~~~~~lfV~nLp~-~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l  593 (675)
                      .+.++|||+|||+ .+++++    |+.+|..||.|..|.|.        +|||||+|.+.++|..||. |||..|.|+.|
T Consensus         8 ~~~~~l~V~nlp~~~~t~~~----l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   75 (96)
T 2kvi_A            8 PPKSRLFIGNLPLKNVSKED----LFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKL   75 (96)
T ss_dssp             -CCEEEEEESSTTSCCCHHH----HHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTB
T ss_pred             CCCCEEEEeCCCcccCCHHH----HHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEE
Confidence            4589999999998 999998    78899999999999984        6899999999999999998 99999999999


Q ss_pred             EEeccccCCC
Q 045516          594 VVDEAKQRGD  603 (675)
Q Consensus       594 ~V~~a~~r~~  603 (675)
                      +|.++.++..
T Consensus        76 ~V~~a~~~~~   85 (96)
T 2kvi_A           76 ILEVSSSNAR   85 (96)
T ss_dssp             CEEEEECCCC
T ss_pred             EEEEcCcCCC
Confidence            9999987544

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.46  E-value=1.6e-13  Score=114.71  Aligned_cols=73  Identities=14%  Similarity=0.228  Sum_probs=67.9

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEE
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVV  595 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V  595 (675)
                      .+..|||+||++.+++++    |+++|.+||.|..|+|..      ++|||||+|.+.++|.+|+. ||+..|+|+.|+|
T Consensus         6 ~~~wL~VgNL~~~~te~~----L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V   75 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPT----LRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFA   75 (89)
T ss_dssp             CCCEEEEECCCTTCCCHH----HHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             ccceEEEeCCCccCCHHH----HHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEE
Confidence            378999999999999998    778888999999999976      48999999999999999998 9999999999999


Q ss_pred             eccc
Q 045516          596 DEAK  599 (675)
Q Consensus       596 ~~a~  599 (675)
                      .++.
T Consensus        76 ~~A~   79 (89)
T 2wbr_A           76 ESPS   79 (89)
T ss_dssp             ECCC
T ss_pred             EECC
Confidence            9984

>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=99.46  E-value=1.7e-13  Score=129.51  Aligned_cols=78  Identities=29%  Similarity=0.521  Sum_probs=72.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCee--EEEE
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRA--IRLD  489 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~--i~V~  489 (675)
                      ...++|||+|||+.+++++|+++|..||.|..|+|+.+. +|.++|||||+|.+.++|.+||. |||..|.|+.  |+|.
T Consensus        86 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~  165 (167)
T 1fxl_A           86 IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVK  165 (167)
T ss_dssp             GTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEE
Confidence            356899999999999999999999999999999999997 89999999999999999999998 9999999975  7777


Q ss_pred             ec
Q 045516          490 FA  491 (675)
Q Consensus       490 ~a  491 (675)
                      |+
T Consensus       166 ~A  167 (167)
T 1fxl_A          166 FA  167 (167)
T ss_dssp             EC
T ss_pred             eC
Confidence            64

>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=99.46  E-value=9.9e-14  Score=118.76  Aligned_cols=77  Identities=23%  Similarity=0.383  Sum_probs=67.5

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCc-EEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCC-ceeCCeee
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGE-ITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSG-TEIGGYSL  593 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~-I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng-~~~~Gr~l  593 (675)
                      ..++|||+|||..+++++    |+++|..||. |..+.+.       ++|||||+|.+.++|.+||. ||| ..|+|+.|
T Consensus         7 ~~~~l~V~nLp~~~t~~~----l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l   75 (93)
T 2cqh_A            7 GMNKLYIGNLSPAVTADD----LRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIM   75 (93)
T ss_dssp             CCCCEEEECCCTTCCHHH----HHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEEC
T ss_pred             CCcEEEEeCCCCCCCHHH----HHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEE
Confidence            478999999999999998    7788899999 6655552       48999999999999999998 999 99999999


Q ss_pred             EEeccccCCCC
Q 045516          594 VVDEAKQRGDF  604 (675)
Q Consensus       594 ~V~~a~~r~~~  604 (675)
                      +|.++.++..+
T Consensus        76 ~v~~a~~~~~~   86 (93)
T 2cqh_A           76 EVDYSVSKKLR   86 (93)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEEccCcccc
Confidence            99999876554

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.46  E-value=7.4e-14  Score=116.42  Aligned_cols=76  Identities=17%  Similarity=0.362  Sum_probs=66.1

Q ss_pred             eEEEEecCCCCcCH--HHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCe-eeE
Q 045516          519 HTIFIKGFDSSVGE--DQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGY-SLV  594 (675)
Q Consensus       519 ~~lfV~nLp~~~te--~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr-~l~  594 (675)
                      ++|||+|||..+++  +.+.+.|+.+|+.||.|..|.|+  ..+|+++|||||+|.+.++|..||. |||..|+|+ .|+
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~   79 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFR   79 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEE
Confidence            68999999999843  11334488999999999999988  4689999999999999999999998 999999999 888


Q ss_pred             Ee
Q 045516          595 VD  596 (675)
Q Consensus       595 V~  596 (675)
                      |.
T Consensus        80 V~   81 (81)
T 2krb_A           80 VN   81 (81)
T ss_dssp             CC
T ss_pred             eC
Confidence            73

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.46  E-value=1.1e-13  Score=119.22  Aligned_cols=80  Identities=34%  Similarity=0.521  Sum_probs=71.4

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      ...++|||+|||..+++++    |+.+|..||.|..|     ..++.++|||||+|.+.++|..||. |||..|+|+.|+
T Consensus        14 ~~~~~l~V~nL~~~~t~~~----l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   84 (96)
T 1fjc_A           14 RAARTLLAKNLSFNITEDE----LKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVS   84 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHH----HHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            3479999999999999998    77899999988766     3568899999999999999999998 999999999999


Q ss_pred             EeccccCCCC
Q 045516          595 VDEAKQRGDF  604 (675)
Q Consensus       595 V~~a~~r~~~  604 (675)
                      |.++.++...
T Consensus        85 v~~a~~~~~~   94 (96)
T 1fjc_A           85 LYYTGEKGGT   94 (96)
T ss_dssp             EEECSSSCCC
T ss_pred             EEEcCCCCCC
Confidence            9999876543

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.46  E-value=2.9e-13  Score=115.17  Aligned_cols=77  Identities=17%  Similarity=0.321  Sum_probs=69.3

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      ...++|||+|||..+++++    |+.+|..||.|..|.|++        +||||+|.+.++|..||. |||..|+|+.|+
T Consensus         7 ~~~~~l~V~nlp~~~t~~~----l~~~F~~~G~v~~~~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   74 (90)
T 2dnp_A            7 GNTWKIFVGNVSAACTSQE----LRSLFERRGRVIECDVVK--------DYAFVHMEKEADAKAAIAQLNGKEVKGKRIN   74 (90)
T ss_dssp             CCSCCEEEESCCTTCCHHH----HHHHHHHHSCEEEEEECS--------SCEEEEESCHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHHcCCCEEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCEECCcEEE
Confidence            3478999999999999998    778888999999999974        399999999999999998 999999999999


Q ss_pred             EeccccCCCC
Q 045516          595 VDEAKQRGDF  604 (675)
Q Consensus       595 V~~a~~r~~~  604 (675)
                      |.++.++...
T Consensus        75 v~~a~~~~~~   84 (90)
T 2dnp_A           75 VELSTKGQKK   84 (90)
T ss_dssp             EEESCCCCCC
T ss_pred             EEECCCCCCC
Confidence            9999876443

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.46  E-value=1.4e-13  Score=121.67  Aligned_cols=80  Identities=20%  Similarity=0.414  Sum_probs=74.0

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      ...++|||+|||..+++++    |+.+|..||.|..|.|+++.  +.++|||||+|.+.++|.+|+. |||..|+|+.|+
T Consensus        27 ~~~~~l~V~nLp~~~te~~----l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~  100 (109)
T 2err_A           27 SQPKRLHVSNIPFRFRDPD----LRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIE  100 (109)
T ss_dssp             TCCCEEEEESCCTTCCHHH----HHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEECCCCcCCHHH----HHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            3479999999999999998    78899999999999999885  4589999999999999999998 999999999999


Q ss_pred             EeccccC
Q 045516          595 VDEAKQR  601 (675)
Q Consensus       595 V~~a~~r  601 (675)
                      |.++.++
T Consensus       101 V~~a~~~  107 (109)
T 2err_A          101 VNNATAR  107 (109)
T ss_dssp             EEECCCS
T ss_pred             EEECCCC
Confidence            9999875

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.45  E-value=4.4e-13  Score=115.03  Aligned_cols=78  Identities=27%  Similarity=0.412  Sum_probs=69.3

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEec
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDE  597 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~~  597 (675)
                      .++|||+|||+.+++++    |+.+|..||.|..|  +.+..+|+   ||||+|.+.+.|..||.||+..|+|+.|+|.+
T Consensus         8 ~~~l~V~nl~~~~t~~~----l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~l~g~~~~g~~l~V~~   78 (94)
T 2e5g_A            8 LRSVFVSGFPRGVDSAQ----LSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLSQSQHSLGGHRLRVRP   78 (94)
T ss_dssp             CCEEEEECCCTTCCHHH----HHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHTCSCCEETTEECCCBC
T ss_pred             CCEEEEECCCCCCCHHH----HHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHhcCCeEECCEEEEEEE
Confidence            68999999999999998    78899999999987  55555555   99999999999999999999999999999998


Q ss_pred             cccCCCC
Q 045516          598 AKQRGDF  604 (675)
Q Consensus       598 a~~r~~~  604 (675)
                      +.++...
T Consensus        79 a~~~~~~   85 (94)
T 2e5g_A           79 REQKEFQ   85 (94)
T ss_dssp             SCCSCCC
T ss_pred             CCcCCCC
Confidence            8765543

>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=99.45  E-value=8.9e-14  Score=123.11  Aligned_cols=81  Identities=11%  Similarity=0.156  Sum_probs=71.1

Q ss_pred             CCCceEEEEecCCCC-cCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hC--CceeCC
Q 045516          515 GQAAHTIFIKGFDSS-VGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MS--GTEIGG  590 (675)
Q Consensus       515 ~~~~~~lfV~nLp~~-~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-ln--g~~~~G  590 (675)
                      ..+.++|||+|||+. +++++    |+++|..||.|..|+|++.      +|||||+|.+.++|..||. ||  +..|.|
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~----L~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~l~G   91 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSA----VLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQG   91 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHH----HHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSS
T ss_pred             CCCCCEEEEeCCCCccCCHHH----HHHHHHhcCCEEEEEEecC------CCEEEEEECCHHHHHHHHHHhccCCceECC
Confidence            445899999999998 99998    8899999999999999754      7999999999999999997 65  567999


Q ss_pred             eeeEEeccccCCCCC
Q 045516          591 YSLVVDEAKQRGDFG  605 (675)
Q Consensus       591 r~l~V~~a~~r~~~~  605 (675)
                      |.|+|.|+..+....
T Consensus        92 r~l~V~~a~~~~~~~  106 (112)
T 1x4f_A           92 RCVKVDLSEKYKKLV  106 (112)
T ss_dssp             SCCEEEEECSCSSSS
T ss_pred             EEEEEEECccccccc
Confidence            999999998765543

>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=99.45  E-value=4.7e-14  Score=124.34  Aligned_cols=81  Identities=21%  Similarity=0.263  Sum_probs=75.2

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCc---EEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeee
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGE---ITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSL  593 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~---I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l  593 (675)
                      ..++|||+|||+.+++++    |+++|..||.   |..|+|+++.. |+++|||||+|.+.++|.+||.||+..|+||.|
T Consensus        10 ~~~~l~V~nLp~~~te~~----l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i   84 (107)
T 2lmi_A           10 DVFLIRAQGLPWSCTMED----VLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALEKHRMYMGQRYV   84 (107)
T ss_dssp             SCCEEEEECCCSSCCSHH----HHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHTTTTCCSSSSCC
T ss_pred             CccEEEEeCCCCCCCHHH----HHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHHhCcceeCCeEE
Confidence            378999999999999998    7789999888   89999999987 999999999999999999999999999999999


Q ss_pred             EEeccccCC
Q 045516          594 VVDEAKQRG  602 (675)
Q Consensus       594 ~V~~a~~r~  602 (675)
                      +|.++.++.
T Consensus        85 ~V~~a~~~~   93 (107)
T 2lmi_A           85 EVYEINNED   93 (107)
T ss_dssp             CCEECCHHH
T ss_pred             EEEECCHHH
Confidence            999987643

>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=99.45  E-value=1.3e-13  Score=123.42  Aligned_cols=79  Identities=14%  Similarity=0.218  Sum_probs=71.3

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hC--CceeCCee
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MS--GTEIGGYS  592 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-ln--g~~~~Gr~  592 (675)
                      .+.++|||+|||+.+++++    |+++|..||.|..|+|+++      +|||||+|.+.++|..||. |+  +..|.|+.
T Consensus        29 ~ps~~LfVgNLp~~vte~d----L~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~   98 (119)
T 2ad9_A           29 VPSRVIHIRKLPIDVTEGE----VISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQP   98 (119)
T ss_dssp             SCCSEEEEESCCTTCCHHH----HHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBC
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeE
Confidence            4579999999999999998    7899999999999999986      7999999999999999998 76  46899999


Q ss_pred             eEEeccccCCCC
Q 045516          593 LVVDEAKQRGDF  604 (675)
Q Consensus       593 l~V~~a~~r~~~  604 (675)
                      |+|.|+.++.-.
T Consensus        99 l~V~~a~~k~~~  110 (119)
T 2ad9_A           99 IYIQFSNHKELK  110 (119)
T ss_dssp             CEEEECSSSSCC
T ss_pred             EEEEEccCCCCC
Confidence            999999876554

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.45  E-value=1.5e-13  Score=121.76  Aligned_cols=77  Identities=21%  Similarity=0.267  Sum_probs=68.9

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccC-cEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEE
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCG-EITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVV  595 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G-~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V  595 (675)
                      .++|||+|||+.+++++    |+++|..|| .|..|.|+..    .++|||||+|.+.++|..||. |||..|+|+.|+|
T Consensus        28 ~~~l~VgnLp~~~te~d----L~~~F~~~G~~v~~v~i~~~----~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V   99 (111)
T 2jvr_A           28 RYRITMKNLPEGCSWQD----LKDLARENSLETTFSSVNTR----DFDGTGALEFPSEEILVEALERLNNIEFRGSVITV   99 (111)
T ss_dssp             CEEEEEECSSCCCCHHH----HHHHHHHHTCCCSEEECSSC----SSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEE
T ss_pred             CCEEEEECCCCCCCHHH----HHHHHHHhCCeeEEEEEEcC----CCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            68999999999999998    778889999 9999999653    479999999999999999998 9999999999999


Q ss_pred             eccccCC
Q 045516          596 DEAKQRG  602 (675)
Q Consensus       596 ~~a~~r~  602 (675)
                      .++....
T Consensus       100 ~~a~~~p  106 (111)
T 2jvr_A          100 ERDDNPP  106 (111)
T ss_dssp             EESCC--
T ss_pred             EECCCCC
Confidence            9987543

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.44  E-value=1.9e-13  Score=119.12  Aligned_cols=82  Identities=23%  Similarity=0.469  Sum_probs=75.2

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEe
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVD  596 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~  596 (675)
                      ..++|||+|||+.+++++    |+.+|..||.|..|+|+++. +|.++|||||+|.+.++|..||. ++..|+|+.|.|.
T Consensus         8 ~~~~l~V~nLp~~~t~~~----l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~-~~~~~~g~~l~v~   81 (102)
T 2xs2_A            8 MPNTVFVGGIDVRMDETE----IRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE-SQINFHGKKLKLG   81 (102)
T ss_dssp             EEEEEEEECCCTTCCHHH----HHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT-CCCEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHH----HHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh-CCCeECCEEEEEE
Confidence            368999999999999998    77899999999999999998 89999999999999999999999 9999999999999


Q ss_pred             ccccCCCC
Q 045516          597 EAKQRGDF  604 (675)
Q Consensus       597 ~a~~r~~~  604 (675)
                      ++.++...
T Consensus        82 ~a~~~~~~   89 (102)
T 2xs2_A           82 PAIRKQNL   89 (102)
T ss_dssp             EEEECC--
T ss_pred             ECCcCcch
Confidence            99876543

>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=99.43  E-value=4.4e-13  Score=112.52  Aligned_cols=74  Identities=24%  Similarity=0.428  Sum_probs=68.4

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-h-CCceeCCeee
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-M-SGTEIGGYSL  593 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-l-ng~~~~Gr~l  593 (675)
                      ...++|||+|||..+++++    |+.+|..||.|..|.|+++      +|||||+|.+.+.|..|+. | |+..|+|+.|
T Consensus        10 ~~~~~l~V~~l~~~~t~~~----l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l   79 (85)
T 2ytc_A           10 KTITTLYVGGLGDTITETD----LRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRL   79 (85)
T ss_dssp             SSCCCEEEECCTTTSCHHH----HHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEEC
T ss_pred             CCccEEEEcCCCCCCCHHH----HHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCEE
Confidence            3478999999999999998    7788999999999999875      7999999999999999998 8 9999999999


Q ss_pred             EEeccc
Q 045516          594 VVDEAK  599 (675)
Q Consensus       594 ~V~~a~  599 (675)
                      +|.|++
T Consensus        80 ~v~~ak   85 (85)
T 2ytc_A           80 NVKWGR   85 (85)
T ss_dssp             CEEECC
T ss_pred             EEEecC
Confidence            999974

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.43  E-value=8.8e-14  Score=125.63  Aligned_cols=80  Identities=15%  Similarity=0.184  Sum_probs=72.4

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcE----EEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCee
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEI----TRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYS  592 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I----~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~  592 (675)
                      ..++|||+|||+.+++++    |++||..||.|    ..|+|+++ .+|+++|||||+|.+.++|.+||.+|+..|+||.
T Consensus        22 ~~~~v~V~nLp~~~te~d----l~~~F~~~g~v~g~v~~v~i~~d-~~gr~~G~aFV~F~~~~~A~~Al~~~~~~l~gR~   96 (123)
T 2dha_A           22 NQVIVRMRGLPFTATAEE----VVAFFGQHCPITGGKEGILFVTY-PDGRPTGDAFVLFACEEYAQNALRKHKDLLGKRY   96 (123)
T ss_dssp             SCCEEEECSCCTTCCHHH----HHHHHHTTSCCTTGGGGEEEEEC-TTSCEEEEEEECCSSHHHHHHHHTTTTEESSSCE
T ss_pred             CCCEEEEeCCCCCCCHHH----HHHHHHhhCCccCCcceEEEEEC-CCCCEeeEEEEEECCHHHHHHHHHhCCCeeCCeE
Confidence            368999999999999999    77888888875    68999988 5899999999999999999999999999999999


Q ss_pred             eEEeccccC
Q 045516          593 LVVDEAKQR  601 (675)
Q Consensus       593 l~V~~a~~r  601 (675)
                      |.|..+.++
T Consensus        97 i~V~~a~~~  105 (123)
T 2dha_A           97 IELFRSTAA  105 (123)
T ss_dssp             ECCEEECHH
T ss_pred             EEEEECCHH
Confidence            999988654

>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=99.43  E-value=1.9e-13  Score=123.82  Aligned_cols=79  Identities=23%  Similarity=0.391  Sum_probs=72.3

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEE--EEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeE
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEIT--RISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLV  594 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~--~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~  594 (675)
                      ..++|||+|||+.+++++    |+++|..| .|.  .|+|+++.. |+++|||||+|.+.++|.+||.+++..|+||.|.
T Consensus        41 ~~~~lfVgnLp~~~te~d----L~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~~~~~l~gR~I~  114 (126)
T 2hgm_A           41 NDGFVRLRGLPFGCTKEE----IVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALGKHKERIGHRYIE  114 (126)
T ss_dssp             SCCEEEEECCCTTCCHHH----HHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHTTTTCCBTTBCCC
T ss_pred             CCCEEEEeCCCCCCCHHH----HHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHCCCEECCEEEE
Confidence            368999999999999998    78999999 566  999999987 9999999999999999999999888999999999


Q ss_pred             EeccccC
Q 045516          595 VDEAKQR  601 (675)
Q Consensus       595 V~~a~~r  601 (675)
                      |.++.++
T Consensus       115 V~~a~~~  121 (126)
T 2hgm_A          115 VFKSSQE  121 (126)
T ss_dssp             CEEECHH
T ss_pred             EEECCHH
Confidence            9987654

>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=99.43  E-value=1.9e-13  Score=130.64  Aligned_cols=78  Identities=29%  Similarity=0.542  Sum_probs=71.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ....++|||+|||+.+++++|+++|+.||.|..|    ..++.++|||||+|.+.++|.+||. |||..|.|+.|+|.|+
T Consensus        96 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  171 (175)
T 1fje_B           96 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT  171 (175)
T ss_dssp             TGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEEC
T ss_pred             cccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEec
Confidence            3457899999999999999999999999988766    5588999999999999999999998 9999999999999998


Q ss_pred             ccc
Q 045516          492 RER  494 (675)
Q Consensus       492 ~~~  494 (675)
                      .++
T Consensus       172 ~~k  174 (175)
T 1fje_B          172 GEK  174 (175)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            754

>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=99.42  E-value=2.5e-13  Score=121.05  Aligned_cols=81  Identities=22%  Similarity=0.408  Sum_probs=73.4

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEE
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVV  595 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V  595 (675)
                      +.++|||+|||..+++++    |+.+|..||.|..|.|+++   +..+|||||+|.+.++|..||. |||..|+|+.|+|
T Consensus         7 ~~~~l~V~nlp~~~t~~~----l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   79 (115)
T 3lqv_A            7 VNRILYIRNLPYKITAEE----MYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVV   79 (115)
T ss_dssp             CCSEEEEESCCTTCCHHH----HHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEE
T ss_pred             CCCEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            378999999999999998    7788999999999999976   4559999999999999999998 9999999999999


Q ss_pred             eccccCCCC
Q 045516          596 DEAKQRGDF  604 (675)
Q Consensus       596 ~~a~~r~~~  604 (675)
                      .|+.++...
T Consensus        80 ~~a~~~~~~   88 (115)
T 3lqv_A           80 LYYNANRAF   88 (115)
T ss_dssp             EECCHHHHT
T ss_pred             EEecCChhh
Confidence            999875443

>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=99.42  E-value=2.5e-13  Score=120.50  Aligned_cols=74  Identities=18%  Similarity=0.257  Sum_probs=68.8

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~  596 (675)
                      .++|||+|||+.+++++    |+.+|..||.|..|.|+.      .+|||||+|.+.++|..||. |||..|+|+.|+|.
T Consensus        10 ~~~l~V~nLp~~~te~~----L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   79 (111)
T 1whx_A           10 KTVILAKNLPAGTLAAE----IQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLE   79 (111)
T ss_dssp             EEEEEEESCCTTCCHHH----HHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCEEEEeCCCCCCCHHH----HHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            68999999999999998    788999999999999976      37899999999999999998 99999999999999


Q ss_pred             ccccC
Q 045516          597 EAKQR  601 (675)
Q Consensus       597 ~a~~r  601 (675)
                      |+...
T Consensus        80 ~a~~~   84 (111)
T 1whx_A           80 WAPIG   84 (111)
T ss_dssp             EEETT
T ss_pred             ECCCC
Confidence            99754

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.42  E-value=2.6e-13  Score=117.99  Aligned_cols=75  Identities=17%  Similarity=0.226  Sum_probs=69.1

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEE
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVV  595 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V  595 (675)
                      ..++|||+|||..+++++    |+.+|..||.|..|+|++      ++|||||+|.+.++|..||. |||..|+|+.|+|
T Consensus        26 ~~~~l~V~nlp~~~~~~~----l~~~f~~~G~i~~~~~~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V   95 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEAD----LIPLFQNFGFILDFKHYP------EKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRT   95 (101)
T ss_dssp             SCCEEEEESCCTTCCHHH----HHHHHHTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHTTCEETTEECCC
T ss_pred             CCCEEEEcCCCcccCHHH----HHHHHHhCCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            368999999999999998    778899999999999984      48999999999999999998 9999999999999


Q ss_pred             eccccC
Q 045516          596 DEAKQR  601 (675)
Q Consensus       596 ~~a~~r  601 (675)
                      .|++++
T Consensus        96 ~~a~~~  101 (101)
T 2la4_A           96 GWGKER  101 (101)
T ss_dssp             CBCCCC
T ss_pred             EeccCC
Confidence            999864

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.42  E-value=1.4e-12  Score=112.60  Aligned_cols=77  Identities=19%  Similarity=0.403  Sum_probs=68.6

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEE
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVV  595 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V  595 (675)
                      ..++|||+||  .+++++    |+.+|..||.|..|.|.      .++|||||+|.+.++|.+||. ||+..|+|+.|+|
T Consensus        14 ~~~~l~V~n~--~~t~~~----l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v   81 (97)
T 1x5p_A           14 KGNTLYVYGE--DMTPTL----LRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKV   81 (97)
T ss_dssp             CCSEEEEECS--SCCHHH----HHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEE
T ss_pred             CCCEEEEcCC--CCCHHH----HHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            4789999996  788887    78999999999999995      458999999999999999997 9999999999999


Q ss_pred             eccccCCCCC
Q 045516          596 DEAKQRGDFG  605 (675)
Q Consensus       596 ~~a~~r~~~~  605 (675)
                      .|+.++....
T Consensus        82 ~~a~~~~~~~   91 (97)
T 1x5p_A           82 NIARKQPMLD   91 (97)
T ss_dssp             ECCSSCCCCC
T ss_pred             EECCCCCCCC
Confidence            9998765543

>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=99.42  E-value=1.1e-13  Score=128.57  Aligned_cols=85  Identities=24%  Similarity=0.367  Sum_probs=71.9

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEE--eccc---CCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeC
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRIS--VPKD---YDTGSVKGIAYLDFTDADSFNKALE-MSGTEIG  589 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~--i~~d---~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~  589 (675)
                      .+.++|||+|||+.+++++    |+.+|..||.|..|.  ++.+   ..+|+++|||||+|.+.++|..||. |||..|.
T Consensus        43 ~~~~~l~V~nLp~~~te~~----L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~  118 (143)
T 3egn_A           43 EPNCRIYVKNLAKHVQEKD----LKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLF  118 (143)
T ss_dssp             SCCSEEEEEEECTTCCHHH----HHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEET
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeC
Confidence            4478999999999999998    778999999987751  2222   3468999999999999999999998 9999999


Q ss_pred             CeeeEEeccccCCCC
Q 045516          590 GYSLVVDEAKQRGDF  604 (675)
Q Consensus       590 Gr~l~V~~a~~r~~~  604 (675)
                      |+.|+|.|++++...
T Consensus       119 g~~l~V~~a~~~~~~  133 (143)
T 3egn_A          119 GKPMVVQFARSARPK  133 (143)
T ss_dssp             TEECEEEECCCSCC-
T ss_pred             CcEEEEEECCCCCCc
Confidence            999999999875543

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.42  E-value=2.2e-13  Score=136.53  Aligned_cols=78  Identities=24%  Similarity=0.376  Sum_probs=70.3

Q ss_pred             CCCCceEEEcCCCCCC---------CHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCccc-
Q 045516          413 SGGSKTLFVGNLPFSV---------EQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQML-  481 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~---------te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~-  481 (675)
                      ....++|||+||++.+         ++++|+.+|++||.|..|+|+.     ++|||||+|.+.++|+.||+ |||..| 
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~-----~kG~AFV~F~~~~~Ae~A~~am~g~~l~  205 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE-----SKNCGFVKFKYQANAEFAKEAMSNQTLL  205 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG-----GGTEEEEEESSHHHHHHHHHHHTTCCCC
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC-----CCCEEEEEeCCHHHHHHHHHHhCCCEEe
Confidence            4567999999999998         7999999999999999999985     48999999999999999997 999999 


Q ss_pred             -----------CCeeEEEEeccccC
Q 045516          482 -----------GNRAIRLDFARERG  495 (675)
Q Consensus       482 -----------~gr~i~V~~a~~~~  495 (675)
                                 .|+.|.|.|+....
T Consensus       206 ~~~~~e~~~~~~gr~L~V~wA~~~p  230 (240)
T 3u1l_A          206 LPSDKEWDDRREGTGLLVKWANEDP  230 (240)
T ss_dssp             CTTSTTGGGGGGSCCCEEEECC---
T ss_pred             ccccccccccCCCCEEEEEEccCCC
Confidence                       89999999997653

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

Probab=99.42  E-value=4.4e-13  Score=118.34  Aligned_cols=78  Identities=27%  Similarity=0.482  Sum_probs=70.3

Q ss_pred             CCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeee
Q 045516          515 GQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSL  593 (675)
Q Consensus       515 ~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l  593 (675)
                      ....++|||+|||..+++++    |+.+|..||.|..|.|+        +|||||+|.+.++|..|+. |||..|+|+.|
T Consensus        28 ~~~~~~l~V~nLp~~~t~~~----L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l   95 (108)
T 2jvo_A           28 ELSNTRLFVRPFPLDVQESE----LNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPL   95 (108)
T ss_dssp             CCSCSEEEECSSCTTCCHHH----HHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEECCCCCCCHHH----HHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEE
Confidence            34579999999999999998    78899999999999997        6899999999999999998 99999999999


Q ss_pred             EEeccccCCCC
Q 045516          594 VVDEAKQRGDF  604 (675)
Q Consensus       594 ~V~~a~~r~~~  604 (675)
                      +|.|+.++..+
T Consensus        96 ~V~~a~~~~~r  106 (108)
T 2jvo_A           96 EVVYSKLPAKR  106 (108)
T ss_dssp             EEESCSCCC--
T ss_pred             EEEEecCCCCC
Confidence            99999876543

>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=99.41  E-value=7.8e-13  Score=114.32  Aligned_cols=75  Identities=20%  Similarity=0.383  Sum_probs=68.7

Q ss_pred             CCCceEEEEecCCC-CcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCee
Q 045516          515 GQAAHTIFIKGFDS-SVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYS  592 (675)
Q Consensus       515 ~~~~~~lfV~nLp~-~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~  592 (675)
                      .++.++|||+|||. .+++++    |+.+|..||.|..|+|.        +|||||+|.+.++|..||. |||..|+|+.
T Consensus        19 ~~~~~~l~V~nLp~~~~t~~~----L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~   86 (97)
T 2xnq_A           19 SHMKSRLFIGNLPLKNVSKED----LFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKK   86 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCHHH----HHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEE
T ss_pred             CCCCCEEEEeCCCcccCCHHH----HHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEE
Confidence            34589999999998 999998    77899999999999983        7899999999999999998 9999999999


Q ss_pred             eEEeccccC
Q 045516          593 LVVDEAKQR  601 (675)
Q Consensus       593 l~V~~a~~r  601 (675)
                      |+|.+++++
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=99.41  E-value=3.9e-13  Score=116.07  Aligned_cols=79  Identities=18%  Similarity=0.349  Sum_probs=69.7

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      ...++|||+|||+.+++++    |+.+|..||.|. +.|+.    +.++|||||+|.+.++|..||. |||..|+|+.|+
T Consensus        17 ~~~~~l~V~nL~~~~t~~~----l~~~F~~~G~v~-~~~~~----~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   87 (97)
T 2e5j_A           17 PLAADVYVGNLPRDARVSD----LKRALRELGSVP-LRLTW----QGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLR   87 (97)
T ss_dssp             CCCCEEEEECCCTTCCHHH----HHHHHHHTTCCC-SEEEE----ETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             CCCCEEEEeCCCCcCcHHH----HHHHHHhcCCEE-EEEEc----CCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEE
Confidence            3478999999999999998    778889999996 66664    3678999999999999999997 999999999999


Q ss_pred             EeccccCCC
Q 045516          595 VDEAKQRGD  603 (675)
Q Consensus       595 V~~a~~r~~  603 (675)
                      |.++.++..
T Consensus        88 V~~a~~~~~   96 (97)
T 2e5j_A           88 VALARQQRD   96 (97)
T ss_dssp             EEECCCCCC
T ss_pred             EEEcCCCCC
Confidence            999987653

>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=99.41  E-value=8e-13  Score=117.41  Aligned_cols=82  Identities=21%  Similarity=0.329  Sum_probs=69.8

Q ss_pred             CCCCceEEEcCCCCCCC-----------HHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcc
Q 045516          413 SGGSKTLFVGNLPFSVE-----------QADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQM  480 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~t-----------e~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~  480 (675)
                      ...+++|||.||.....           +++|+++|.+||.|..|.| .+.  .++|||||+|.+.++|.+||. |||..
T Consensus        12 ~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~--~~~G~afV~f~~~~~A~~Ai~~lng~~   88 (112)
T 2dit_A           12 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR--HPDGVASVSFRDPEEADYCIQTLDGRW   88 (112)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT--CTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC--CCCEEEEEEECCHHHHHHHHHHcCCCE
Confidence            34579999999954432           5899999999999999976 443  479999999999999999997 99999


Q ss_pred             cCCeeEEEEeccccCCC
Q 045516          481 LGNRAIRLDFARERGAY  497 (675)
Q Consensus       481 ~~gr~i~V~~a~~~~~~  497 (675)
                      |.||.|+|.++.++..+
T Consensus        89 ~~gr~l~v~~a~~~~~~  105 (112)
T 2dit_A           89 FGGRQITAQAWDGTTDY  105 (112)
T ss_dssp             ETTEECEEEECCSCCCS
T ss_pred             ECCcEEEEEEeCCCCCc
Confidence            99999999999765443

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.40  E-value=8.4e-13  Score=127.17  Aligned_cols=83  Identities=18%  Similarity=0.334  Sum_probs=76.5

Q ss_pred             CCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeee
Q 045516          515 GQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSL  593 (675)
Q Consensus       515 ~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l  593 (675)
                      ....++|||+|||+.+++++    |+++|..||.|..|.|+.+. +|.++|||||+|.+.++|..||. ||+..|+|+.|
T Consensus        85 ~~~~~~l~V~nLp~~~te~~----L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l  159 (177)
T 2f3j_A           85 VETGAKLLVSNLDFGVSDAD----IQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPM  159 (177)
T ss_dssp             CTTCEEEEEECCCSCCCHHH----HHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBC
T ss_pred             CCCCCEEEEeCCCCCCCHHH----HHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEE
Confidence            34579999999999999998    77888899999999999998 89999999999999999999998 99999999999


Q ss_pred             EEeccccCC
Q 045516          594 VVDEAKQRG  602 (675)
Q Consensus       594 ~V~~a~~r~  602 (675)
                      +|.|+....
T Consensus       160 ~V~~a~~~~  168 (177)
T 2f3j_A          160 DIQLVASQI  168 (177)
T ss_dssp             EEEEESSGG
T ss_pred             EEEEecCCC
Confidence            999987643

>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=99.40  E-value=4.3e-12  Score=131.11  Aligned_cols=85  Identities=27%  Similarity=0.456  Sum_probs=79.0

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      .+.++|||+|||+.+++++|+.+|.++|..||.|..|+|++   +|+++|||||+|.+.++|.+||. |||..|.|+.|+
T Consensus         7 ~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   83 (282)
T 3pgw_A            7 RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   83 (282)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEE
Confidence            44899999999999999999999999999999999999987   58899999999999999999997 999999999999


Q ss_pred             EeccccCCC
Q 045516          595 VDEAKQRGD  603 (675)
Q Consensus       595 V~~a~~r~~  603 (675)
                      |.|+.....
T Consensus        84 v~~a~~~~~   92 (282)
T 3pgw_A           84 IQYAKTDSD   92 (282)
T ss_pred             EEEeccCcc
Confidence            999976553

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.39  E-value=5.8e-13  Score=118.80  Aligned_cols=78  Identities=17%  Similarity=0.226  Sum_probs=69.2

Q ss_pred             ceEEEEecC----CCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCC----HHH----HHHHHH---
Q 045516          518 AHTIFIKGF----DSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTD----ADS----FNKALE---  582 (675)
Q Consensus       518 ~~~lfV~nL----p~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~----~e~----A~~Al~---  582 (675)
                      ...|||+||    ++.+++..    |+.+|..||.|..|.++.|+.||+++|||||+|.+    ++.    |.+|+.   
T Consensus         2 p~kI~VgnL~~~~~~~tte~~----Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~   77 (136)
T 2j8a_A            2 SCEIVVYPAQDSTTTNIQDIS----IKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHE   77 (136)
T ss_dssp             CCEEEEEESSSSCCCCCCHHH----HHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTT
T ss_pred             CcEEEEeCCCCCCCCCCCHHH----HHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhh
Confidence            378999999    99999998    78899999999999999999999999999999996    433    778865   


Q ss_pred             hCCceeCCeeeEEeccc
Q 045516          583 MSGTEIGGYSLVVDEAK  599 (675)
Q Consensus       583 lng~~~~Gr~l~V~~a~  599 (675)
                      |||..|+||.|+|.+.+
T Consensus        78 lng~~I~Gr~irV~ln~   94 (136)
T 2j8a_A           78 SSGCFIMGFKFEVILNK   94 (136)
T ss_dssp             TTCEEETTEEEEEEECC
T ss_pred             hcCCeecCcEEEEEECc
Confidence            79999999999999764

>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=99.38  E-value=6.1e-13  Score=112.60  Aligned_cols=79  Identities=20%  Similarity=0.405  Sum_probs=67.2

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEe
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVD  596 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~  596 (675)
                      ..++|||+|||..+++++    |+.+|..||.|..|+|+++     ++|||||+|.+.++|.+|+.. ...+.|+.|+|.
T Consensus         4 ~~~~l~V~nLp~~~te~~----l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~~-~~~~~g~~l~v~   73 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDE----LREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE-DLIIKGISVHIS   73 (88)
T ss_dssp             CCCEEEEESCCSSSCHHH----HHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTTC-EEEETTEEEEEE
T ss_pred             CCcEEEEeCCCCCCCHHH----HHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhcC-CceeCCEEEEEE
Confidence            379999999999999998    7899999999999999875     689999999999999754333 456699999999


Q ss_pred             ccccCCCCC
Q 045516          597 EAKQRGDFG  605 (675)
Q Consensus       597 ~a~~r~~~~  605 (675)
                      ++.++....
T Consensus        74 ~a~~~~~~~   82 (88)
T 1wf0_A           74 NAEPKHNSN   82 (88)
T ss_dssp             CCCCCCCCC
T ss_pred             ecCCCCCCC
Confidence            998766543

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.38  E-value=1.2e-12  Score=114.93  Aligned_cols=83  Identities=13%  Similarity=0.213  Sum_probs=71.6

Q ss_pred             CceEEEEecCCC--CcCHHHHHHHHHhhhcccCcEEEEEecccCCC-CCeeeEEEEEeCCHHHHHHHHH-hCCceeCCee
Q 045516          517 AAHTIFIKGFDS--SVGEDQVRASLEEHFGSCGEITRISVPKDYDT-GSVKGIAYLDFTDADSFNKALE-MSGTEIGGYS  592 (675)
Q Consensus       517 ~~~~lfV~nLp~--~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~t-G~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~  592 (675)
                      ++++|+|.||..  .+. +++.+.|+++|++||.|..|.|++++.+ ++++|||||+|.+.++|.+|+. |||+.|+||.
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 PTKVVLLRNMVGAGEVD-EDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRV   85 (105)
T ss_dssp             CCSEEEEESSSCSCCC----CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCEEEEEcCCChHHhh-HHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcE
Confidence            479999999963  232 3456679999999999999999998654 6899999999999999999998 9999999999


Q ss_pred             eEEecccc
Q 045516          593 LVVDEAKQ  600 (675)
Q Consensus       593 l~V~~a~~  600 (675)
                      |+|.++..
T Consensus        86 i~v~~a~~   93 (105)
T 2pe8_A           86 VKACFYNL   93 (105)
T ss_dssp             CEEEECCH
T ss_pred             EEEEEcCH
Confidence            99999875

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

Probab=99.36  E-value=1.8e-12  Score=111.49  Aligned_cols=78  Identities=15%  Similarity=0.273  Sum_probs=70.0

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEE-ecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRIS-VPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~-i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      ..++|||+|||+.+++++    |+.+|..||.|..|+ |+.+..+|.    |||+|.+.+.|..||. |||..|+|+.|+
T Consensus        14 ~~~~l~V~nlp~~~t~~~----l~~~F~~~G~v~~~~~i~~~~~~~~----afV~f~~~~~a~~Ai~~l~g~~~~g~~l~   85 (96)
T 2e44_A           14 RIRKLQIRNIPPHLQWEV----LDSLLVQYGVVESCEQVNTDSETAV----VNVTYSSKDQARQALDKLNGFQLENFTLK   85 (96)
T ss_dssp             SCCCEEEEEECSSSCHHH----HHHHHHHHSCEEEEEEECCSSSSEE----EEEEESSHHHHHHHHHHHTTCBCSSCBCE
T ss_pred             CCCEEEEEcCCCCCCHHH----HHHHHHhcCCeEEEEEeecCCCCCE----EEEEECCHHHHHHHHHHhCCCEECCcEEE
Confidence            368999999999999998    778888999999994 888765443    9999999999999998 999999999999


Q ss_pred             EeccccCC
Q 045516          595 VDEAKQRG  602 (675)
Q Consensus       595 V~~a~~r~  602 (675)
                      |.++.++.
T Consensus        86 V~~a~~~~   93 (96)
T 2e44_A           86 VAYIPDEM   93 (96)
T ss_dssp             EEECCCCC
T ss_pred             EEEcCccc
Confidence            99998874

>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=99.36  E-value=2.4e-13  Score=119.21  Aligned_cols=71  Identities=23%  Similarity=0.390  Sum_probs=63.9

Q ss_pred             EcCCCCCCCHHHHHHHh------------hhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEE
Q 045516          421 VGNLPFSVEQADVQNFF------------SEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIR  487 (675)
Q Consensus       421 V~nLp~~~te~~L~~~F------------~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~  487 (675)
                      +.||++.+++++|+++|            ++||.|.+|+|+++.+++++|||||+|.+.++|.+|+. |||..|.||.|+
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~   99 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH   99 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEEE
Confidence            56677777888777766            99999999999998888999999999999999999997 999999999999


Q ss_pred             EEec
Q 045516          488 LDFA  491 (675)
Q Consensus       488 V~~a  491 (675)
                      |.|+
T Consensus       100 v~~s  103 (104)
T 1jmt_A          100 AELS  103 (104)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            9886

>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=99.36  E-value=1.6e-12  Score=115.16  Aligned_cols=78  Identities=17%  Similarity=0.368  Sum_probs=69.1

Q ss_pred             CCceEEEE--ecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCcee----
Q 045516          516 QAAHTIFI--KGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEI----  588 (675)
Q Consensus       516 ~~~~~lfV--~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~----  588 (675)
                      .+.++|||  +||++.+++++    |+++|++||.|..|.|+.+      +|||||+|.+.++|.+|+. |||..|    
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~----L~~~F~~fG~v~~v~i~~~------rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~l   92 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQ----LLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVVDDL   92 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHH----HHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEECTT
T ss_pred             CCCCEEEEECCCCCCCCCHHH----HHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHhCCCEEcccc
Confidence            34789999  66999999998    7899999999999998764      7999999999999999998 999998    


Q ss_pred             -CCeeeEEeccccCCC
Q 045516          589 -GGYSLVVDEAKQRGD  603 (675)
Q Consensus       589 -~Gr~l~V~~a~~r~~  603 (675)
                       .|+.|.|.|+....-
T Consensus        93 g~g~~l~v~~a~~~p~  108 (114)
T 2cq2_A           93 GQKITLYLNFVEKVQW  108 (114)
T ss_dssp             SCEEECEEEEESCCCC
T ss_pred             CCCcEEEEEecccCcc
Confidence             789999999875443

>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=99.35  E-value=8.1e-13  Score=130.41  Aligned_cols=76  Identities=22%  Similarity=0.277  Sum_probs=68.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCe--EEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCe----eEE
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEV--VDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNR----AIR  487 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I--~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr----~i~  487 (675)
                      .+++|||+|||+.+++++|+++|++||.|  ..|+|+.+. +..+|||||+|.+.++|.+||. |||..|.|+    +|.
T Consensus       122 p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~-~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~  200 (205)
T 3tyt_A          122 PSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK-SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYT  200 (205)
T ss_dssp             CCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC-SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEE
T ss_pred             CcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC-CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceE
Confidence            46899999999999999999999999999  899998776 5557999999999999999997 999999887    577


Q ss_pred             EEec
Q 045516          488 LDFA  491 (675)
Q Consensus       488 V~~a  491 (675)
                      |.|+
T Consensus       201 vk~~  204 (205)
T 3tyt_A          201 LKLC  204 (205)
T ss_dssp             CEEE
T ss_pred             EEec
Confidence            7664

>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=99.35  E-value=1.4e-12  Score=114.38  Aligned_cols=79  Identities=27%  Similarity=0.331  Sum_probs=69.5

Q ss_pred             CCceEEEcCC--CCCC--------CHHHHHHHhhhCCCeEEEEEeeCCC---CCcccEEEEEecCHHHHHHHHH-hCCcc
Q 045516          415 GSKTLFVGNL--PFSV--------EQADVQNFFSEVAEVVDVRLSSDAD---GRFKGYGHVEFASVEDAHKAIE-LNGQM  480 (675)
Q Consensus       415 ~~~tlfV~nL--p~~~--------te~~L~~~F~~~G~I~~v~i~~~~~---g~~kG~afV~F~~~e~A~~Al~-l~g~~  480 (675)
                      .++.|+|.||  |..+        .+++|+++|++||.|.+|+|+++..   ++++|||||+|.+.++|.+||. |||..
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~   83 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   83 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCE
Confidence            4789999998  4343        3478999999999999999998873   4689999999999999999997 99999


Q ss_pred             cCCeeEEEEeccc
Q 045516          481 LGNRAIRLDFARE  493 (675)
Q Consensus       481 ~~gr~i~V~~a~~  493 (675)
                      |.||.|+|.+...
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

>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=99.34  E-value=7.3e-12  Score=111.15  Aligned_cols=87  Identities=17%  Similarity=0.347  Sum_probs=72.9

Q ss_pred             CCCceEEEEecCCCCcC-------HHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCc
Q 045516          515 GQAAHTIFIKGFDSSVG-------EDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGT  586 (675)
Q Consensus       515 ~~~~~~lfV~nLp~~~t-------e~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~  586 (675)
                      ..+.++|+|.||.....       .+++.+.|+.+|.+||.|..|.| .+.   .++|||||+|.+.++|.+||. |||.
T Consensus        12 ~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng~   87 (112)
T 2dit_A           12 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDGR   87 (112)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTTC
T ss_pred             CCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCCC
Confidence            34589999999954433       23467789999999999999966 443   379999999999999999997 9999


Q ss_pred             eeCCeeeEEeccccCCCCC
Q 045516          587 EIGGYSLVVDEAKQRGDFG  605 (675)
Q Consensus       587 ~~~Gr~l~V~~a~~r~~~~  605 (675)
                      .|+|+.|+|.++.++..+.
T Consensus        88 ~~~gr~l~v~~a~~~~~~~  106 (112)
T 2dit_A           88 WFGGRQITAQAWDGTTDYQ  106 (112)
T ss_dssp             EETTEECEEEECCSCCCSS
T ss_pred             EECCcEEEEEEeCCCCCcc
Confidence            9999999999998876654

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.33  E-value=3.4e-12  Score=115.65  Aligned_cols=78  Identities=22%  Similarity=0.233  Sum_probs=69.8

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeE-EEEEeCCHHHHHHHHH-hCCceeCC--eee
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGI-AYLDFTDADSFNKALE-MSGTEIGG--YSL  593 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~-afV~F~~~e~A~~Al~-lng~~~~G--r~l  593 (675)
                      ...|||+||++.+++++    |+++|++||.|..|+|+...     +|| |||+|.+.++|..|+. |||..|.|  +.|
T Consensus        28 VL~I~V~NL~~~vte~~----L~~lFs~yG~V~~V~i~~~~-----~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~L   98 (130)
T 3zzy_A           28 VLRIIVENLFYPVTLDV----LHQIFSKFGTVLKIITFTKN-----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTL   98 (130)
T ss_dssp             EEEEEEESCCSCCCHHH----HHHHHTTSSCEEEEEEEEET-----TEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEE
T ss_pred             eEEEEECCCCCCCCHHH----HHHHHhCcCCEEEEEEEcCC-----CCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEE
Confidence            56778999999999998    88999999999999988642     677 9999999999999998 99999988  999


Q ss_pred             EEeccccCCCC
Q 045516          594 VVDEAKQRGDF  604 (675)
Q Consensus       594 ~V~~a~~r~~~  604 (675)
                      +|.|+++..-.
T Consensus        99 rI~~ak~~~l~  109 (130)
T 3zzy_A           99 RIDFSKLTSLN  109 (130)
T ss_dssp             EEEECSCSSCC
T ss_pred             EEEecCCCcee
Confidence            99999876543

>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=99.33  E-value=3.2e-12  Score=108.64  Aligned_cols=78  Identities=19%  Similarity=0.406  Sum_probs=62.4

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVV  595 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V  595 (675)
                      .+.++|||+|||+.+++++    |+++|++||.|..|+|+++     ++|||||+|.+.++|.. +......++|+.|.|
T Consensus         9 ~~~~~l~V~~Lp~~~te~~----L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~-~~~~~~~~~g~~v~v   78 (89)
T 3d2w_A            9 HHGSKVFVGRCTEDMTAEE----LQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS-LCGEDLIIKGISVHI   78 (89)
T ss_dssp             --CCEEEEESCCTTCCHHH----HHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH-HTTCEEEETTEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH-HcCCCcccCCEEEEE
Confidence            3479999999999999998    7899999999999999985     69999999999999883 222234457999999


Q ss_pred             eccccCCC
Q 045516          596 DEAKQRGD  603 (675)
Q Consensus       596 ~~a~~r~~  603 (675)
                      .++.++..
T Consensus        79 ~~a~~k~~   86 (89)
T 3d2w_A           79 SNAEPKHN   86 (89)
T ss_dssp             EECC----
T ss_pred             EEcCCCCc
Confidence            99987654

>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=99.32  E-value=3.9e-12  Score=111.56  Aligned_cols=86  Identities=13%  Similarity=0.271  Sum_probs=73.8

Q ss_pred             CCceEEEEecCCC--CcC----HHHHHHHHHhhhcccCcEEEEEecccCCC--CCeeeEEEEEeCCHHHHHHHHH-hCCc
Q 045516          516 QAAHTIFIKGFDS--SVG----EDQVRASLEEHFGSCGEITRISVPKDYDT--GSVKGIAYLDFTDADSFNKALE-MSGT  586 (675)
Q Consensus       516 ~~~~~lfV~nLp~--~~t----e~~i~~~L~~~F~~~G~I~~v~i~~d~~t--G~~rG~afV~F~~~e~A~~Al~-lng~  586 (675)
                      .++++|+|.|+-.  .+.    ..+|.+.|+++|++||.|..|.|+++..+  ++++||+||+|.+.++|.+|+. |||+
T Consensus         3 ~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~   82 (105)
T 3v4m_A            3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   82 (105)
T ss_dssp             SCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            3588999999832  332    35688889999999999999999998765  4689999999999999999998 9999


Q ss_pred             eeCCeeeEEeccccC
Q 045516          587 EIGGYSLVVDEAKQR  601 (675)
Q Consensus       587 ~~~Gr~l~V~~a~~r  601 (675)
                      .|+||.|+|.+....
T Consensus        83 ~f~GR~i~v~~~~~~   97 (105)
T 3v4m_A           83 KFANRVVVTKYCDPD   97 (105)
T ss_dssp             EETTEECEEEEECHH
T ss_pred             EeCCCEEEEEEeCHH
Confidence            999999999988643

>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=99.32  E-value=4.3e-12  Score=107.41  Aligned_cols=74  Identities=12%  Similarity=0.243  Sum_probs=67.9

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~  596 (675)
                      .++|||+|||+.+++++    |+++|..| .|..|+|.      +++|||||+|.+.++|.+||. |||..|+|+.|+|.
T Consensus         5 ~~~l~V~nLp~~~t~~~----l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~   73 (88)
T 1wg1_A            5 SSGILVKNLPQDSNCQE----VHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQ   73 (88)
T ss_dssp             CCCEEEESCCSSCCHHH----HHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCEEEEeCCCCCCCHHH----HHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEE
Confidence            68999999999999998    78999999 99999884      568999999999999999998 99999999999999


Q ss_pred             ccccCC
Q 045516          597 EAKQRG  602 (675)
Q Consensus       597 ~a~~r~  602 (675)
                      ++....
T Consensus        74 ~a~~~~   79 (88)
T 1wg1_A           74 LQPTDA   79 (88)
T ss_dssp             ECCCCC
T ss_pred             EcCCCc
Confidence            986543

>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=99.32  E-value=2.7e-12  Score=131.42  Aligned_cols=81  Identities=30%  Similarity=0.354  Sum_probs=73.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-h-CCcccC---CeeEEEE
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-L-NGQMLG---NRAIRLD  489 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l-~g~~~~---gr~i~V~  489 (675)
                      ..++|||+|||+.+++++|+++|..||.|..|+|+.+.+|+++|||||+|.+.++|.+||. | ++..+.   +++|.|.
T Consensus        95 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~  174 (261)
T 3sde_A           95 HGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVE  174 (261)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEE
T ss_pred             cCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEe
Confidence            4689999999999999999999999999999999999999999999999999999999998 8 555555   9999999


Q ss_pred             eccccC
Q 045516          490 FARERG  495 (675)
Q Consensus       490 ~a~~~~  495 (675)
                      ++....
T Consensus       175 ~~~~~~  180 (261)
T 3sde_A          175 PMEQFD  180 (261)
T ss_dssp             ECCCEE
T ss_pred             eccccC
Confidence            987653

>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=99.32  E-value=9.3e-12  Score=121.56  Aligned_cols=78  Identities=21%  Similarity=0.388  Sum_probs=71.7

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEec
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDE  597 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~~  597 (675)
                      .++|||+|||+.+++++    |+.+|+.||.|..|+|+++. +|.++|||||+|.+.++|..||.+.+..|+|+.|+|.+
T Consensus       109 ~~~l~V~nLp~~~t~~~----L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~~~~~~Gr~l~V~~  183 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDD----IKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILF  183 (193)
T ss_dssp             HTEEEEECCCTTCCHHH----HHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCTTCEETTEECEEEE
T ss_pred             cCEEEecCCCCcCCHHH----HHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhCCCeECCEEEEEEE
Confidence            58999999999999988    88999999999999999986 49999999999999999999999666799999999998


Q ss_pred             ccc
Q 045516          598 AKQ  600 (675)
Q Consensus       598 a~~  600 (675)
                      ...
T Consensus       184 ~~~  186 (193)
T 2voo_A          184 KDD  186 (193)
T ss_dssp             TTT
T ss_pred             hHH
Confidence            764

>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=99.31  E-value=3.1e-12  Score=120.37  Aligned_cols=78  Identities=22%  Similarity=0.219  Sum_probs=69.9

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCC--eeeE
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGG--YSLV  594 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~G--r~l~  594 (675)
                      ..+|||+||++.+++++    |+++|++||.|..|.|+..    ..+|||||+|.+.++|..|+. |||..|.|  +.|+
T Consensus        46 vl~l~VgNL~~~vted~----L~~~Fs~fG~V~~V~i~~k----~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~  117 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDV----LHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLR  117 (164)
T ss_dssp             EEEEEECSCCSCCCHHH----HHHHHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEE
T ss_pred             eEEEEEeCcCCCCCHHH----HHHHHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEE
Confidence            57789999999999998    7889999999999999754    257999999999999999998 99999965  9999


Q ss_pred             EeccccCCC
Q 045516          595 VDEAKQRGD  603 (675)
Q Consensus       595 V~~a~~r~~  603 (675)
                      |.|++++.-
T Consensus       118 V~~Ak~~~l  126 (164)
T 1sjr_A          118 IDFSKLTSL  126 (164)
T ss_dssp             EEECSSSSC
T ss_pred             EEEecCCcc
Confidence            999988643

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.31  E-value=2.4e-12  Score=125.69  Aligned_cols=76  Identities=29%  Similarity=0.443  Sum_probs=70.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCC-CeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccC-CeeEEEEe
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVA-EVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLG-NRAIRLDF  490 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G-~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~-gr~i~V~~  490 (675)
                      ..+++|||+|||+.+++++|+++|..|| .|..|+|+.+    .+|||||+|.+.++|.+||. |||..|. |+.|+|.|
T Consensus       118 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~  193 (198)
T 1qm9_A          118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF  193 (198)
T ss_dssp             CCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST----TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEE
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC----CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEe
Confidence            3479999999999999999999999999 9999999764    27999999999999999998 9999999 99999999


Q ss_pred             ccc
Q 045516          491 ARE  493 (675)
Q Consensus       491 a~~  493 (675)
                      +.+
T Consensus       194 a~~  196 (198)
T 1qm9_A          194 SKS  196 (198)
T ss_dssp             ECC
T ss_pred             ecc
Confidence            864

>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=99.31  E-value=3.8e-12  Score=113.98  Aligned_cols=79  Identities=22%  Similarity=0.276  Sum_probs=69.3

Q ss_pred             CCceEEEcCCCC-----CCCHHHHHHHhhhCCCeEEEEEeeCC-----CCCcccEEEEEecCHHHHHHHHH-hCCcccCC
Q 045516          415 GSKTLFVGNLPF-----SVEQADVQNFFSEVAEVVDVRLSSDA-----DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGN  483 (675)
Q Consensus       415 ~~~tlfV~nLp~-----~~te~~L~~~F~~~G~I~~v~i~~~~-----~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~g  483 (675)
                      .+++|+|.||-.     .--+++|+++|++||.|.+|+|+++.     +++++||+||+|.+.++|.+|+. |||..|.|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            478999999942     23478999999999999999999875     24678999999999999999997 99999999


Q ss_pred             eeEEEEeccc
Q 045516          484 RAIRLDFARE  493 (675)
Q Consensus       484 r~i~V~~a~~  493 (675)
                      |.|+|.|+..
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999999753

>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=99.30  E-value=4.4e-12  Score=127.19  Aligned_cols=76  Identities=29%  Similarity=0.443  Sum_probs=70.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCC-CeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccC-CeeEEEEe
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVA-EVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLG-NRAIRLDF  490 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G-~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~-gr~i~V~~  490 (675)
                      ...++|||+|||+.+++++|+++|..|| .|..|+|+..    .+|||||+|.+.++|.+||. |||..|. |+.|+|.|
T Consensus       149 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~  224 (229)
T 2adc_A          149 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF  224 (229)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEE
T ss_pred             CCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEE
Confidence            3468999999999999999999999999 9999999653    37999999999999999998 9999999 99999999


Q ss_pred             ccc
Q 045516          491 ARE  493 (675)
Q Consensus       491 a~~  493 (675)
                      +.+
T Consensus       225 a~~  227 (229)
T 2adc_A          225 SKS  227 (229)
T ss_dssp             CSS
T ss_pred             ecC
Confidence            864

>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=99.30  E-value=5.2e-12  Score=106.32  Aligned_cols=71  Identities=21%  Similarity=0.484  Sum_probs=64.2

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhccc----C-------cEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCC
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSC----G-------EITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSG  585 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~----G-------~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng  585 (675)
                      ..++|||+|||+.+++++    |+++|..|    |       .|..|++.++      +|||||+|.+.++|.+||.|||
T Consensus         5 ~~~~l~V~nLp~~~t~~~----l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~~l~g   74 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEA----MMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAMAFDG   74 (87)
T ss_dssp             GGGEEEEESCCTTCCHHH----HHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHGGGTT
T ss_pred             CCCEEEEeCCCCCCCHHH----HHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHHhcCC
Confidence            479999999999999998    56666667    8       9999999876      7999999999999999999999


Q ss_pred             ceeCCeeeEEec
Q 045516          586 TEIGGYSLVVDE  597 (675)
Q Consensus       586 ~~~~Gr~l~V~~  597 (675)
                      ..|+|+.|+|.+
T Consensus        75 ~~~~g~~l~V~r   86 (87)
T 2hzc_A           75 IIFQGQSLKIRR   86 (87)
T ss_dssp             CEETTEECEEEC
T ss_pred             CEECCeEEEEeC
Confidence            999999999974

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.30  E-value=6.5e-12  Score=113.26  Aligned_cols=76  Identities=22%  Similarity=0.267  Sum_probs=67.1

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeE-EEEEeCCHHHHHHHHH-hCCceeCC--eee
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGI-AYLDFTDADSFNKALE-MSGTEIGG--YSL  593 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~-afV~F~~~e~A~~Al~-lng~~~~G--r~l  593 (675)
                      ...|||+||++.+++++    |+++|+.||.|..|+|+..      .|| |||+|.+.++|..|+. |||..|.|  +.|
T Consensus        25 vl~l~V~NL~~~vt~~~----L~~~Fs~yG~V~~v~i~~~------~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l   94 (124)
T 2e5i_A           25 VLLLSIQNPLYPITVDV----LYTVCNPVGKVQRIVIFKR------NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTL   94 (124)
T ss_dssp             EEEEEEESCCSCCCHHH----HHHHHTTTSCEEEEEEEES------SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEE
T ss_pred             EEEEEEcCcCCCCCHHH----HHHHHHhcCCEEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEE
Confidence            34567999999999998    8899999999999999652      276 9999999999999998 99999987  689


Q ss_pred             EEeccccCCC
Q 045516          594 VVDEAKQRGD  603 (675)
Q Consensus       594 ~V~~a~~r~~  603 (675)
                      +|.|++++.-
T Consensus        95 ~V~~Ak~~~l  104 (124)
T 2e5i_A           95 KIEYARPTRL  104 (124)
T ss_dssp             EEECCSCSCC
T ss_pred             EEEEecCCcc
Confidence            9999988754

>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=99.29  E-value=5.2e-12  Score=113.08  Aligned_cols=84  Identities=15%  Similarity=0.358  Sum_probs=72.8

Q ss_pred             CceEEEEecCCCCcC-HHHHHHHHHhhhcccCcEEEEEecccCC----CCCeeeEEEEEeCCHHHHHHHHH-hCCceeCC
Q 045516          517 AAHTIFIKGFDSSVG-EDQVRASLEEHFGSCGEITRISVPKDYD----TGSVKGIAYLDFTDADSFNKALE-MSGTEIGG  590 (675)
Q Consensus       517 ~~~~lfV~nLp~~~t-e~~i~~~L~~~F~~~G~I~~v~i~~d~~----tG~~rG~afV~F~~~e~A~~Al~-lng~~~~G  590 (675)
                      ++++|+|.|+-.... .++|.+.|+++|++||.|..|.|+++..    +++++||+||+|.+.++|.+|+. |||++|+|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            589999999853321 2457788999999999999999999864    46789999999999999999998 99999999


Q ss_pred             eeeEEecccc
Q 045516          591 YSLVVDEAKQ  600 (675)
Q Consensus       591 r~l~V~~a~~  600 (675)
                      |.|+|.|...
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999999854

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.27  E-value=1.5e-11  Score=109.53  Aligned_cols=75  Identities=20%  Similarity=0.406  Sum_probs=65.7

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCC---CCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeee
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDT---GSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSL  593 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~t---G~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l  593 (675)
                      .++|||+|||+.+++++    |+++|.+||.|. +.++.+..+   |+++|||||+|.+.++|.+||. |+  .|+|+.|
T Consensus         8 ~~~lfVgnLp~~~te~~----L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~   80 (114)
T 2dnl_A            8 SRKVFVGGLPPDIDEDE----ITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLY   80 (114)
T ss_dssp             CCCEEEECCCTTCCHHH----HHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEE
T ss_pred             CCEEEEcCCCCCCCHHH----HHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEE
Confidence            68999999999999998    789999999999 889888877   7999999999999999999998 73  4777777


Q ss_pred             EEeccc
Q 045516          594 VVDEAK  599 (675)
Q Consensus       594 ~V~~a~  599 (675)
                      .+....
T Consensus        81 ~~~~~~   86 (114)
T 2dnl_A           81 LCVSSP   86 (114)
T ss_dssp             EEECCS
T ss_pred             EeccCC
Confidence            666543

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.25  E-value=4.6e-11  Score=103.56  Aligned_cols=75  Identities=21%  Similarity=0.283  Sum_probs=64.7

Q ss_pred             CCceEEEcCCC-------CCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeE
Q 045516          415 GSKTLFVGNLP-------FSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAI  486 (675)
Q Consensus       415 ~~~tlfV~nLp-------~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i  486 (675)
                      ..++|.|.-..       ..+++++|+++|++||.|..|+|+    ++++|||||+|.+.++|..||. +++  +.|++|
T Consensus         9 ~~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~----~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l   82 (100)
T 2d9o_A            9 GTPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLS----SKKPGTAVVEFATVKAAELAVQNEVG--LVDNPL   82 (100)
T ss_dssp             SSCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEE----SSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBC
T ss_pred             ccceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEc----cCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeE
Confidence            35678877665       468999999999999999999998    4679999999999999999998 544  679999


Q ss_pred             EEEeccccC
Q 045516          487 RLDFARERG  495 (675)
Q Consensus       487 ~V~~a~~~~  495 (675)
                      +|.|+..+.
T Consensus        83 ~V~~a~~~~   91 (100)
T 2d9o_A           83 KISWLEGQP   91 (100)
T ss_dssp             EEECSSCCC
T ss_pred             EEEEccCCC
Confidence            999987654

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.22  E-value=1.3e-11  Score=123.70  Aligned_cols=82  Identities=24%  Similarity=0.412  Sum_probs=68.1

Q ss_pred             CCceEEEEecCCCCcC-----HHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCcee-
Q 045516          516 QAAHTIFIKGFDSSVG-----EDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEI-  588 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~t-----e~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~-  588 (675)
                      ...++|||+||+..++     ...+.+.|+.+|+.||.|..|+|+..      +|||||+|.+.++|..|+. |||..| 
T Consensus       132 ~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~------kG~AFV~F~~~~~Ae~A~~am~g~~l~  205 (240)
T 3u1l_A          132 KKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES------KNCGFVKFKYQANAEFAKEAMSNQTLL  205 (240)
T ss_dssp             CCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHHHTTCCCC
T ss_pred             cCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC------CCEEEEEeCCHHHHHHHHHHhCCCEEe
Confidence            3479999999999872     12233448899999999999999875      8999999999999999998 999999 


Q ss_pred             -----------CCeeeEEeccccCCC
Q 045516          589 -----------GGYSLVVDEAKQRGD  603 (675)
Q Consensus       589 -----------~Gr~l~V~~a~~r~~  603 (675)
                                 .|+.|.|.|+....+
T Consensus       206 ~~~~~e~~~~~~gr~L~V~wA~~~pn  231 (240)
T 3u1l_A          206 LPSDKEWDDRREGTGLLVKWANEDPD  231 (240)
T ss_dssp             CTTSTTGGGGGGSCCCEEEECC----
T ss_pred             ccccccccccCCCCEEEEEEccCCCC
Confidence                       899999999987554

>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=99.20  E-value=5.1e-11  Score=105.87  Aligned_cols=80  Identities=14%  Similarity=0.220  Sum_probs=71.1

Q ss_pred             CceEEEEecCCCCcC------HHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeC
Q 045516          517 AAHTIFIKGFDSSVG------EDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIG  589 (675)
Q Consensus       517 ~~~~lfV~nLp~~~t------e~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~  589 (675)
                      ++++|.|.|+-....      ..+|.+.|+++|++||.|..|.|+++.    .+||+||+|.+.++|.+|+. |||++|+
T Consensus         6 ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f~   81 (114)
T 3s6e_A            6 ATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWFA   81 (114)
T ss_dssp             CCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEET
T ss_pred             CCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEEC
Confidence            478999999865443      588999999999999999999998763    48999999999999999998 9999999


Q ss_pred             CeeeEEecccc
Q 045516          590 GYSLVVDEAKQ  600 (675)
Q Consensus       590 Gr~l~V~~a~~  600 (675)
                      ||.|+|.|+..
T Consensus        82 GR~i~v~~~~~   92 (114)
T 3s6e_A           82 GKMITAAYVPL   92 (114)
T ss_dssp             TEECEEEEECH
T ss_pred             CEEEEEEEEcH
Confidence            99999999854

>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=99.19  E-value=1.4e-11  Score=107.80  Aligned_cols=75  Identities=16%  Similarity=0.329  Sum_probs=64.0

Q ss_pred             EecCCCCcCHHHHH-------HHHHhhh-cccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeee
Q 045516          523 IKGFDSSVGEDQVR-------ASLEEHF-GSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSL  593 (675)
Q Consensus       523 V~nLp~~~te~~i~-------~~L~~~F-~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l  593 (675)
                      +.||+..+++++|+       +.|+.+| ++||.|..|.|+++.. ++++|||||.|.+.++|.+|+. |||+.|+||.|
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~-~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i   98 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLG-DHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSS-SSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCC-CCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            45666666776554       5567777 9999999999998864 7899999999999999999998 99999999999


Q ss_pred             EEecc
Q 045516          594 VVDEA  598 (675)
Q Consensus       594 ~V~~a  598 (675)
                      +|.|+
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99886

>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=99.16  E-value=4.3e-11  Score=126.21  Aligned_cols=75  Identities=21%  Similarity=0.341  Sum_probs=65.5

Q ss_pred             CCCCceEEEcC--CCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCccc---CCe--
Q 045516          413 SGGSKTLFVGN--LPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQML---GNR--  484 (675)
Q Consensus       413 ~~~~~tlfV~n--Lp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~---~gr--  484 (675)
                      ...+++|||+|  |++.+|+++|+++|++||.|..|+|..     ++|||||+|.+.++|++||+ |||..+   .|+  
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~-----~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~   89 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-----NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKI   89 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT-----TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEE
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCccccccCCce
Confidence            45678999999  589999999999999999999998864     48999999999999999998 999988   355  


Q ss_pred             eEEEEecc
Q 045516          485 AIRLDFAR  492 (675)
Q Consensus       485 ~i~V~~a~  492 (675)
                      .|+|.|..
T Consensus        90 ~ly~~~~~   97 (345)
T 3tht_A           90 TLYLNFVE   97 (345)
T ss_dssp             ECEEEECS
T ss_pred             EEEEEEee
Confidence            57777764

>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=99.14  E-value=1e-10  Score=103.94  Aligned_cols=77  Identities=16%  Similarity=0.215  Sum_probs=65.8

Q ss_pred             CCCceEEEcCCCC--C--------CCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccC
Q 045516          414 GGSKTLFVGNLPF--S--------VEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLG  482 (675)
Q Consensus       414 ~~~~tlfV~nLp~--~--------~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~  482 (675)
                      ..+++|.|.||=.  .        --+++|+++|++||.|.+|+|.++.   .+||+||.|.+.++|.+||. |||..|+
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~---~~G~~fV~f~~~e~A~~Ai~~lnG~~f~   81 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS---AQGNVYVKCPSIAAAIAAVNALHGRWFA   81 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC---TTCCEEEECSSHHHHHHHHHHHTTCEET
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC---CcEEEEEEECCHHHHHHHHHHhCCCEEC
Confidence            3578999999932  2        1245789999999999999997652   58999999999999999997 9999999


Q ss_pred             CeeEEEEeccc
Q 045516          483 NRAIRLDFARE  493 (675)
Q Consensus       483 gr~i~V~~a~~  493 (675)
                      ||.|+|.|+..
T Consensus        82 GR~i~v~~~~~   92 (114)
T 3s6e_A           82 GKMITAAYVPL   92 (114)
T ss_dssp             TEECEEEEECH
T ss_pred             CEEEEEEEEcH
Confidence            99999999854

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.05  E-value=1e-09  Score=95.01  Aligned_cols=66  Identities=15%  Similarity=0.214  Sum_probs=56.4

Q ss_pred             CCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEeccccCCCC
Q 045516          528 SSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVDEAKQRGDF  604 (675)
Q Consensus       528 ~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~~a~~r~~~  604 (675)
                      ..+++++    |+.+|.+||.|..|+|+     ++++|||||+|.+.++|..||. +++  +.|+.|+|.|++++...
T Consensus        27 ~~~te~~----L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~~~~~   93 (100)
T 2d9o_A           27 GGYSKDV----LLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEGQPQD   93 (100)
T ss_dssp             CSCCHHH----HHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSCCCCC
T ss_pred             CCCCHHH----HHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccCCCCC
Confidence            4577777    88999999999999998     3679999999999999999998 544  68999999999876543

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.04  E-value=8.8e-10  Score=92.21  Aligned_cols=79  Identities=19%  Similarity=0.315  Sum_probs=70.3

Q ss_pred             CCCceEEEEecCC----CCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCC
Q 045516          515 GQAAHTIFIKGFD----SSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGG  590 (675)
Q Consensus       515 ~~~~~~lfV~nLp----~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~G  590 (675)
                      +++..||+|..++    .+.-.++|...|.+.|..||.|..|+|+.+.        +||+|.+.+.|.+||.|||..|+|
T Consensus         4 GPpd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~mnG~~v~G   75 (91)
T 2dnr_A            4 GSSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLSLNGKELLN   75 (91)
T ss_dssp             CCSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGGGTTCEETT
T ss_pred             CCCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHhcCCeEeCC
Confidence            5668899999887    3556677888899999999999999999974        899999999999999999999999


Q ss_pred             eeeEEeccccC
Q 045516          591 YSLVVDEAKQR  601 (675)
Q Consensus       591 r~l~V~~a~~r  601 (675)
                      |.|+|.++++.
T Consensus        76 r~LkV~lkt~d   86 (91)
T 2dnr_A           76 RTITIALKSPS   86 (91)
T ss_dssp             EEEEEEECCCS
T ss_pred             eEEEEEeCCCC
Confidence            99999998763

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.91  E-value=1.9e-09  Score=90.20  Aligned_cols=71  Identities=24%  Similarity=0.301  Sum_probs=61.5

Q ss_pred             CceEEEcCCC----CCCCH----HHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEE
Q 045516          416 SKTLFVGNLP----FSVEQ----ADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIR  487 (675)
Q Consensus       416 ~~tlfV~nLp----~~~te----~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~  487 (675)
                      .-||+|.-++    .+.-.    .+|.+.|.+||.|..|+|..+       .+||+|.+.++|.+||.|||..|.||.|+
T Consensus         7 d~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d-------~~fVtF~d~~sAlaAi~mnG~~v~Gr~Lk   79 (91)
T 2dnr_A            7 GGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVED-------KMWVTFLEGSSALNVLSLNGKELLNRTIT   79 (91)
T ss_dssp             SCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSS-------SEEEEESSHHHHHHGGGGTTCEETTEEEE
T ss_pred             CCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecC-------CEEEEECChHHHHHHHhcCCeEeCCeEEE
Confidence            4688888877    23333    578999999999999999965       39999999999999999999999999999


Q ss_pred             EEeccc
Q 045516          488 LDFARE  493 (675)
Q Consensus       488 V~~a~~  493 (675)
                      |.++++
T Consensus        80 V~lkt~   85 (91)
T 2dnr_A           80 IALKSP   85 (91)
T ss_dssp             EEECCC
T ss_pred             EEeCCC
Confidence            999864

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.89  E-value=3.4e-09  Score=94.39  Aligned_cols=73  Identities=15%  Similarity=0.115  Sum_probs=64.9

Q ss_pred             CCceEEEcCCCCC-CCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecC-HHHHHHHHH-h--CCcccCCeeEEEE
Q 045516          415 GSKTLFVGNLPFS-VEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFAS-VEDAHKAIE-L--NGQMLGNRAIRLD  489 (675)
Q Consensus       415 ~~~tlfV~nLp~~-~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~-~e~A~~Al~-l--~g~~~~gr~i~V~  489 (675)
                      .++.|||+||++. ++.++|+++|+.||.|..|.|.++.     -+|||.|.+ ...|..|+. |  ++..|.|..+++.
T Consensus        17 ~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~-----~tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~e   91 (121)
T 1owx_A           17 IGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGA-----KEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWE   91 (121)
T ss_dssp             CCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTC-----SEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEE
T ss_pred             CCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCC-----CEEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEE
Confidence            4689999999999 9999999999999999999998764     369999999 889999997 7  5888999988887


Q ss_pred             ecc
Q 045516          490 FAR  492 (675)
Q Consensus       490 ~a~  492 (675)
                      +..
T Consensus        92 vL~   94 (121)
T 1owx_A           92 VLE   94 (121)
T ss_dssp             ECC
T ss_pred             ECC
Confidence            654

>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=98.84  E-value=3.7e-09  Score=88.86  Aligned_cols=79  Identities=18%  Similarity=0.340  Sum_probs=69.0

Q ss_pred             CCCCceEEEEecCCCC-----cCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCcee
Q 045516          514 RGQAAHTIFIKGFDSS-----VGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEI  588 (675)
Q Consensus       514 ~~~~~~~lfV~nLp~~-----~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~  588 (675)
                      .+++..||+|..++..     +-.+++...|.++|..||.|..|+|+.+.        +||+|.+.+.|.+||.|||..|
T Consensus        11 ~GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~ldG~~v   82 (95)
T 1ufw_A           11 QGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLDVDGMKV   82 (95)
T ss_dssp             CCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHHGGGSEE
T ss_pred             cCCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHhcCCeee
Confidence            4567899999998743     44567777899999999999999999983        9999999999999999999999


Q ss_pred             CCeeeEEecccc
Q 045516          589 GGYSLVVDEAKQ  600 (675)
Q Consensus       589 ~Gr~l~V~~a~~  600 (675)
                      +||.|+|.+-.+
T Consensus        83 ~Gr~L~V~~k~~   94 (95)
T 1ufw_A           83 KGRAVKISGPSS   94 (95)
T ss_dssp             TTEEEEEECCCC
T ss_pred             CCeEEEEeccCC
Confidence            999999997643

>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=98.81  E-value=7.5e-09  Score=109.12  Aligned_cols=75  Identities=17%  Similarity=0.390  Sum_probs=64.2

Q ss_pred             CCCceEEEEec--CCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeC--
Q 045516          515 GQAAHTIFIKG--FDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIG--  589 (675)
Q Consensus       515 ~~~~~~lfV~n--Lp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~--  589 (675)
                      ..++++|||+|  |++.+++++    |+++|++||.|..|.|++      .||||||+|.+.++|.+||+ |||..+.  
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~----L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~   84 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQ----LLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDD   84 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHH----HHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECT
T ss_pred             CCCCCEEEEEcCCCCCCCCHHH----HHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccccc
Confidence            45589999999  578999998    789999999999998865      37999999999999999998 9999883  


Q ss_pred             -Ce--eeEEeccc
Q 045516          590 -GY--SLVVDEAK  599 (675)
Q Consensus       590 -Gr--~l~V~~a~  599 (675)
                       |+  .|.|.|..
T Consensus        85 ~g~~~~ly~~~~~   97 (345)
T 3tht_A           85 LGQKITLYLNFVE   97 (345)
T ss_dssp             TSCEEECEEEECS
T ss_pred             cCCceEEEEEEee
Confidence             45  57777763

>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=98.72  E-value=6.7e-09  Score=87.26  Aligned_cols=71  Identities=17%  Similarity=0.211  Sum_probs=61.0

Q ss_pred             CCceEEEcCCCCC-----CCH----HHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCee
Q 045516          415 GSKTLFVGNLPFS-----VEQ----ADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRA  485 (675)
Q Consensus       415 ~~~tlfV~nLp~~-----~te----~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~  485 (675)
                      ..-||+|..|+..     .-.    .+|.+.|.+||.|+.|+|..++       +||+|.+.+.|.+||.|||..|.||.
T Consensus        14 pD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~-------~fVtF~d~~sAl~AI~ldG~~v~Gr~   86 (95)
T 1ufw_A           14 LDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ-------MLVTFADSHSALSVLDVDGMKVKGRA   86 (95)
T ss_dssp             TTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE-------EEEECSCSHHHHHHHHGGGSEETTEE
T ss_pred             CCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc-------EEEEEcChHHHHHHHhcCCeeeCCeE
Confidence            4569999998743     222    5689999999999999999763       99999999999999999999999999


Q ss_pred             EEEEecc
Q 045516          486 IRLDFAR  492 (675)
Q Consensus       486 i~V~~a~  492 (675)
                      |+|.+..
T Consensus        87 L~V~~k~   93 (95)
T 1ufw_A           87 VKISGPS   93 (95)
T ss_dssp             EEEECCC
T ss_pred             EEEeccC
Confidence            9998753

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.61  E-value=9.2e-08  Score=95.05  Aligned_cols=77  Identities=22%  Similarity=0.279  Sum_probs=65.6

Q ss_pred             CceEEEcCCC-----CCCCHHHHHHHhhhCCCeEEEEEeeCC-----CCCcccEEEEEecCHHHHHHHHH-hCCcccCCe
Q 045516          416 SKTLFVGNLP-----FSVEQADVQNFFSEVAEVVDVRLSSDA-----DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNR  484 (675)
Q Consensus       416 ~~tlfV~nLp-----~~~te~~L~~~F~~~G~I~~v~i~~~~-----~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr  484 (675)
                      .+.|.+.|+-     ..-.+++|++.|.+||.|..|.|+++.     +++++||+||+|.+.++|.+||. |||..|.||
T Consensus       124 s~v~~l~n~v~~~e~~~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr  203 (222)
T 3dxb_A          124 STVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGR  203 (222)
T ss_dssp             CSEEEEESSCCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSS
T ss_pred             cccchhhcCCCHHHHHHHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCe
Confidence            4566666652     334678899999999999999998654     35899999999999999999998 999999999


Q ss_pred             eEEEEecc
Q 045516          485 AIRLDFAR  492 (675)
Q Consensus       485 ~i~V~~a~  492 (675)
                      .|+|.+..
T Consensus       204 ~i~~~~~~  211 (222)
T 3dxb_A          204 KVVAEVYD  211 (222)
T ss_dssp             BCEEEECC
T ss_pred             EEEEEEcC
Confidence            99999975

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.58  E-value=1.8e-07  Score=92.86  Aligned_cols=68  Identities=19%  Similarity=0.398  Sum_probs=60.0

Q ss_pred             HHHHHHHHhhhcccCcEEEEEeccc----CCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEecccc
Q 045516          533 DQVRASLEEHFGSCGEITRISVPKD----YDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVDEAKQ  600 (675)
Q Consensus       533 ~~i~~~L~~~F~~~G~I~~v~i~~d----~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~~a~~  600 (675)
                      +++...|.+.|.+||.|..|.|+++    ..+++++|++||+|.+.++|.+|+. |||++|+||.|++.+...
T Consensus       140 ~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~  212 (222)
T 3dxb_A          140 DDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQ  212 (222)
T ss_dssp             TTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCH
T ss_pred             HHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCH
Confidence            3455679999999999999999854    4456999999999999999999998 999999999999998753

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.56  E-value=2e-07  Score=83.03  Aligned_cols=74  Identities=12%  Similarity=0.113  Sum_probs=64.0

Q ss_pred             CCCceEEEEecCCCC-cCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCC-HHHHHHHHH-h--CCceeC
Q 045516          515 GQAAHTIFIKGFDSS-VGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTD-ADSFNKALE-M--SGTEIG  589 (675)
Q Consensus       515 ~~~~~~lfV~nLp~~-~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~-~e~A~~Al~-l--ng~~~~  589 (675)
                      ...+..|||+||+.. ++.++    |+++|..||.|.+|.|.++..      .|||.|.+ ...|..|+. |  ++..|+
T Consensus        15 ~~~G~il~v~~l~~~~~sred----Lke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~   84 (121)
T 1owx_A           15 EKIGCLLKFSGDLDDQTCRED----LHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLR   84 (121)
T ss_dssp             CCCCCEEEEEESCCSSCCHHH----HHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTT
T ss_pred             ccCCeEEEEecCCCCcCCHHH----HHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEe
Confidence            455899999999999 99887    889999999999999999854      59999999 789999987 7  478899


Q ss_pred             CeeeEEecc
Q 045516          590 GYSLVVDEA  598 (675)
Q Consensus       590 Gr~l~V~~a  598 (675)
                      |..+++...
T Consensus        85 g~~~~~evL   93 (121)
T 1owx_A           85 NKEVTWEVL   93 (121)
T ss_dssp             SSSEEEEEC
T ss_pred             CcEEEEEEC
Confidence            988888654

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.19  E-value=4.4e-06  Score=71.53  Aligned_cols=71  Identities=21%  Similarity=0.193  Sum_probs=65.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhC-----CCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHH-HhCCcccCCeeEEE
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEV-----AEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI-ELNGQMLGNRAIRL  488 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~-----G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al-~l~g~~~~gr~i~V  488 (675)
                      ..++|-|-|||.+++...|+.|+..|     |.|..|.|+.+     -+-|+|+|.+...|.+|. .|||..|.||.|+|
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pD-----H~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~   94 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSD-----FNGAIIIFRDSKFAAKMLMILNGSQFQGKVIRS   94 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETT-----TTEEEEECSCHHHHHHHHHHHSSEEETTEEEEE
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecC-----CCceEEEEccchhhHHHHhhcCCeeecCeEEEe
Confidence            46899999999999999999999999     99999999987     566999999999999998 59999999999998


Q ss_pred             Ee
Q 045516          489 DF  490 (675)
Q Consensus       489 ~~  490 (675)
                      .-
T Consensus        95 gT   96 (117)
T 2l9w_A           95 GT   96 (117)
T ss_dssp             EC
T ss_pred             cC
Confidence            54

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.12  E-value=1.3e-05  Score=68.11  Aligned_cols=89  Identities=18%  Similarity=0.260  Sum_probs=74.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhh-----CCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEE
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSE-----VAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRL  488 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~-----~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V  488 (675)
                      ...++|.|.|||..+.++.|.-||+.     =|+|..|....       +-|+|+|.+...|++.|....+.|.|.+|.|
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~-------~~AvItF~d~~va~rVL~k~~H~L~~~~LsV   78 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG-------CGGVLTFREPADAERVLAQADHELHGAQLSL   78 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET-------TEEEEEESSHHHHHHHHTCSCCBSSSSBCEE
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC-------CcEEEEEcChHHHHHHhcCCcceecCeEEEE
Confidence            45689999999999999999999997     25788888762       6799999999999999998888999999999


Q ss_pred             EeccccCCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcC
Q 045516          489 DFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVG  531 (675)
Q Consensus       489 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~t  531 (675)
                      .....+.                      ..+|++.||+..+.
T Consensus        79 ~P~~~~~----------------------~~r~ll~gl~~~t~   99 (104)
T 2dhx_A           79 RPAPPRA----------------------PARLLLQGLPPGTS   99 (104)
T ss_dssp             EECCCCC----------------------CCCCCCCSCCCCCC
T ss_pred             EcCCCCC----------------------cceEeeecCCCCCC
Confidence            7754332                      56788888887764

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=97.89  E-value=4.4e-05  Score=65.38  Aligned_cols=74  Identities=19%  Similarity=0.229  Sum_probs=65.1

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhh-hcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHH-HhCCceeCCeeeEE
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEH-FGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKAL-EMSGTEIGGYSLVV  595 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~-F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al-~lng~~~~Gr~l~V  595 (675)
                      .++|-|-|||..++...|+.+|..+ +-.-|.|..|.+..|.      +-|+|+|.+...|.+|. .|+|..|.||.|+|
T Consensus        21 ~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~   94 (117)
T 2l9w_A           21 ETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKMLMILNGSQFQGKVIRS   94 (117)
T ss_dssp             TSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHHHHHSSEEETTEEEEE
T ss_pred             CcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHHhhcCCeeecCeEEEe
Confidence            6899999999999999988877765 4455999999999994      56999999999999996 59999999999999


Q ss_pred             ec
Q 045516          596 DE  597 (675)
Q Consensus       596 ~~  597 (675)
                      .-
T Consensus        95 gT   96 (117)
T 2l9w_A           95 GT   96 (117)
T ss_dssp             EC
T ss_pred             cC
Confidence            64

>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=97.49  E-value=0.00018  Score=61.48  Aligned_cols=77  Identities=19%  Similarity=0.197  Sum_probs=66.7

Q ss_pred             ceEEEEecCCCCc-CHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEE
Q 045516          518 AHTIFIKGFDSSV-GEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVV  595 (675)
Q Consensus       518 ~~~lfV~nLp~~~-te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V  595 (675)
                      .++|+|.||+..+ ..++++..|+.+|..|+.+....+.+...      -..|.|.+.++|.+|.. ||+..|+|+.|+|
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSFR------Rirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~   78 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFK------RVRINFSNPLSAADARLRLHKTEFLGKEMKL   78 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTT------EEEEECSSTTHHHHHHHTSTTSEETTEECEE
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcce------EEEEEeCChHHHHHHHHHhccceecCceeEE
Confidence            5889999998866 77788788999999999888877777642      36899999999999976 9999999999999


Q ss_pred             ecccc
Q 045516          596 DEAKQ  600 (675)
Q Consensus       596 ~~a~~  600 (675)
                      .++.+
T Consensus        79 YFgq~   83 (104)
T 1wey_A           79 YFAQT   83 (104)
T ss_dssp             ECCCC
T ss_pred             EecCC
Confidence            99974

>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=97.38  E-value=0.00031  Score=60.00  Aligned_cols=74  Identities=18%  Similarity=0.171  Sum_probs=62.2

Q ss_pred             CCceEEEcCCCCCC-C----HHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEE
Q 045516          415 GSKTLFVGNLPFSV-E----QADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRL  488 (675)
Q Consensus       415 ~~~tlfV~nLp~~~-t----e~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V  488 (675)
                      -.++|+|.||+..+ .    ...|+.+|..|+.+....+.+.     -.-..|.|.+.++|.+|-. ||+..|+|+.|+|
T Consensus         4 ~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkS-----FRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~   78 (104)
T 1wey_A            4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS-----FKRVRINFSNPLSAADARLRLHKTEFLGKEMKL   78 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT-----TTEEEEECSSTTHHHHHHHTSTTSEETTEECEE
T ss_pred             CCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCc-----ceEEEEEeCChHHHHHHHHHhccceecCceeEE
Confidence            35799999998655 2    2678999999999888776643     4567899999999999986 9999999999999


Q ss_pred             Eeccc
Q 045516          489 DFARE  493 (675)
Q Consensus       489 ~~a~~  493 (675)
                      .++..
T Consensus        79 YFgq~   83 (104)
T 1wey_A           79 YFAQT   83 (104)
T ss_dssp             ECCCC
T ss_pred             EecCC
Confidence            99873

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=97.28  E-value=0.00057  Score=60.00  Aligned_cols=71  Identities=17%  Similarity=0.258  Sum_probs=60.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCC-eeEEEEec
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGN-RAIRLDFA  491 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~g-r~i~V~~a  491 (675)
                      ..+.|.|-++|... ...|..+|++||.|+.....     ....+-+|.|.+..+|++||..||..|.| ..|-|..+
T Consensus        23 ~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~-----~~~NWihI~Y~s~~~A~rAL~kNG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           23 DDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS-----NTGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPC   94 (119)
T ss_dssp             GGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC-----SSSSEEEEEESSHHHHHHHHTTTTCEETTTEECEEEEC
T ss_pred             CCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC-----CCCCeEEEEeCCHHHHHHHHHhCCeEecCCEEEEEEEC
Confidence            46889999999885 77899999999999998873     23679999999999999999999999975 55666554

>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=97.20  E-value=0.00094  Score=56.03  Aligned_cols=66  Identities=14%  Similarity=0.214  Sum_probs=55.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-C--CCcccEEEEEecCHHHHHHHHH-hCCcccC
Q 045516          417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-D--GRFKGYGHVEFASVEDAHKAIE-LNGQMLG  482 (675)
Q Consensus       417 ~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~--g~~kG~afV~F~~~e~A~~Al~-l~g~~~~  482 (675)
                      +.|.|++||+++|++++.+.+..+..+....++... .  -.....|||.|.+.+++..... ++|+.|.
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~   71 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEE
Confidence            579999999999999999999999888777776554 1  2245679999999999999997 9998884

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=97.06  E-value=0.0011  Score=58.07  Aligned_cols=71  Identities=15%  Similarity=0.194  Sum_probs=57.9

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCC-eeeEEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGG-YSLVVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~G-r~l~V~  596 (675)
                      .+.|.|-+++......     +-.+|.+||.|........      ..+.+|.|.+..+|.+||..||..|+| ..|-|.
T Consensus        24 ~~wVtVFGFp~~~~~~-----VL~~F~~~G~Iv~~~~~~~------~NWihI~Y~s~~~A~rAL~kNG~ii~g~~mIGV~   92 (119)
T 1wwh_A           24 DTWVTVFGFPQASASY-----ILLQFAQYGNILKHVMSNT------GNWMHIRYQSKLQARKALSKDGRIFGESIMIGVK   92 (119)
T ss_dssp             GGEEEEECCCGGGHHH-----HHHHHHTTSCEEEEEECSS------SSEEEEEESSHHHHHHHHTTTTCEETTTEECEEE
T ss_pred             CCEEEEECCCHHHHHH-----HHHHHHhhCcEEEeccCCC------CCeEEEEeCCHHHHHHHHHhCCeEecCCEEEEEE
Confidence            6889999998876543     6678999999999887322      579999999999999999999999985 666666


Q ss_pred             ccc
Q 045516          597 EAK  599 (675)
Q Consensus       597 ~a~  599 (675)
                      ...
T Consensus        93 p~~   95 (119)
T 1wwh_A           93 PCI   95 (119)
T ss_dssp             ECC
T ss_pred             ECC
Confidence            543

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.88  E-value=0.006  Score=51.83  Aligned_cols=79  Identities=15%  Similarity=0.215  Sum_probs=63.2

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhh-cccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHF-GSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F-~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~  596 (675)
                      ..+|.|.|||..+.++.|.-+|+... +.-|.|..|....        +-|+|.|.+...|.+.|....+.|+|..|.|.
T Consensus         8 ~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k~~H~L~~~~LsV~   79 (104)
T 2dhx_A            8 GVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQADHELHGAQLSLR   79 (104)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTCSCCBSSSSBCEEE
T ss_pred             ccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcCCcceecCeEEEEE
Confidence            68999999999999887555555432 3346888887755        46899999999999999988899999999998


Q ss_pred             ccccCCCC
Q 045516          597 EAKQRGDF  604 (675)
Q Consensus       597 ~a~~r~~~  604 (675)
                      ...++...
T Consensus        80 P~~~~~~~   87 (104)
T 2dhx_A           80 PAPPRAPA   87 (104)
T ss_dssp             ECCCCCCC
T ss_pred             cCCCCCcc
Confidence            77666554

>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=96.51  E-value=0.008  Score=50.47  Aligned_cols=54  Identities=19%  Similarity=0.316  Sum_probs=44.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE  475 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~  475 (675)
                      +-.+.|+| ++|......+|.++|+.||.|. |+.+.|      ..|||.|.+++.|..||.
T Consensus        14 ~r~HVf~l-~FP~ewKt~DI~~lFs~fggv~-I~WidD------TsAlvvf~~~~~a~~al~   67 (100)
T 1whv_A           14 KRDHVLHV-TFPKEWKTSDLYQLFSAFGNIQ-ISWIDD------TSAFVSLSQPEQVQIAVN   67 (100)
T ss_dssp             CCCSEEEE-ECCTTCCHHHHHHHHTTTCSCC-CEEEET------TEEEEECSCHHHHHHHHH
T ss_pred             CCCeEEEE-eCChhhhhHHHHHHhhccCCEE-EEEEcC------CeEEEEecCHHHHHHHHH
Confidence            34566777 9999999999999999999665 444443      589999999999999997

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.44  E-value=0.0036  Score=55.66  Aligned_cols=78  Identities=18%  Similarity=0.210  Sum_probs=57.9

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEE-EEecccCC------------CC-CeeeEEEEEeCCHHHHHHHHHh
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITR-ISVPKDYD------------TG-SVKGIAYLDFTDADSFNKALEM  583 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~-v~i~~d~~------------tG-~~rG~afV~F~~~e~A~~Al~l  583 (675)
                      ...|.|-++|......     +-.+|++||.|.. +.+.+...            .+ ....+..|+|.+..+|.+||..
T Consensus         7 e~~VtVFGFp~~~~~~-----VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~   81 (132)
T 3p3d_A            7 ELAILVFGYPETMANQ-----VIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLE   81 (132)
T ss_dssp             -CEEEEECCCGGGHHH-----HHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTT
T ss_pred             ceEEEEEecCHHHHHH-----HHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHh
Confidence            4678888998877765     4568999999876 32222100            00 1357899999999999999999


Q ss_pred             CCceeCCeeeEEecccc
Q 045516          584 SGTEIGGYSLVVDEAKQ  600 (675)
Q Consensus       584 ng~~~~Gr~l~V~~a~~  600 (675)
                      ||..|+|..|-|....+
T Consensus        82 NG~ii~G~mIGV~Py~~   98 (132)
T 3p3d_A           82 NGAVFNGVLLGVIPYTK   98 (132)
T ss_dssp             TTCEETTEECEEEECCH
T ss_pred             CCeEeCcEEEEEEECCH
Confidence            99999999888877653

>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=96.14  E-value=0.005  Score=51.88  Aligned_cols=53  Identities=19%  Similarity=0.335  Sum_probs=43.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hC
Q 045516          417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LN  477 (675)
Q Consensus       417 ~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~  477 (675)
                      +.|+| ++|......+|..+|+.||.| .|+.+.|      ..|||.|.+++.|..||. ++
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fggv-~I~WidD------TsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDD------TSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSEEE-EEEEEET------TEEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccCCE-EEEEEcC------CeEEEEecCHHHHHHHHHhcc
Confidence            45666 999999999999999999944 4555543      589999999999999998 54

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=95.88  E-value=0.013  Score=52.05  Aligned_cols=76  Identities=12%  Similarity=0.157  Sum_probs=56.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhhCCCeEEEE-EeeC--------C-----CC-CcccEEEEEecCHHHHHHHHHhCCcc
Q 045516          416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVR-LSSD--------A-----DG-RFKGYGHVEFASVEDAHKAIELNGQM  480 (675)
Q Consensus       416 ~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~-i~~~--------~-----~g-~~kG~afV~F~~~e~A~~Al~l~g~~  480 (675)
                      ...|.|=+.|... ...|..+|++||.|+.-. +.+.        .     .. ...++..|.|.+..+|.+||..||..
T Consensus         7 e~~VtVFGFp~~~-~~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~NG~i   85 (132)
T 3p3d_A            7 ELAILVFGYPETM-ANQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLENGAV   85 (132)
T ss_dssp             -CEEEEECCCGGG-HHHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTTTTCE
T ss_pred             ceEEEEEecCHHH-HHHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHhCCeE
Confidence            4567777886554 566888999999997732 1110        0     01 13678899999999999999999999


Q ss_pred             cCCeeEEEEecc
Q 045516          481 LGNRAIRLDFAR  492 (675)
Q Consensus       481 ~~gr~i~V~~a~  492 (675)
                      |.|..|-|.+..
T Consensus        86 i~G~mIGV~Py~   97 (132)
T 3p3d_A           86 FNGVLLGVIPYT   97 (132)
T ss_dssp             ETTEECEEEECC
T ss_pred             eCcEEEEEEECC
Confidence            999977777664

>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=95.62  E-value=0.049  Score=45.51  Aligned_cols=67  Identities=12%  Similarity=0.198  Sum_probs=50.3

Q ss_pred             eEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCC--CeeeEEEEEeCCHHHHHHHHH-hCCceeC
Q 045516          519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTG--SVKGIAYLDFTDADSFNKALE-MSGTEIG  589 (675)
Q Consensus       519 ~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG--~~rG~afV~F~~~e~A~~Al~-lng~~~~  589 (675)
                      ..|.|++||++++++++.+.|..    +..+....++....+.  ..-.-|||.|.+.+++....+ ++|+.|-
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~----~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~   71 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQP----MPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCS----CCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcC----cccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEE
Confidence            47899999999999996655554    4566666665543222  234569999999999999988 9999884

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=95.54  E-value=0.0092  Score=50.32  Aligned_cols=67  Identities=9%  Similarity=0.127  Sum_probs=49.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC--CC-CcccEEEEEecCHHHHHHHHH-hCCcccC
Q 045516          416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA--DG-RFKGYGHVEFASVEDAHKAIE-LNGQMLG  482 (675)
Q Consensus       416 ~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~--~g-~~kG~afV~F~~~e~A~~Al~-l~g~~~~  482 (675)
                      +-.|.|++||+.+|+++|.+.+..+=.+....++...  .+ ..-..|||.|.+.+++....+ ++|..|.
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~   79 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFL   79 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEE
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEE
Confidence            4579999999999999988888776554322222211  11 123568999999999999997 9998873

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.25  E-value=0.008  Score=65.39  Aligned_cols=62  Identities=13%  Similarity=0.163  Sum_probs=46.7

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccC
Q 045516          416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLG  482 (675)
Q Consensus       416 ~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~  482 (675)
                      .|+|||. +|..+++.+|.++|++||.|.++.+..+.    .-|+.|+|.+.+++..++........
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~----g~~~~vef~~~~~~~~~~~~~~~p~~  114 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF----GLYAVVEFCQKESIGSLQNGTHTPXX  114 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS----SEEEEEECC---CCHHHHSSCCCCCC
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC----CeEEEEEeCCHHHHHHHHhccCCCcc
Confidence            3899998 79999999999999999999999998653    47999999999999988764444443

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=92.87  E-value=0.21  Score=42.08  Aligned_cols=69  Identities=13%  Similarity=0.160  Sum_probs=47.9

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCC--CeeeEEEEEeCCHHHHHHHHH-hCCceeCC
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTG--SVKGIAYLDFTDADSFNKALE-MSGTEIGG  590 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG--~~rG~afV~F~~~e~A~~Al~-lng~~~~G  590 (675)
                      +-.|.|+.||++++++++.+.|..+    -.+.+..++....+.  ..-.-|||.|.+.+++..-.+ ++|..|-+
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~----~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D   80 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPL----PAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLD   80 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCC----SSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEEC
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCc----CccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEe
Confidence            5789999999999999955444443    334444443332221  122458999999999999988 99988843

>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=92.67  E-value=0.32  Score=40.81  Aligned_cols=52  Identities=21%  Similarity=0.392  Sum_probs=40.8

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE  582 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~  582 (675)
                      .+.++| +||..+...+    |.++|..||.| .|+.+-|       ..|||.|.+++.|..||.
T Consensus        16 ~HVf~l-~FP~ewKt~D----I~~lFs~fggv-~I~WidD-------TsAlvvf~~~~~a~~al~   67 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSD----LYQLFSAFGNI-QISWIDD-------TSAFVSLSQPEQVQIAVN   67 (100)
T ss_dssp             CSEEEE-ECCTTCCHHH----HHHHHTTTCSC-CCEEEET-------TEEEEECSCHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHH----HHHHhhccCCE-EEEEEcC-------CeEEEEecCHHHHHHHHH
Confidence            566667 9999999988    78899999833 2333333       469999999999999998

>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=92.47  E-value=0.16  Score=42.80  Aligned_cols=54  Identities=19%  Similarity=0.342  Sum_probs=42.6

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hC
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MS  584 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-ln  584 (675)
                      .+.++| +||..+...+    |.++|..||. ..|+.+-|       ..|||.|.+++.|..||. ++
T Consensus         6 ~HV~~l-~FP~ewKt~D----i~~lFs~fgg-v~I~WidD-------TsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            6 DHVLHV-TFPKEWKTSD----LYQLFSAFGN-IQISWIDD-------TSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEEE-ECCTTCCHHH----HHHHTTTSEE-EEEEEEET-------TEEEEEEEEECHHHHHHHHHT
T ss_pred             CeEEEE-eCChhhhhHH----HHHHHhccCC-EEEEEEcC-------CeEEEEecCHHHHHHHHHhcc
Confidence            456666 9999999988    8899999993 34444444       369999999999999998 54

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=86.32  E-value=0.36  Score=52.42  Aligned_cols=56  Identities=14%  Similarity=0.237  Sum_probs=42.5

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHh
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEM  583 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~l  583 (675)
                      .+.|||. ++..+++.+    |.++|++||.|..+.+..+.     .-|+.|+|.+.+.+..++..
T Consensus        53 ~rsv~v~-~~~~~~~~~----l~~y~~~~g~i~~~~~~~~~-----g~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENK----FLKYLSQFGPINNHFFYESF-----GLYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             HTEEEEE-ECCC---CH----HHHHHGGGSCCCCEEEECSS-----SEEEEEECC---CCHHHHSS
T ss_pred             cceEEEE-cCCCCCHHH----HHHHHHhcCCcceEEEEccC-----CeEEEEEeCCHHHHHHHHhc
Confidence            6899997 688888888    88999999999999988764     37999999999999988753

>2pk2_A Cyclin-T1, protein TAT; TAR, twinning, transcription regulation P- TEFB, cell cycle; 2.67A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 2w2h_C

Probab=80.35  E-value=0.34  Score=51.12  Aligned_cols=17  Identities=12%  Similarity=0.124  Sum_probs=10.9

Q ss_pred             CCcCHHHHHHHHHhhhc
Q 045516          528 SSVGEDQVRASLEEHFG  544 (675)
Q Consensus       528 ~~~te~~i~~~L~~~F~  544 (675)
                      ..++.++|++....+..
T Consensus       227 ~~vt~~~l~~i~~~il~  243 (358)
T 2pk2_A          227 ATVTLELLDELTHEFLQ  243 (358)
T ss_dssp             SSCCHHHHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHHHH
Confidence            35677777776666644

---

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	675
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	6e-24
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	5e-17
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	4e-10
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	6e-17
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	1e-16
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	1e-16
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	6e-08
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	2e-16
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	2e-11
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	3e-16
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	9e-08
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	1e-15
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	1e-07
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	1e-15
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	5e-10
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-15
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-08
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	2e-15
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	4e-11
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	1e-14
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	8e-06
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	2e-14
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	5e-08
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-14
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-09
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-14
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-08
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	3e-14
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	2e-09
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	4e-14
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	4e-07
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	5e-14
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	8e-09
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	5e-14
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	3e-08
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	6e-14
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	1e-13
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	7e-08
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	1e-13
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	2e-08
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-13
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-09
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	2e-13
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	2e-13
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	4e-09
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-13
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-08
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	2e-13
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	4e-05
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-13
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	6e-10
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	3e-13
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	1e-06
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	3e-13
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	3e-13
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	8e-06
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	3e-13
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	4e-07
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	4e-13
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	7e-08
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	5e-13
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	6e-07
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	5e-13
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	2e-06
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	5e-13
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	1e-08
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	7e-13
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	5e-07
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	8e-13
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	1e-04
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	1e-12
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	5e-06
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	1e-12
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	1e-08
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-12
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	6e-06
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	2e-12
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	2e-07
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	2e-12
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	8e-08
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	2e-12
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	3e-12
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	3e-08
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	3e-12
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	4e-12
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	8e-08
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	7e-12
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	9e-12
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	1e-11
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	3e-06
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	1e-11
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	1e-11
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	1e-05
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-11
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	1e-06
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	2e-11
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	1e-06
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	4e-11
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	2e-05
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-11
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-07
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	6e-11
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	5e-09
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	6e-11
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	3e-06
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	7e-11
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	9e-11
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	9e-11
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	4e-09
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	1e-10
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	2e-10
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	2e-10
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	3e-10
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	4e-10
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	6e-10
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	2e-07
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 6e-10
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	2e-09
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	3e-09
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	3e-09
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	3e-09
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	2e-04
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-09
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	5e-09
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	5e-09
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	5e-09
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	9e-09
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	0.004
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	2e-08
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	1e-07
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	2e-07
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-07
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-04
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	2e-06
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	6e-05
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	1e-04

>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 = 97.4 bits (241), Expect = 6e-24
 Identities = 40/189 (21%), Positives = 74/189 (39%), Gaps = 17/189 (8%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAI 474
            + LF+G L F      +++ F +   + D  +  D +  R +G+G V +A+VE+   A+
Sbjct: 6   LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 65

Query: 475 ELNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQ 534
                 +  R +    A  R                          IF+ G      E  
Sbjct: 66  NARPHKVDGRVVEPKRAVSREDSQRPGAHLTV------------KKIFVGGIKEDTEEHH 113

Query: 535 VRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLV 594
               L ++F   G+I  I +  D  +G  +G A++ F D DS +K +      + G++  
Sbjct: 114 ----LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCE 169

Query: 595 VDEAKQRGD 603
           V +A  + +
Sbjct: 170 VRKALSKQE 178

>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 = 74.6 bits (183), Expect = 5e-17
 Identities = 25/88 (28%), Positives = 42/88 (47%), Gaps = 4/88 (4%)

Query: 411 PQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD--GRFKGYGHVEFASVE 468
           P+   +  + V N+PF   Q +++  FS   E+  VRL       G  +G+G V+F + +
Sbjct: 3   PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQ 62

Query: 469 DAHKAIE--LNGQMLGNRAIRLDFARER 494
           DA KA     +   L  R + L++A   
Sbjct: 63  DAKKAFNALCHSTHLYGRRLVLEWADSE 90

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 54.9 bits (132), Expect = 4e-10
 Identities = 20/91 (21%), Positives = 37/91 (40%), Gaps = 7/91 (7%)

Query: 514 RGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYD-TGSVKGIAYLDFT 572
           + Q    I ++       + +    + E F + GE+  + +PK    TG+ +G  ++DF 
Sbjct: 4   KKQTTSKILVRNIPFQANQRE----IRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFI 59

Query: 573 DADSFNKALE--MSGTEIGGYSLVVDEAKQR 601
                 KA       T + G  LV++ A   
Sbjct: 60  TKQDAKKAFNALCHSTHLYGRRLVLEWADSE 90

>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 = 74.3 bits (182), Expect = 6e-17
 Identities = 29/97 (29%), Positives = 49/97 (50%), Gaps = 1/97 (1%)

Query: 399 ESGKKAAQTPFTPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADG-RFK 457
           +S  +      +P+   ++T+F   L   +   D+++FFS V +V DVR+ SD +  R K
Sbjct: 1   KSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSK 60

Query: 458 GYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARER 494
           G  +VEF  ++    AI L GQ L    I +  ++  
Sbjct: 61  GIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQAE 97

>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 = 73.0 bits (179), Expect = 1e-16
 Identities = 25/74 (33%), Positives = 33/74 (44%), Gaps = 1/74 (1%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LN 477
           L V NL F V  AD+Q  F+E   +    +  D  GR  G   V F    DA KA++  N
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 62

Query: 478 GQMLGNRAIRLDFA 491
           G  L  R + +   
Sbjct: 63  GVPLDGRPMNIQLV 76

>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 = 73.1 bits (179), Expect = 1e-16
 Identities = 25/81 (30%), Positives = 39/81 (48%), Gaps = 2/81 (2%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAI 474
           S TL+VGNL F   +  +   FS+  ++  + +  D       G+  VE+ S  DA  A+
Sbjct: 7   SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAM 66

Query: 475 E-LNGQMLGNRAIRLDFARER 494
             +NG  L +R IR D+    
Sbjct: 67  RYINGTRLDDRIIRTDWDAGF 87

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.4 bits (115), Expect = 6e-08
 Identities = 17/100 (17%), Positives = 37/100 (37%), Gaps = 14/100 (14%)

Query: 516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDAD 575
           + + T+++        E+Q    + E F   G+I +I +  D    +  G  ++++    
Sbjct: 5   KKSCTLYVGNLSFYTTEEQ----IYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRA 60

Query: 576 SFNKALE-MSGTEIGGYSLVVDEAKQRGDFGSGGGRSGGR 614
               A+  ++GT +    +  D            G   GR
Sbjct: 61  DAENAMRYINGTRLDDRIIRTDWDA---------GFKEGR 91

>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 = 72.3 bits (177), Expect = 2e-16
 Identities = 20/77 (25%), Positives = 42/77 (54%), Gaps = 2/77 (2%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFK-GYGHVEFASVEDAHKAIE- 475
           +L+VG+L   V +A +   FS    ++ +R+  D   R   GY +V F    DA +A++ 
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 476 LNGQMLGNRAIRLDFAR 492
           +N  ++  + +R+ +++
Sbjct: 62  MNFDVIKGKPVRIMWSQ 78

>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 = 58.0 bits (140), Expect = 2e-11
 Identities = 20/82 (24%), Positives = 35/82 (42%), Gaps = 5/82 (6%)

Query: 520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNK 579
           ++++      V E      L E F   G I  I V +D  T    G AY++F       +
Sbjct: 2   SLYVGDLHPDVTEAM----LYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAER 57

Query: 580 ALE-MSGTEIGGYSLVVDEAKQ 600
           AL+ M+   I G  + +  +++
Sbjct: 58  ALDTMNFDVIKGKPVRIMWSQR 79

>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 = 72.3 bits (177), Expect = 3e-16
 Identities = 18/84 (21%), Positives = 39/84 (46%), Gaps = 6/84 (7%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE 475
           + T++ G +   +    ++  FS   +++++R+        KGY  V F++ E A  AI 
Sbjct: 18  NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF-----PEKGYSFVRFSTHESAAHAIV 72

Query: 476 -LNGQMLGNRAIRLDFARERGAYT 498
            +NG  +    ++  + +E    T
Sbjct: 73  SVNGTTIEGHVVKCYWGKESPDMT 96

>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 = 48.0 bits (114), Expect = 9e-08
 Identities = 18/85 (21%), Positives = 35/85 (41%), Gaps = 11/85 (12%)

Query: 520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNK 579
           T++  G  S + +      + + F   G+I  I V  +     V+      F+  +S   
Sbjct: 20  TVYCGGIASGLTDQL----MRQTFSPFGQIMEIRVFPEKGYSFVR------FSTHESAAH 69

Query: 580 ALE-MSGTEIGGYSLVVDEAKQRGD 603
           A+  ++GT I G+ +     K+  D
Sbjct: 70  AIVSVNGTTIEGHVVKCYWGKESPD 94

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 70.5 bits (172), Expect = 1e-15
 Identities = 23/82 (28%), Positives = 42/82 (51%), Gaps = 5/82 (6%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE 475
           ++TL   NL F++ + +++  F +  E+  V       G+ KG  ++EF S  DA K +E
Sbjct: 16  ARTLLAKNLSFNITEDELKEVFEDALEIRLVSQD----GKSKGIAYIEFKSEADAEKNLE 71

Query: 476 -LNGQMLGNRAIRLDFARERGA 496
              G  +  R++ L +  E+G 
Sbjct: 72  EKQGAEIDGRSVSLYYTGEKGG 93

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 48.1 bits (114), Expect = 1e-07
 Identities = 25/88 (28%), Positives = 39/88 (44%), Gaps = 10/88 (11%)

Query: 516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDAD 575
           +AA T+  K    ++ ED+    L+E F        + +      G  KGIAY++F    
Sbjct: 14  RAARTLLAKNLSFNITEDE----LKEVFEDA-----LEIRLVSQDGKSKGIAYIEFKSEA 64

Query: 576 SFNKALE-MSGTEIGGYSLVVDEAKQRG 602
              K LE   G EI G S+ +    ++G
Sbjct: 65  DAEKNLEEKQGAEIDGRSVSLYYTGEKG 92

>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 = 70.0 bits (171), Expect = 1e-15
 Identities = 20/79 (25%), Positives = 37/79 (46%), Gaps = 2/79 (2%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDV-RLSSDADGRFKGYGHVEFASVEDAHKAI 474
           +  L V  LP  +   ++   F  +  +     +     G   GY  V+F S  D+ +AI
Sbjct: 2   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 61

Query: 475 E-LNGQMLGNRAIRLDFAR 492
           + LNG  + N+ +++ +AR
Sbjct: 62  KVLNGITVRNKRLKVSYAR 80

>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 = 54.2 bits (130), Expect = 5e-10
 Identities = 18/81 (22%), Positives = 35/81 (43%), Gaps = 5/81 (6%)

Query: 520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNK 579
            + +      + + +    L   F + G I    + +DY TG   G A++DFT      +
Sbjct: 4   NLIVNYLPQDMTDRE----LYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 59

Query: 580 ALE-MSGTEIGGYSLVVDEAK 599
           A++ ++G  +    L V  A+
Sbjct: 60  AIKVLNGITVRNKRLKVSYAR 80

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 69.7 bits (170), Expect = 2e-15
 Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 5/81 (6%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD----GRFKGYGHVEFASVEDAHKAI 474
           LF+ NL FS  +  ++  FS+V  +    +S   +        G+G VE+   E A KA+
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 475 E-LNGQMLGNRAIRLDFARER 494
           + L G  +    + +  +   
Sbjct: 61  KQLQGHTVDGHKLEVRISERA 81

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 49.6 bits (118), Expect = 2e-08
 Identities = 17/85 (20%), Positives = 33/85 (38%), Gaps = 8/85 (9%)

Query: 521 IFIKGFDSSVGEDQVRASLEEHFGSCGEITR---ISVPKDYDTGSVKGIAYLDFTDADSF 577
           +FIK  + S  E+     L+  F   G I                  G  ++++   +  
Sbjct: 1   LFIKNLNFSTTEET----LKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQA 56

Query: 578 NKALE-MSGTEIGGYSLVVDEAKQR 601
            KAL+ + G  + G+ L V  +++ 
Sbjct: 57  QKALKQLQGHTVDGHKLEVRISERA 81

>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 = 69.2 bits (169), Expect = 2e-15
 Identities = 17/74 (22%), Positives = 32/74 (43%), Gaps = 1/74 (1%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAIELN 477
           +F+G L +   Q  ++ +F +  EV +  +  D    R +G+G V F       K +  +
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62

Query: 478 GQMLGNRAIRLDFA 491
              L ++ I    A
Sbjct: 63  RHELDSKTIDPKVA 76

>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 = 57.3 bits (138), Expect = 4e-11
 Identities = 20/78 (25%), Positives = 33/78 (42%), Gaps = 4/78 (5%)

Query: 521 IFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKA 580
           +FI G      ++     L E+FG  GE+    V +D  T   +G  ++ F D    +K 
Sbjct: 3   MFIGGLSWQTTQEG----LREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV 58

Query: 581 LEMSGTEIGGYSLVVDEA 598
           L  S  E+   ++    A
Sbjct: 59  LAQSRHELDSKTIDPKVA 76

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 68.1 bits (166), Expect = 1e-14
 Identities = 16/83 (19%), Positives = 39/83 (46%), Gaps = 3/83 (3%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE 475
           ++ L++ NLP+ +   ++ + F +   +  +R         +G  +V +  + DA  A +
Sbjct: 7   NRILYIRNLPYKITAEEMYDIFGKYGPIRQIR--VGNTPETRGTAYVVYEDIFDAKNACD 64

Query: 476 -LNGQMLGNRAIRLDFARERGAY 497
            L+G  + NR + + +     A+
Sbjct: 65  HLSGFNVCNRYLVVLYYNANRAF 87

>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 = 43.1 bits (101), Expect = 8e-06
 Identities = 17/83 (20%), Positives = 32/83 (38%), Gaps = 8/83 (9%)

Query: 520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNK 579
            ++I+     +  ++    + + FG  G I +I V         +G AY+ + D      
Sbjct: 9   ILYIRNLPYKITAEE----MYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKN 61

Query: 580 ALE-MSGTEIGGYSLVVDEAKQR 601
           A + +SG  +    LVV      
Sbjct: 62  ACDHLSGFNVCNRYLVVLYYNAN 84

>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 = 67.0 bits (163), Expect = 2e-14
 Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 2/81 (2%)

Query: 415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI 474
           G   +F+ NL  S++   + + FS    ++  ++  D +G    YG V F + E A +AI
Sbjct: 7   GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKG-YGFVHFETQEAAERAI 65

Query: 475 E-LNGQMLGNRAIRLDFARER 494
           E +NG +L +R + +   + R
Sbjct: 66  EKMNGMLLNDRKVFVGRFKSR 86

>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 = 48.5 bits (115), Expect = 5e-08
 Identities = 26/97 (26%), Positives = 41/97 (42%), Gaps = 11/97 (11%)

Query: 508 SFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIA 567
           S +K G G     IFIK  D S+        L + F + G I    V  D +    KG  
Sbjct: 2   SLRKSGVG----NIFIKNLDKSIDNKA----LYDTFSAFGNILSCKVVCDENGS--KGYG 51

Query: 568 YLDFTDADSFNKALE-MSGTEIGGYSLVVDEAKQRGD 603
           ++ F   ++  +A+E M+G  +    + V   K R +
Sbjct: 52  FVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKE 88

>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 = 67.1 bits (163), Expect = 2e-14
 Identities = 18/92 (19%), Positives = 44/92 (47%), Gaps = 9/92 (9%)

Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD------ADGRFKGYGHVEFASVEDA 470
           + L+VGN+PF + +  + +FF+    +  +  +           + K +  +EF SV++ 
Sbjct: 2   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 61

Query: 471 HKAIELNGQMLGNRAIRLDFARERGAYTPYSG 502
            +A+  +G +   +++++    +   Y P  G
Sbjct: 62  TQAMAFDGIIFQGQSLKIRRPHD---YQPLPG 90

>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 = 53.2 bits (127), Expect = 2e-09
 Identities = 13/87 (14%), Positives = 29/87 (33%), Gaps = 9/87 (10%)

Query: 518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPK-----DYDTGSVKGIAYLDFT 572
           A  +++      + E+ +     + F +   +  ++               K  A+L+F 
Sbjct: 1   ARRLYVGNIPFGITEEAMM----DFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFR 56

Query: 573 DADSFNKALEMSGTEIGGYSLVVDEAK 599
             D   +A+   G    G SL +    
Sbjct: 57  SVDETTQAMAFDGIIFQGQSLKIRRPH 83

>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 = 66.6 bits (162), Expect = 2e-14
 Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 2/81 (2%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRF-KGYGHVEFASVEDAHKAI 474
            + L+VG L   V+   +   F    ++ D+++  D +    +G+  VEF   EDA  AI
Sbjct: 5   KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 64

Query: 475 E-LNGQMLGNRAIRLDFARER 494
           + +N   L  R IR++ A+  
Sbjct: 65  DNMNESELFGRTIRVNLAKPM 85

>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 = 50.0 bits (119), Expect = 2e-08
 Identities = 23/83 (27%), Positives = 43/83 (51%), Gaps = 5/83 (6%)

Query: 520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNK 579
            +++ G    V +      L   F   G+IT I +P DY+T   +G A+++F  A+    
Sbjct: 7   VLYVGGLAEEVDDKV----LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 62

Query: 580 ALE-MSGTEIGGYSLVVDEAKQR 601
           A++ M+ +E+ G ++ V+ AK  
Sbjct: 63  AIDNMNESELFGRTIRVNLAKPM 85

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.9 bits (160), Expect = 3e-14
 Identities = 29/80 (36%), Positives = 44/80 (55%), Gaps = 3/80 (3%)

Query: 416 SKT-LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKA 473
           SKT L V  LP ++ Q + ++ F  + E+   +L  D   G+  GYG V +   +DA KA
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 474 IE-LNGQMLGNRAIRLDFAR 492
           I  LNG  L  + I++ +AR
Sbjct: 61  INTLNGLRLQTKTIKVSYAR 80

>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 = 52.8 bits (126), Expect = 2e-09
 Identities = 16/81 (19%), Positives = 36/81 (44%), Gaps = 5/81 (6%)

Query: 520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNK 579
            + +     ++ +++        FGS GEI    + +D  TG   G  ++++ D     K
Sbjct: 4   NLIVNYLPQNMTQEE----FRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEK 59

Query: 580 ALE-MSGTEIGGYSLVVDEAK 599
           A+  ++G  +   ++ V  A+
Sbjct: 60  AINTLNGLRLQTKTIKVSYAR 80

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 65.9 bits (160), Expect = 4e-14
 Identities = 13/82 (15%), Positives = 36/82 (43%), Gaps = 3/82 (3%)

Query: 416 SKTLFVGNLPFSV-EQADVQNFFSEVAEVVDVRLSSDADG--RFKGYGHVEFASVEDAHK 472
            + + + NL   + ++  ++  F     +  + + +             + F + + A +
Sbjct: 4   GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAER 63

Query: 473 AIELNGQMLGNRAIRLDFARER 494
           A+++N  +LGNR I +  A ++
Sbjct: 64  ALQMNRSLLGNREISVSLADKK 85

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 45.9 bits (108), Expect = 4e-07
 Identities = 19/83 (22%), Positives = 40/83 (48%), Gaps = 4/83 (4%)

Query: 520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDY-DTGSVKGIAYLDFTDADSFN 578
            I I+   + + ++ +   L E F   G I +I++P    +       A++ F + DS  
Sbjct: 6   EIMIRNLSTELLDENL---LRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAE 62

Query: 579 KALEMSGTEIGGYSLVVDEAKQR 601
           +AL+M+ + +G   + V  A ++
Sbjct: 63  RALQMNRSLLGNREISVSLADKK 85

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.8 bits (160), Expect = 5e-14
 Identities = 15/84 (17%), Positives = 40/84 (47%), Gaps = 7/84 (8%)

Query: 416 SKTLFVGNLPFSVEQADVQ----NFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAH 471
           + T+++ NL   +++ +++      FS   +++D+ +      + +G   V F  V  A 
Sbjct: 3   NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILV--SRSLKMRGQAFVIFKEVSSAT 60

Query: 472 KAIE-LNGQMLGNRAIRLDFARER 494
            A+  + G    ++ +R+ +A+  
Sbjct: 61  NALRSMQGFPFYDKPMRIQYAKTD 84

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.2 bits (122), Expect = 8e-09
 Identities = 23/86 (26%), Positives = 38/86 (44%), Gaps = 4/86 (4%)

Query: 519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFN 578
           HTI+I   +  + +D+++ SL   F   G+I  I V +       +G A++ F +  S  
Sbjct: 4   HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKM---RGQAFVIFKEVSSAT 60

Query: 579 KALE-MSGTEIGGYSLVVDEAKQRGD 603
            AL  M G       + +  AK   D
Sbjct: 61  NALRSMQGFPFYDKPMRIQYAKTDSD 86

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 65.5 bits (159), Expect = 5e-14
 Identities = 23/88 (26%), Positives = 43/88 (48%), Gaps = 3/88 (3%)

Query: 411 PQ-SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGY-GHVEFASVE 468
           PQ S     LFV ++    ++ ++Q  F +  E+ ++ L+ D    F      VE+ + +
Sbjct: 1   PQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHK 60

Query: 469 DAHKAIE-LNGQMLGNRAIRLDFARERG 495
            A  A E LNG  +  + I++D+   +G
Sbjct: 61  QALAAKEALNGAEIMGQTIQVDWCFVKG 88

>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 = 49.3 bits (117), Expect = 3e-08
 Identities = 24/85 (28%), Positives = 38/85 (44%), Gaps = 5/85 (5%)

Query: 519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFN 578
             +F+        ED+    ++E F   GEI  I +  D  TG  KG A +++       
Sbjct: 8   WILFVTSIHEEAQEDE----IQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQAL 63

Query: 579 KALE-MSGTEIGGYSLVVDEAKQRG 602
            A E ++G EI G ++ VD    +G
Sbjct: 64  AAKEALNGAEIMGQTIQVDWCFVKG 88

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.5 bits (159), Expect = 6e-14
 Identities = 16/78 (20%), Positives = 37/78 (47%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE 475
           ++++++   P      D++ +  +  +V+++++       FKG   V F S+E A K +E
Sbjct: 6   NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE 65

Query: 476 LNGQMLGNRAIRLDFARE 493
             GQ      + + F  +
Sbjct: 66  TPGQKYKETDLLILFKDD 83

>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 = 64.6 bits (157), Expect = 1e-13
 Identities = 18/78 (23%), Positives = 33/78 (42%), Gaps = 4/78 (5%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFK-GYGHVEFASVEDAHKAIE- 475
            L+V NLP ++    +   F +   +V   +  D       G   V +   E+A +AI  
Sbjct: 8   NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 67

Query: 476 LNGQML--GNRAIRLDFA 491
           LN  +   G++ + +  A
Sbjct: 68  LNNVIPEGGSQPLSVRLA 85

>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 = 48.0 bits (114), Expect = 7e-08
 Identities = 18/82 (21%), Positives = 39/82 (47%), Gaps = 7/82 (8%)

Query: 520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNK 579
            +++     ++ +DQ    L+  FG  G I + ++ +D  TG  +G+A++ +   +   +
Sbjct: 8   NLYVTNLPRTITDDQ----LDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQE 63

Query: 580 ALE-MSGTEIGGYS--LVVDEA 598
           A+  ++     G S  L V  A
Sbjct: 64  AISALNNVIPEGGSQPLSVRLA 85

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.3 bits (156), Expect = 1e-13
 Identities = 18/76 (23%), Positives = 35/76 (46%), Gaps = 1/76 (1%)

Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAIE 475
           + LF+G L F      +++ F +   + D  +  D +  R +G+G V +A+VE+   A+ 
Sbjct: 7   RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66

Query: 476 LNGQMLGNRAIRLDFA 491
                +  R +    A
Sbjct: 67  ARPHKVDGRVVEPKRA 82

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.0 bits (119), Expect = 2e-08
 Identities = 15/79 (18%), Positives = 31/79 (39%), Gaps = 4/79 (5%)

Query: 520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNK 579
            +FI G      ++     L  HF   G +T   V +D +T   +G  ++ +   +  + 
Sbjct: 8   KLFIGGLSFETTDES----LRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 63

Query: 580 ALEMSGTEIGGYSLVVDEA 598
           A+     ++ G  +    A
Sbjct: 64  AMNARPHKVDGRVVEPKRA 82

>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 = 64.3 bits (156), Expect = 1e-13
 Identities = 22/82 (26%), Positives = 35/82 (42%), Gaps = 2/82 (2%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAI 474
           +  LF+G LP  +    V+   +    +    L  D A G  KGY   E+  +    +AI
Sbjct: 1   AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 60

Query: 475 E-LNGQMLGNRAIRLDFARERG 495
             LNG  LG++ + +  A    
Sbjct: 61  AGLNGMQLGDKKLLVQRASVGA 82

>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 = 51.9 bits (124), Expect = 3e-09
 Identities = 24/86 (27%), Positives = 45/86 (52%), Gaps = 5/86 (5%)

Query: 518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSF 577
           AH +FI G  + + +DQ    ++E   S G +   ++ KD  TG  KG A+ ++ D +  
Sbjct: 1   AHKLFIGGLPNYLNDDQ----VKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVT 56

Query: 578 NKALE-MSGTEIGGYSLVVDEAKQRG 602
           ++A+  ++G ++G   L+V  A    
Sbjct: 57  DQAIAGLNGMQLGDKKLLVQRASVGA 82

>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 = 64.3 bits (156), Expect = 2e-13
 Identities = 25/86 (29%), Positives = 44/86 (51%), Gaps = 2/86 (2%)

Query: 410 TPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVED 469
           +      K L V N+PF     D++  F +  +++DV +  + +   KG+G V F +  D
Sbjct: 5   SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-ERGSKGFGFVTFENSAD 63

Query: 470 AHKAIE-LNGQMLGNRAIRLDFARER 494
           A +A E L+G ++  R I ++ A  R
Sbjct: 64  ADRAREKLHGTVVEGRKIEVNNATAR 89

>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 = 63.6 bits (154), Expect = 2e-13
 Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 1/74 (1%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRF-KGYGHVEFASVEDAHKAIELN 477
           +FVG L  +    DV+++F +  +V D  L  D      +G+G V F S +   K  E++
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61

Query: 478 GQMLGNRAIRLDFA 491
              + N+ +    A
Sbjct: 62  FHEINNKMVECKKA 75

>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 = 51.7 bits (123), Expect = 4e-09
 Identities = 15/78 (19%), Positives = 30/78 (38%), Gaps = 4/78 (5%)

Query: 521 IFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKA 580
           IF+ G   +   +     ++ +F   G++    +  D  T   +G  ++ F   D   K 
Sbjct: 2   IFVGGLSVNTTVED----VKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKV 57

Query: 581 LEMSGTEIGGYSLVVDEA 598
            E+   EI    +   +A
Sbjct: 58  CEIHFHEINNKMVECKKA 75

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.5 bits (154), Expect = 2e-13
 Identities = 20/70 (28%), Positives = 34/70 (48%), Gaps = 1/70 (1%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRF-KGYGHVEFASVEDAHKAIELN 477
           +F+G L +   + D++++FS+  EVVD  L  D      +G+G V F   E   K ++  
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61

Query: 478 GQMLGNRAIR 487
              L  + I 
Sbjct: 62  EHKLNGKVID 71

>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 = 49.2 bits (117), Expect = 2e-08
 Identities = 16/78 (20%), Positives = 36/78 (46%), Gaps = 4/78 (5%)

Query: 521 IFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKA 580
           +FI G      +      L+++F   GE+   ++  D  TG  +G  ++ F +++S +K 
Sbjct: 2   MFIGGLSWDTTKKD----LKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKV 57

Query: 581 LEMSGTEIGGYSLVVDEA 598
           ++    ++ G  +    A
Sbjct: 58  MDQKEHKLNGKVIDPKRA 75

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 63.8 bits (155), Expect = 2e-13
 Identities = 20/85 (23%), Positives = 37/85 (43%), Gaps = 6/85 (7%)

Query: 415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI 474
               LFVGNLP  + + +++  F +  +  +V        + KG+G +   +   A  A 
Sbjct: 7   QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVF-----IHKDKGFGFIRLETRTLAEIAK 61

Query: 475 E-LNGQMLGNRAIRLDFARERGAYT 498
             L+   L  + +R+ FA    + T
Sbjct: 62  VELDNMPLRGKQLRVRFACHSASLT 86

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.3 bits (94), Expect = 4e-05
 Identities = 12/83 (14%), Positives = 26/83 (31%), Gaps = 11/83 (13%)

Query: 520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNK 579
            +F+      + E++    + + F   G+   + + KD   G ++               
Sbjct: 10  RLFVGNLPPDITEEE----MRKLFEKYGKAGEVFIHKDKGFGFIR------LETRTLAEI 59

Query: 580 ALE-MSGTEIGGYSLVVDEAKQR 601
           A   +    + G  L V  A   
Sbjct: 60  AKVELDNMPLRGKQLRVRFACHS 82

>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 = 64.3 bits (156), Expect = 2e-13
 Identities = 19/80 (23%), Positives = 38/80 (47%), Gaps = 1/80 (1%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAI 474
            + LF+G L F   +  ++N++ +  ++ D  +  D A  R +G+G V F+S+ +   A+
Sbjct: 20  FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM 79

Query: 475 ELNGQMLGNRAIRLDFARER 494
                 +  R +    A  R
Sbjct: 80  AARPHSIDGRVVEPKRAVAR 99

>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 = 54.7 bits (131), Expect = 6e-10
 Identities = 17/87 (19%), Positives = 33/87 (37%), Gaps = 4/87 (4%)

Query: 519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFN 578
             +FI G      E+     L  ++   G++T   V +D  +   +G  ++ F+     +
Sbjct: 21  RKLFIGGLSFETTEES----LRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVD 76

Query: 579 KALEMSGTEIGGYSLVVDEAKQRGDFG 605
            A+      I G  +    A  R + G
Sbjct: 77  AAMAARPHSIDGRVVEPKRAVAREESG 103

>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 = 63.5 bits (154), Expect = 3e-13
 Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 2/79 (2%)

Query: 415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVD-VRLSSDADGRFKGYGHVEFASVEDAHKA 473
           G   + V N+PF+V   ++ +FF     +   V L  +  G   G   V F S ++A  A
Sbjct: 8   GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 67

Query: 474 IE-LNGQMLGNRAIRLDFA 491
           +  LN + +G+R ++L   
Sbjct: 68  VIDLNDRPIGSRKVKLVLG 86

>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 = 44.7 bits (105), Expect = 1e-06
 Identities = 14/81 (17%), Positives = 27/81 (33%), Gaps = 5/81 (6%)

Query: 519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFN 578
             I ++    +V  D+    + + F     I      K  + G   G A + F   D   
Sbjct: 10  TIIKVQNMPFTVSIDE----ILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEAT 65

Query: 579 KALE-MSGTEIGGYSLVVDEA 598
            A+  ++   IG   + +   
Sbjct: 66  AAVIDLNDRPIGSRKVKLVLG 86

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.2 bits (153), Expect = 3e-13
 Identities = 24/80 (30%), Positives = 41/80 (51%), Gaps = 3/80 (3%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRL--SSDADGRFKGYGHVEFASVEDAHKAIE- 475
           +F+GNL   +++  + + FS    ++           G  KGY  + FAS + +  AIE 
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 476 LNGQMLGNRAIRLDFARERG 495
           +NGQ L NR I + +A ++ 
Sbjct: 61  MNGQYLCNRPITVSYAFKKD 80

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.5 bits (154), Expect = 3e-13
 Identities = 20/80 (25%), Positives = 33/80 (41%), Gaps = 2/80 (2%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRF-KGYGHVEFASVEDAHKAI 474
           +  L V  LP+   + D++ +FS   EV+ V++  D      KG+G V F   E   K +
Sbjct: 8   TSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVM 67

Query: 475 ELNGQMLGNRAIRLDFARER 494
                M+  R         +
Sbjct: 68  S-QRHMIDGRWCDCKLPNSK 86

>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 = 42.7 bits (100), Expect = 8e-06
 Identities = 19/84 (22%), Positives = 33/84 (39%), Gaps = 5/84 (5%)

Query: 520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNK 579
            + + G      E      L+E+F + GE+  + V KD  TG  KG  ++ FT+ ++  K
Sbjct: 10  DLIVLGLPWKTTEQD----LKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVK 65

Query: 580 ALEMSGTEIGGYSLVVDEAKQRGD 603
            +      I G          +  
Sbjct: 66  VMS-QRHMIDGRWCDCKLPNSKQS 88

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.2 bits (153), Expect = 3e-13
 Identities = 23/74 (31%), Positives = 34/74 (45%), Gaps = 2/74 (2%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKG-YGHVEFASVEDAHKAI 474
           +  L V  L     + D++  FS+   + DV +  D   R    +  V F +V+DA +A 
Sbjct: 9   NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 68

Query: 475 E-LNGQMLGNRAIR 487
           E  NG  L  R IR
Sbjct: 69  ERANGMELDGRRIR 82

>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 = 46.2 bits (109), Expect = 4e-07
 Identities = 19/78 (24%), Positives = 32/78 (41%), Gaps = 5/78 (6%)

Query: 519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFN 578
             + + G      E      L E F   G I  +S+  D  +   +G A++ F + D   
Sbjct: 10  CCLGVFGLSLYTTERD----LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAK 65

Query: 579 KALE-MSGTEIGGYSLVV 595
           +A E  +G E+ G  + V
Sbjct: 66  EAKERANGMELDGRRIRV 83

>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 = 63.1 bits (153), Expect = 4e-13
 Identities = 19/81 (23%), Positives = 37/81 (45%), Gaps = 2/81 (2%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRF-KGYGHVEFASVEDAHKAI 474
           + T+ V NL     + D+Q  F     +  + L+ D      KG+  + F   EDA +AI
Sbjct: 8   NATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAI 67

Query: 475 E-LNGQMLGNRAIRLDFARER 494
             ++G    +  + +++A+  
Sbjct: 68  AGVSGFGYDHLILNVEWAKPS 88

>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 = 48.5 bits (115), Expect = 7e-08
 Identities = 26/91 (28%), Positives = 38/91 (41%), Gaps = 5/91 (5%)

Query: 514 RGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTD 573
           R     TI +        E      L+E F   G I+RI + KD  TG  KG A++ F  
Sbjct: 4   RADDNATIRVTNLSEDTRETD----LQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHR 59

Query: 574 ADSFNKALE-MSGTEIGGYSLVVDEAKQRGD 603
            +   +A+  +SG       L V+ AK   +
Sbjct: 60  REDAARAIAGVSGFGYDHLILNVEWAKPSTN 90

>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 = 62.8 bits (152), Expect = 5e-13
 Identities = 22/78 (28%), Positives = 37/78 (47%), Gaps = 4/78 (5%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFK-GYGHVEFASVEDAHKAIE- 475
            L+V  LP ++ Q +++  FS+   ++  R+  D       G G + F    +A +AI+ 
Sbjct: 8   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 67

Query: 476 LNGQMLG--NRAIRLDFA 491
           LNGQ        I + FA
Sbjct: 68  LNGQKPSGATEPITVKFA 85

>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 = 45.4 bits (107), Expect = 6e-07
 Identities = 16/82 (19%), Positives = 37/82 (45%), Gaps = 7/82 (8%)

Query: 520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNK 579
            +++ G   ++ + +    LE+ F   G I    +  D  TG  +G+ ++ F       +
Sbjct: 8   NLYVSGLPKTMTQKE----LEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEE 63

Query: 580 ALE-MSGTEIGGYS--LVVDEA 598
           A++ ++G +  G +  + V  A
Sbjct: 64  AIKGLNGQKPSGATEPITVKFA 85

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 63.0 bits (152), Expect = 5e-13
 Identities = 25/84 (29%), Positives = 43/84 (51%)

Query: 411 PQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDA 470
            +S     LF+GNL  +   A+++   SE+    D+ +     G  + +G+V+F S ED 
Sbjct: 8   SESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDL 67

Query: 471 HKAIELNGQMLGNRAIRLDFARER 494
            KA+EL G  +    I+L+  + R
Sbjct: 68  EKALELTGLKVFGNEIKLEKPKGR 91

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 44.6 bits (104), Expect = 2e-06
 Identities = 18/95 (18%), Positives = 40/95 (42%), Gaps = 5/95 (5%)

Query: 507 NSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGI 566
           +   +G        +FI   + +    +++               ++V     TG+ +  
Sbjct: 2   SHMVEGSESTTPFNLFIGNLNPNKSVAELK----VAISELFAKNDLAVVDV-RTGTNRKF 56

Query: 567 AYLDFTDADSFNKALEMSGTEIGGYSLVVDEAKQR 601
            Y+DF  A+   KALE++G ++ G  + +++ K R
Sbjct: 57  GYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGR 91

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.1 bits (153), Expect = 5e-13
 Identities = 24/81 (29%), Positives = 37/81 (45%), Gaps = 2/81 (2%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKG-YGHVEFASVEDAHKAI 474
             T++VG L   V +  +   F +   VV+  +  D        YG VEF S EDA  AI
Sbjct: 9   DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 68

Query: 475 E-LNGQMLGNRAIRLDFARER 494
           + ++   L  + IR++ A   
Sbjct: 69  KIMDMIKLYGKPIRVNKASAH 89

>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 = 50.4 bits (120), Expect = 1e-08
 Identities = 21/83 (25%), Positives = 39/83 (46%), Gaps = 5/83 (6%)

Query: 520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNK 579
           T+++ G D  V E      L E F   G +    +PKD  TG  +G  +++F   +  + 
Sbjct: 11  TVYVGGLDEKVSEPL----LWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADY 66

Query: 580 ALE-MSGTEIGGYSLVVDEAKQR 601
           A++ M   ++ G  + V++A   
Sbjct: 67  AIKIMDMIKLYGKPIRVNKASAH 89

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.3 bits (151), Expect = 7e-13
 Identities = 16/80 (20%), Positives = 36/80 (45%), Gaps = 8/80 (10%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI- 474
             TL+V     +     ++  FS    ++D+          +    V +  +E A +A+ 
Sbjct: 5   GNTLYVYGEDMTPT--LLRGAFSPFGNIIDLS-----MDPPRNCAFVTYEKMESADQAVA 57

Query: 475 ELNGQMLGNRAIRLDFARER 494
           ELNG  + +  ++++ AR++
Sbjct: 58  ELNGTQVESVQLKVNIARKQ 77

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.4 bits (107), Expect = 5e-07
 Identities = 17/83 (20%), Positives = 38/83 (45%), Gaps = 13/83 (15%)

Query: 520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNK 579
           T+++ G D  +        L   F   G I  +S+            A++ +   +S ++
Sbjct: 7   TLYVYGED--MTPTL----LRGAFSPFGNIIDLSMDPPR------NCAFVTYEKMESADQ 54

Query: 580 AL-EMSGTEIGGYSLVVDEAKQR 601
           A+ E++GT++    L V+ A+++
Sbjct: 55  AVAELNGTQVESVQLKVNIARKQ 77

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.3 bits (151), Expect = 8e-13
 Identities = 21/81 (25%), Positives = 39/81 (48%), Gaps = 6/81 (7%)

Query: 415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI 474
             K L+V NL  S  +  ++  F+ +      R+      + + Y  V F++ EDA +A+
Sbjct: 7   SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV-----KKIRDYAFVHFSNREDAVEAM 61

Query: 475 E-LNGQMLGNRAIRLDFARER 494
           + LNG++L    I +  A+  
Sbjct: 62  KALNGKVLDGSPIEVTLAKPV 82

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.9 bits (90), Expect = 1e-04
 Identities = 14/83 (16%), Positives = 35/83 (42%), Gaps = 11/83 (13%)

Query: 520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNK 579
            ++++    S  E+     +E+ F +        V K       +  A++ F++ +   +
Sbjct: 10  ILYVRNLMLSTSEEM----IEKEFNNIKPGAVERVKKI------RDYAFVHFSNREDAVE 59

Query: 580 ALE-MSGTEIGGYSLVVDEAKQR 601
           A++ ++G  + G  + V  AK  
Sbjct: 60  AMKALNGKVLDGSPIEVTLAKPV 82

>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 = 62.0 bits (150), Expect = 1e-12
 Identities = 19/78 (24%), Positives = 39/78 (50%), Gaps = 2/78 (2%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE 475
            +TL+VGNL   V +  +   FS++      ++ ++       Y  VEF    DA  A+ 
Sbjct: 8   PRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITE-HTSNDPYCFVEFYEHRDAAAALA 66

Query: 476 -LNGQMLGNRAIRLDFAR 492
            +NG+ +  + +++++A 
Sbjct: 67  AMNGRKILGKEVKVNWAT 84

>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 = 43.1 bits (101), Expect = 5e-06
 Identities = 16/82 (19%), Positives = 30/82 (36%), Gaps = 7/82 (8%)

Query: 519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFN 578
            T+++      V E      + + F   G     S     +  S     +++F +     
Sbjct: 9   RTLYVGNLSRDVTEVL----ILQLFSQIGPCK--SCKMITEHTSNDPYCFVEFYEHRDAA 62

Query: 579 KALE-MSGTEIGGYSLVVDEAK 599
            AL  M+G +I G  + V+ A 
Sbjct: 63  AALAAMNGRKILGKEVKVNWAT 84

>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 = 61.1 bits (148), Expect = 1e-12
 Identities = 16/74 (21%), Positives = 28/74 (37%), Gaps = 1/74 (1%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRF-KGYGHVEFASVEDAHKAIELN 477
           +FVG L     +  ++ +F    EV  + L  D      +G+  + F   E   K +E  
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61

Query: 478 GQMLGNRAIRLDFA 491
              +G     +  A
Sbjct: 62  YHNVGLSKCEIKVA 75

>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 = 49.6 bits (118), Expect = 1e-08
 Identities = 19/78 (24%), Positives = 34/78 (43%), Gaps = 4/78 (5%)

Query: 521 IFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKA 580
           IF+ G      E++    + E+FG  GE+  I +P D  T   +G  ++ F + +   K 
Sbjct: 2   IFVGGLSPDTPEEK----IREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKI 57

Query: 581 LEMSGTEIGGYSLVVDEA 598
           +E     +G     +  A
Sbjct: 58  MEKKYHNVGLSKCEIKVA 75

>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 = 61.4 bits (149), Expect = 2e-12
 Identities = 20/93 (21%), Positives = 46/93 (49%), Gaps = 9/93 (9%)

Query: 404 AAQTPFTPQSGGSKTLFVGNL-PFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHV 462
           +  +  T     +  +F+GNL    V+++DV+  FS+  ++V   +        KG+  V
Sbjct: 3   SGSSGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV-------HKGFAFV 55

Query: 463 EFASVEDAHKAIE-LNGQMLGNRAIRLDFARER 494
           ++ +  +A  A+   +G+M+  + + ++ A E 
Sbjct: 56  QYVNERNARAAVAGEDGRMIAGQVLDINLAAEP 88

>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 = 42.9 bits (101), Expect = 6e-06
 Identities = 23/105 (21%), Positives = 38/105 (36%), Gaps = 12/105 (11%)

Query: 506 SNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKG 565
           S S  K         +FI   ++ V +      +E  F   G+I   SV         KG
Sbjct: 3   SGSSGKTDPRSMNSRVFIGNLNTLVVKKS---DVEAIFSKYGKIVGCSVH--------KG 51

Query: 566 IAYLDFTDADSFNKALE-MSGTEIGGYSLVVDEAKQRGDFGSGGG 609
            A++ + +  +   A+    G  I G  L ++ A +     SG  
Sbjct: 52  FAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPKVNRSGPS 96

>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 = 61.0 bits (147), Expect = 2e-12
 Identities = 18/77 (23%), Positives = 36/77 (46%), Gaps = 2/77 (2%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVV-DVRLSSDADGRFKGYGHVEFASVEDAHKAIE- 475
           TL++ N P S  Q ++++   ++  V   +RL S      + + +++  S EDA   +E 
Sbjct: 3   TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK 62

Query: 476 LNGQMLGNRAIRLDFAR 492
           LNG  +    +    + 
Sbjct: 63  LNGLKIEGYTLVTKVSN 79

>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 = 47.1 bits (111), Expect = 2e-07
 Identities = 14/81 (17%), Positives = 31/81 (38%), Gaps = 5/81 (6%)

Query: 520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNK 579
           T+++  F  S  +      + +       +            + +  AY+D T  +    
Sbjct: 3   TLWMTNFPPSYTQRN----IRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARY 58

Query: 580 ALE-MSGTEIGGYSLVVDEAK 599
            +E ++G +I GY+LV   + 
Sbjct: 59  CVEKLNGLKIEGYTLVTKVSN 79

>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 = 61.2 bits (148), Expect = 2e-12
 Identities = 20/85 (23%), Positives = 36/85 (42%), Gaps = 3/85 (3%)

Query: 411 PQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDA 470
           P       ++VGNLP  +   D+++ F +   + D+ L +        +  VEF    DA
Sbjct: 9   PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN--RRGGPPFAFVEFEDPRDA 66

Query: 471 HKAIE-LNGQMLGNRAIRLDFARER 494
             A+   +G       +R++F R  
Sbjct: 67  EDAVYGRDGYDYDGYRLRVEFPRSG 91

>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 = 48.1 bits (114), Expect = 8e-08
 Identities = 21/106 (19%), Positives = 35/106 (33%), Gaps = 12/106 (11%)

Query: 501 SGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDT 560
           SGG       +G  G     I++      +        +E+ F   G I  I +      
Sbjct: 1   SGGGVI----RGPAGNNDCRIYVGNLPPDIRTKD----IEDVFYKYGAIRDIDLKNRRGG 52

Query: 561 GSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVDEAKQRGDFG 605
                 A+++F D      A+    G +  GY L V+  +     G
Sbjct: 53  ---PPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGTG 95

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.8 bits (147), Expect = 2e-12
 Identities = 18/83 (21%), Positives = 36/83 (43%), Gaps = 5/83 (6%)

Query: 413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHK 472
           S GS  +FVG     + + +++ FFS+  +V+DV         F+ +  V FA  + A  
Sbjct: 2   SSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVF----IPKPFRAFAFVTFADDQIAQS 57

Query: 473 AIELNGQMLGNRAIRLDFARERG 495
                  ++   ++ +  A  + 
Sbjct: 58  LCG-EDLIIKGISVHISNAEPKH 79

>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 = 60.5 bits (146), Expect = 3e-12
 Identities = 12/76 (15%), Positives = 30/76 (39%), Gaps = 1/76 (1%)

Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKG-YGHVEFASVEDAHKAIE 475
           K +FVG +    E+  ++++F +  ++  + + +D     K  +  V F   +   K + 
Sbjct: 3   KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 62

Query: 476 LNGQMLGNRAIRLDFA 491
                +      +  A
Sbjct: 63  QKYHTVNGHNCEVRKA 78

>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 = 48.9 bits (116), Expect = 3e-08
 Identities = 21/79 (26%), Positives = 36/79 (45%), Gaps = 4/79 (5%)

Query: 520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNK 579
            IF+ G      E      L ++F   G+I  I +  D  +G  +G A++ F D DS +K
Sbjct: 4   KIFVGGIKEDTEEHH----LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK 59

Query: 580 ALEMSGTEIGGYSLVVDEA 598
            +      + G++  V +A
Sbjct: 60  IVIQKYHTVNGHNCEVRKA 78

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.1 bits (145), Expect = 3e-12
 Identities = 18/80 (22%), Positives = 39/80 (48%), Gaps = 7/80 (8%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-L 476
            L++GNL  +V   D++  F +    +  ++         GY  V++     A +AIE L
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPLAGQV-----LLKSGYAFVDYPDQNWAIRAIETL 57

Query: 477 NGQM-LGNRAIRLDFARERG 495
           +G++ L  + + +D++  + 
Sbjct: 58  SGKVELHGKIMEVDYSVSKK 77

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.9 bits (147), Expect = 4e-12
 Identities = 29/96 (30%), Positives = 49/96 (51%), Gaps = 5/96 (5%)

Query: 400 SGKKAAQTPFTPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKG 458
           SG   ++ P +P      T F+GNLP+ V +  ++ FF  +           ++  R KG
Sbjct: 3   SGSSGSRLPKSP----PYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKG 58

Query: 459 YGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARER 494
           +G+ EF  ++    A+ LN + LGN+ IR+D A + 
Sbjct: 59  FGYAEFEDLDSLLSALSLNEESLGNKRIRVDVADQA 94

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.6 bits (115), Expect = 8e-08
 Identities = 24/94 (25%), Positives = 37/94 (39%), Gaps = 5/94 (5%)

Query: 519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFN 578
           +T F+      V E+     ++E F            +  +   +KG  Y +F D DS  
Sbjct: 16  YTAFLGNLPYDVTEES----IKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLL 71

Query: 579 KALEMSGTEIGGYSLVVDEAKQRGDFGSGGGRSG 612
            AL ++   +G   + VD A Q  D    G  SG
Sbjct: 72  SALSLNEESLGNKRIRVDVADQAQD-KDSGPSSG 104

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.2 bits (145), Expect = 7e-12
 Identities = 23/98 (23%), Positives = 37/98 (37%), Gaps = 6/98 (6%)

Query: 415 GSKTLFVGNL-PFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKA 473
           G+  L V NL P  V    +   F    +V  V++        K    V+ A    A  A
Sbjct: 1   GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKI----LFNKKENALVQMADGNQAQLA 56

Query: 474 IE-LNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQ 510
           +  LNG  L  + IR+  ++ +    P  G  +    +
Sbjct: 57  MSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTK 94

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.4 bits (143), Expect = 9e-12
 Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 5/81 (6%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE 475
           S TL + N+P SV + D++  FS    VV          + +    ++  SVE+A +A+ 
Sbjct: 10  SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGF---KFFQKDRKMALIQMGSVEEAVQALI 66

Query: 476 -LNGQMLG-NRAIRLDFARER 494
            L+   LG N  +R+ F++  
Sbjct: 67  DLHNHDLGENHHLRVSFSKST 87

>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 = 59.3 bits (143), Expect = 1e-11
 Identities = 17/83 (20%), Positives = 32/83 (38%), Gaps = 6/83 (7%)

Query: 418 TLFVGNLPFSVEQADVQNFFSE---VAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI 474
            LF+G +P   ++ ++    ++       V V  S+    + +G+  VE+ S   A  A 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 475 E---LNGQMLGNRAIRLDFARER 494
                    L    I +D+A   
Sbjct: 63  RKLMPGRIQLWGHQIAVDWAEPE 85

>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 = 43.9 bits (103), Expect = 3e-06
 Identities = 13/87 (14%), Positives = 32/87 (36%), Gaps = 5/87 (5%)

Query: 520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNK 579
            +FI G       +++   + +      ++  I      D    +G A++++    +   
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDV--IVYASAADKMKNRGFAFVEYESHRAAAM 60

Query: 580 ALE---MSGTEIGGYSLVVDEAKQRGD 603
           A         ++ G+ + VD A+   D
Sbjct: 61  ARRKLMPGRIQLWGHQIAVDWAEPEID 87

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.0 bits (142), Expect = 1e-11
 Identities = 24/84 (28%), Positives = 39/84 (46%), Gaps = 2/84 (2%)

Query: 413 SGGSKTLFVGNLPFSVEQADV-QNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAH 471
           +     LFVG L F   +  + Q F         V +      R +G+G V F +++DA 
Sbjct: 2   ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAK 61

Query: 472 KAIE-LNGQMLGNRAIRLDFARER 494
            A+  +NG+ +  R IR+D A + 
Sbjct: 62  DAMMAMNGKSVDGRQIRVDQAGKS 85

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.4 bits (143), Expect = 1e-11
 Identities = 17/79 (21%), Positives = 35/79 (44%), Gaps = 1/79 (1%)

Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADG-RFKGYGHVEFASVEDAHKAIE 475
             +FVG LP+    A ++ +F    ++ +  + +D    + +GYG V  A    A +A +
Sbjct: 11  TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 70

Query: 476 LNGQMLGNRAIRLDFARER 494
               ++  R   ++ A   
Sbjct: 71  DPNPIIDGRKANVNLAYLG 89

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.4 bits (99), Expect = 1e-05
 Identities = 20/101 (19%), Positives = 34/101 (33%), Gaps = 11/101 (10%)

Query: 514 RGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTD 573
           +      IF+ G      +      L ++F   G+I    V  D  TG  +G  ++   D
Sbjct: 6   KDTTFTKIFVGGLPYHTTDAS----LRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMAD 61

Query: 574 ADSFNKALEMSGTEIGGYSLVVDEA-------KQRGDFGSG 607
             +  +A +     I G    V+ A         +  F  G
Sbjct: 62  RAAAERACKDPNPIIDGRKANVNLAYLGAKPRSLQTGFAIG 102

>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 = 59.0 bits (142), Expect = 2e-11
 Identities = 27/95 (28%), Positives = 45/95 (47%), Gaps = 5/95 (5%)

Query: 413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRF-KGYGHVEFASVEDAH 471
           S GS  LFV NL ++  + D++  FS    + ++    D+  +  KG+  V F   E A 
Sbjct: 5   SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAV 64

Query: 472 KAIE-LNGQMLGNRAIRLDFA---RERGAYTPYSG 502
           KA   ++GQ+   R + +  +   +E     P SG
Sbjct: 65  KAYAEVDGQVFQGRMLHVLPSTIKKEASQSGPSSG 99

>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 = 45.1 bits (106), Expect = 1e-06
 Identities = 22/99 (22%), Positives = 40/99 (40%), Gaps = 5/99 (5%)

Query: 515 GQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDA 574
              +  +F++    +  E+     LE+ F + G ++ +  P D  T   KG A++ F   
Sbjct: 5   SSGSGRLFVRNLSYTSSEED----LEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFP 60

Query: 575 DSFNKALE-MSGTEIGGYSLVVDEAKQRGDFGSGGGRSG 612
           +   KA   + G    G  L V  +  + +    G  SG
Sbjct: 61  EHAVKAYAEVDGQVFQGRMLHVLPSTIKKEASQSGPSSG 99

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 59.9 bits (144), Expect = 2e-11
 Identities = 24/108 (22%), Positives = 48/108 (44%), Gaps = 2/108 (1%)

Query: 399 ESGKKAAQTPFTPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADG-RFK 457
           +  +    T   P+    + L V  +P +V++  ++  F     +  V++  D +  + +
Sbjct: 25  QQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSR 84

Query: 458 GYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARERGAYTPYSGGN 504
           GYG V+F S   A +AI  LNG  + N+ +++  A         +G  
Sbjct: 85  GYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAGAV 132

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 46.4 bits (109), Expect = 1e-06
 Identities = 25/132 (18%), Positives = 43/132 (32%), Gaps = 16/132 (12%)

Query: 497 YTPYSGGNESNSFQKGGRGQ-----------AAHTIFIKGFDSSVGEDQVRASLEEHFGS 545
           Y PY    +    Q+  +                 + +    ++V E Q    L + F  
Sbjct: 10  YDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQ----LRQLFER 65

Query: 546 CGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVDEAKQRGDF 604
            G I  + +  D +T   +G  ++ F    S  +A+  ++G  I    L V  A      
Sbjct: 66  YGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQR 125

Query: 605 GSGGGRSGGRGG 616
               G  G   G
Sbjct: 126 PGIAGAVGDGNG 137

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.2 bits (140), Expect = 4e-11
 Identities = 30/81 (37%), Positives = 46/81 (56%), Gaps = 2/81 (2%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADG-RFKGYGHVEFASVEDAHKAI 474
            +++FVGN+P+   +  +++ FSEV  VV  RL  D +  + KGYG  E+   E A  A+
Sbjct: 8   LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAM 67

Query: 475 E-LNGQMLGNRAIRLDFARER 494
             LNG+    RA+R+D A   
Sbjct: 68  RNLNGREFSGRALRVDNAASE 88

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.1 bits (98), Expect = 2e-05
 Identities = 23/101 (22%), Positives = 45/101 (44%), Gaps = 7/101 (6%)

Query: 516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDAD 575
           ++  ++F+        E+Q    L++ F   G +    +  D +TG  KG  + ++ D +
Sbjct: 6   RSLRSVFVGNIPYEATEEQ----LKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61

Query: 576 SFNKALE-MSGTEIGGYSLVVDEAKQRGDFGSGGGRSGGRG 615
           +   A+  ++G E  G +L VD A    +      +S G G
Sbjct: 62  TALSAMRNLNGREFSGRALRVDNAASEKN--KEELKSLGTG 100

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.8 bits (139), Expect = 5e-11
 Identities = 26/95 (27%), Positives = 40/95 (42%), Gaps = 3/95 (3%)

Query: 410 TPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVED 469
           + QS     + +  LP+   + D+ NFFS +  +         DGR  G   VEFA+ ED
Sbjct: 9   SFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEI-GPDGRVTGEADVEFATHED 67

Query: 470 AHKAIELNGQMLGNRAIRLDFA--RERGAYTPYSG 502
           A  A+  +   + +R + L            P SG
Sbjct: 68  AVAAMAKDKANMQHRYVELFLNSTAGTSGSGPSSG 102

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.3 bits (109), Expect = 5e-07
 Identities = 24/112 (21%), Positives = 41/112 (36%), Gaps = 11/112 (9%)

Query: 501 SGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDT 560
           S G+  +SFQ        H + ++G      E+ +      +F S     R+ +    D 
Sbjct: 2   SSGSSGSSFQS----TTGHCVHMRGLPYRATENDIY-----NFFSPLNPMRVHIEIGPD- 51

Query: 561 GSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDEAKQRGDFGSGGGRSG 612
           G V G A ++F   +    A+      +    + +      G  GS G  SG
Sbjct: 52  GRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLNSTAGTSGS-GPSSG 102

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.5 bits (138), Expect = 6e-11
 Identities = 21/104 (20%), Positives = 38/104 (36%), Gaps = 6/104 (5%)

Query: 413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAH 471
           +       + N+PFS+ + DV  F   +    +        +G+  G   V+F + +DA 
Sbjct: 5   NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDAR 64

Query: 472 KAIELNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRG 515
           K+  L+ + L  R   +                E N   +G  G
Sbjct: 65  KSERLHRKKLNGREAFVHVVTLED-----MREIEKNPPAQGKSG 103

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.2 bits (124), Expect = 5e-09
 Identities = 15/107 (14%), Positives = 28/107 (26%), Gaps = 6/107 (5%)

Query: 511 KGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLD 570
           +G    A     I     S+ +  V     +                 + G   G A + 
Sbjct: 1   EGDVNSAKVCAHITNIPFSITKMDVL----QFLEGIPVDENAVHVLVDNNGQGLGQALVQ 56

Query: 571 FTDADSFNKALEMSGTEIGGYSLVVDEA--KQRGDFGSGGGRSGGRG 615
           F + D   K+  +   ++ G    V     +   +        G  G
Sbjct: 57  FKNEDDARKSERLHRKKLNGREAFVHVVTLEDMREIEKNPPAQGKSG 103

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.4 bits (138), Expect = 6e-11
 Identities = 18/81 (22%), Positives = 32/81 (39%), Gaps = 2/81 (2%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVD-VRLSSDADGRFKGYGHVEFASVEDAHKAI 474
              LF+ +LP      D+   F     VV             K +G V + +   A  AI
Sbjct: 18  GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAI 77

Query: 475 E-LNGQMLGNRAIRLDFARER 494
           + +NG  +G + +++   R +
Sbjct: 78  QSMNGFQIGMKRLKVQLKRSK 98

>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 = 43.9 bits (103), Expect = 3e-06
 Identities = 19/85 (22%), Positives = 33/85 (38%), Gaps = 5/85 (5%)

Query: 520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNK 579
            +FI       G+      L + F   G +    V  D  T   K   ++ + +  S   
Sbjct: 20  NLFIYHLPQEFGDQD----LLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQA 75

Query: 580 ALE-MSGTEIGGYSLVVDEAKQRGD 603
           A++ M+G +IG   L V   + + D
Sbjct: 76  AIQSMNGFQIGMKRLKVQLKRSKND 100

>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 = 57.5 bits (138), Expect = 7e-11
 Identities = 17/81 (20%), Positives = 37/81 (45%), Gaps = 2/81 (2%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRF-KGYGHVEFASVEDAHKAI 474
           +K L++ NL   V + D+ + F+   E     +         +G   + F + E A +A+
Sbjct: 18  NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQAL 77

Query: 475 E-LNGQMLGNRAIRLDFARER 494
             +NG  L  + + ++F + +
Sbjct: 78  HLVNGYKLYGKILVIEFGKNK 98

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 56.7 bits (136), Expect = 9e-11
 Identities = 21/87 (24%), Positives = 35/87 (40%), Gaps = 8/87 (9%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFK-GYGHVEFASVEDAHKAI 474
            KT+F+ NL F  E+  +     +  ++  VR+    D     G    +F + E A K +
Sbjct: 8   GKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCL 67

Query: 475 E-------LNGQMLGNRAIRLDFARER 494
                     G  L  R +++D A  R
Sbjct: 68  AAASLEAEGGGLKLDGRQLKVDLAVTR 94

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 56.0 bits (134), Expect = 9e-11
 Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 1/74 (1%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELN 477
           T+ V NLP S  Q  V  +F     ++ V + +D+  +   +  +EFA  + A  AI   
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDV-ADSLKKNFRFARIEFARYDGALAAITKT 60

Query: 478 GQMLGNRAIRLDFA 491
            +++G   I +   
Sbjct: 61  HKVVGQNEIIVSHL 74

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 51.4 bits (122), Expect = 4e-09
 Identities = 15/79 (18%), Positives = 30/79 (37%), Gaps = 6/79 (7%)

Query: 520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNK 579
           T+ +K    S  +++V     ++F  CG I  + V            A ++F   D    
Sbjct: 2   TVLVKNLPKSYNQNKVY----KYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALA 55

Query: 580 ALEMSGTEIGGYSLVVDEA 598
           A+  +   +G   ++V   
Sbjct: 56  AITKTHKVVGQNEIIVSHL 74

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 56.7 bits (136), Expect = 1e-10
 Identities = 14/94 (14%), Positives = 30/94 (31%), Gaps = 11/94 (11%)

Query: 413 SGGSKTLFVGNLPFSV-----EQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASV 467
           S GS  L        V      +A  ++ F    +    +       +      + F++ 
Sbjct: 2   SSGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYF-----KSFKRVRINFSNP 56

Query: 468 EDAHKAIE-LNGQMLGNRAIRLDFARERGAYTPY 500
             A  A   L+      + ++L FA+     + +
Sbjct: 57  LSAADARLRLHKTEFLGKEMKLYFAQTLHIGSSH 90

>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 = 55.9 bits (134), Expect = 2e-10
 Identities = 18/89 (20%), Positives = 36/89 (40%), Gaps = 10/89 (11%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD---------ADGRFKGYGHVEFAS 466
           +  ++V  L  SV   D+ +FF +   V   + +             G+ KG   V +  
Sbjct: 8   NSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYED 67

Query: 467 VEDAHKAIE-LNGQMLGNRAIRLDFARER 494
              A  A+E  +G+      +++  AR++
Sbjct: 68  PPTAKAAVEWFDGKDFQGSKLKVSLARKK 96

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.2 bits (135), Expect = 2e-10
 Identities = 17/93 (18%), Positives = 33/93 (35%), Gaps = 6/93 (6%)

Query: 411 PQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDA 470
                   + V NL + V    +   FS+   V+ +          +    +++A    A
Sbjct: 2   AGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIIT---FTKNNQFQALLQYADPVSA 58

Query: 471 HKAIE-LNGQML--GNRAIRLDFARERGAYTPY 500
             A   L+GQ +      +R+DF++       Y
Sbjct: 59  QHAKLSLDGQNIYNACCTLRIDFSKLTSLNVKY 91

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.4 bits (130), Expect = 3e-10
 Identities = 15/71 (21%), Positives = 27/71 (38%), Gaps = 2/71 (2%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLS-SDADGRFKGYGHVEFASVEDAHKAIE-L 476
           L++  L       D+        ++V  +        + KGYG V+F S   A KA+  L
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 477 NGQMLGNRAIR 487
               +  +  +
Sbjct: 61  KASGVQAQMAK 71

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.4 bits (130), Expect = 4e-10
 Identities = 16/93 (17%), Positives = 27/93 (29%), Gaps = 9/93 (9%)

Query: 413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHK 472
           S GS  + V NLP      +V +   +          +           V   + E A  
Sbjct: 2   SSGSSGILVKNLPQDSNCQEVHDLLKDYDLKYCYVDRNK------RTAFVTLLNGEQAQN 55

Query: 473 AIE-LNGQMLGNRAIRLDFARE--RGAYTPYSG 502
           AI+  +      + + +            P SG
Sbjct: 56  AIQMFHQYSFRGKDLIVQLQPTDALLCSGPSSG 88

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 53.8 bits (129), Expect = 6e-10
 Identities = 11/69 (15%), Positives = 28/69 (40%), Gaps = 6/69 (8%)

Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELN 477
            + V   P +     +   F++   ++   +S+        + H+ + S   A KA+  +
Sbjct: 6   WVTVFGFPQASAS-YILLQFAQYGNILKHVMSNT-----GNWMHIRYQSKLQARKALSKD 59

Query: 478 GQMLGNRAI 486
           G++ G   +
Sbjct: 60  GRIFGESIM 68

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.9 bits (111), Expect = 2e-07
 Identities = 10/76 (13%), Positives = 21/76 (27%), Gaps = 11/76 (14%)

Query: 519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFN 578
             + + GF  +     +       F   G I +  +             ++ +       
Sbjct: 5   TWVTVFGFPQASASYILL-----QFAQYGNILKHVMSNT------GNWMHIRYQSKLQAR 53

Query: 579 KALEMSGTEIGGYSLV 594
           KAL   G   G   ++
Sbjct: 54  KALSKDGRIFGESIMI 69

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.7 bits (131), Expect = 6e-10
 Identities = 13/73 (17%), Positives = 27/73 (36%), Gaps = 1/73 (1%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LN 477
           + +        +        +  EV ++ +  +      G  +V+F   EDA KA+  LN
Sbjct: 30  VEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLN 89

Query: 478 GQMLGNRAIRLDF 490
            +    + I  + 
Sbjct: 90  NRWFNGQPIHAEL 102

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 52.5 bits (125), Expect = 2e-09
 Identities = 22/91 (24%), Positives = 39/91 (42%), Gaps = 10/91 (10%)

Query: 405 AQTPFTPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEF 464
           AQT   P    ++ LF+ NLP    +  +   F++     +VR              VEF
Sbjct: 1   AQTEQPP----NQILFLTNLPEETNEMMLSMLFNQFPGFKEVR----LVPNRHDIAFVEF 52

Query: 465 ASVEDAHKAIE-LNGQML-GNRAIRLDFARE 493
            +   ++ A E L G  +    A+++ FA++
Sbjct: 53  TTELQSNAAKEALQGFKITPTHAMKITFAKK 83

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.2 bits (124), Expect = 3e-09
 Identities = 15/82 (18%), Positives = 31/82 (37%), Gaps = 8/82 (9%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE 475
           S+ L +  LP  V + +V        +V ++        + K    +E A+ E A   + 
Sbjct: 8   SRVLHIRKLPGEVTETEVIALGLPFGKVTNIL-----MLKGKNQAFLELATEEAAITMVN 62

Query: 476 ---LNGQMLGNRAIRLDFARER 494
                   L N+ I + ++  +
Sbjct: 63  YYSAVTPHLRNQPIYIQYSNHK 84

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.4 bits (125), Expect = 3e-09
 Identities = 17/86 (19%), Positives = 38/86 (44%), Gaps = 8/86 (9%)

Query: 412 QSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAH 471
           ++  +  L+VG L  +   A +   F     +  +        +   + ++++ S++ A 
Sbjct: 13  KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTID-----HVKGDSFAYIQYESLDAAQ 67

Query: 472 KAIE-LNGQMLG--NRAIRLDFARER 494
            A   + G  LG  +R +R+DFA+  
Sbjct: 68  AACAKMRGFPLGGPDRRLRVDFAKSG 93

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.2 bits (125), Expect = 3e-09
 Identities = 18/91 (19%), Positives = 30/91 (32%), Gaps = 9/91 (9%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAE--------VVDVRLSSDADGRFKGYGHVEFASV 467
            + + + N+   ++  D     +E+ E           +R     D    G   V F   
Sbjct: 8   ERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDP 67

Query: 468 EDAHKAI-ELNGQMLGNRAIRLDFARERGAY 497
           E+A   I  L+G+  G R I          Y
Sbjct: 68  EEADYCIQTLDGRWFGGRQITAQAWDGTTDY 98

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.7 bits (90), Expect = 2e-04
 Identities = 12/74 (16%), Positives = 28/74 (37%), Gaps = 5/74 (6%)

Query: 532 EDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKAL-EMSGTEIGG 590
            +++R  L       G+I ++ +   +      G+A + F D +  +  +  + G   GG
Sbjct: 29  LNEIREDLRVECSKFGQIRKLLLFDRHP----DGVASVSFRDPEEADYCIQTLDGRWFGG 84

Query: 591 YSLVVDEAKQRGDF 604
             +         D+
Sbjct: 85  RQITAQAWDGTTDY 98

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.5 bits (125), Expect = 4e-09
 Identities = 19/110 (17%), Positives = 39/110 (35%), Gaps = 12/110 (10%)

Query: 400 SGKKAAQTPFTPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGY 459
           SG   +    +     S  + V  L  SV +AD+     +   +  V +       FK  
Sbjct: 3   SGSSGSHHKVSV----SPVVHVRGLCESVVEADLVEALEKFGTICYVMMM-----PFKRQ 53

Query: 460 GHVEFASVEDAHKAIE---LNGQMLGNRAIRLDFARERGAYTPYSGGNES 506
             VEF +++ A + +         +  +    +++  +    P + G  S
Sbjct: 54  ALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITRPGNSGPSS 103

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.1 bits (124), Expect = 5e-09
 Identities = 18/83 (21%), Positives = 33/83 (39%), Gaps = 1/83 (1%)

Query: 411 PQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDA 470
            Q      L++ NLP S+++ +++N      +V+  R+  D+ G  +G G     S E  
Sbjct: 13  QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKC 72

Query: 471 HKAIE-LNGQMLGNRAIRLDFAR 492
              I   NG+ +           
Sbjct: 73  EAVIGHFNGKFIKTPPGVSAPTE 95

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.4 bits (122), Expect = 5e-09
 Identities = 19/91 (20%), Positives = 29/91 (31%), Gaps = 7/91 (7%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LN 477
           + V  LP S    D+++   E  +V              G G VEF   ED   A+  L+
Sbjct: 3   VVVSGLPPSGSWQDLKDHMREAGDVCYAD------VYRDGTGVVEFVRKEDMTYAVRKLD 56

Query: 478 GQMLGNRAIRLDFARERGAYTPYSGGNESNS 508
                +      + R +           S S
Sbjct: 57  NTKFRSHEGETAYIRVKVDGPRSPSYGRSRS 87

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.9 bits (124), Expect = 5e-09
 Identities = 19/78 (24%), Positives = 31/78 (39%), Gaps = 4/78 (5%)

Query: 421 VGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRF---KGYGHVEFASVEDAHKAI-EL 476
           + +  +     DV++  S+   V  + +    DG      G   VEF SV D  KA+  L
Sbjct: 19  LDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGL 78

Query: 477 NGQMLGNRAIRLDFARER 494
            G+   NR +   +    
Sbjct: 79  TGRKFANRVVVTKYCDPD 96

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.4 bits (122), Expect = 9e-09
 Identities = 26/98 (26%), Positives = 50/98 (51%), Gaps = 3/98 (3%)

Query: 398 AESGKKAAQTPFTPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRF 456
           + SG+K +++    ++G    +++  LPF  E   V +FF ++  V D    +   +G+ 
Sbjct: 2   SPSGQKRSRSRSPHEAG--FCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKA 59

Query: 457 KGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARER 494
            G G VEF +  D   A+  + Q +GNR I++    ++
Sbjct: 60  TGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPITKK 97

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.2 bits (80), Expect = 0.004
 Identities = 12/86 (13%), Positives = 27/86 (31%), Gaps = 4/86 (4%)

Query: 516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDAD 575
           +A   +++KG         V     + F     +           G   G  +++F +  
Sbjct: 16  EAGFCVYLKGLPFEAENKHVI----DFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEA 71

Query: 576 SFNKALEMSGTEIGGYSLVVDEAKQR 601
            +  AL      +G   + V    ++
Sbjct: 72  DYKAALCRHKQYMGNRFIQVHPITKK 97

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 50.5 bits (120), Expect = 2e-08
 Identities = 17/85 (20%), Positives = 28/85 (32%), Gaps = 7/85 (8%)

Query: 411 PQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDA 470
           P       + V  LP S    D+++   E  +V           +  G G VE+   ED 
Sbjct: 10  PTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYAD------VQKDGMGMVEYLRKEDM 63

Query: 471 HKAIE-LNGQMLGNRAIRLDFARER 494
             A+  L+     +      + R  
Sbjct: 64  EYALRKLDDTKFRSHEGETSYIRVY 88

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.2 bits (114), Expect = 1e-07
 Identities = 14/84 (16%), Positives = 32/84 (38%), Gaps = 9/84 (10%)

Query: 411 PQSGGSKTLFV--GNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVE 468
             S  +++L V  G L   V +  +     +   V  +          K Y    + + E
Sbjct: 13  TVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALL-----MPPNKPYSFARYRTTE 67

Query: 469 DAHKAIE-LNG-QMLGNRAIRLDF 490
           ++ +A   LNG +++ +   ++  
Sbjct: 68  ESKRAYVTLNGKEVVDDLGQKITL 91

>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 = 47.1 bits (111), Expect = 2e-07
 Identities = 14/78 (17%), Positives = 33/78 (42%), Gaps = 8/78 (10%)

Query: 418 TLFVGNLPFSVEQADV---QNFFSEVAEVVDVRLSSDADGR----FKGYGHVEFASVEDA 470
            +FV  L   +   +V     +F +  ++  V +++              +V +   EDA
Sbjct: 10  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 69

Query: 471 HKAIE-LNGQMLGNRAIR 487
            +AI+ +N  ++  R ++
Sbjct: 70  LRAIQCVNNVVVDGRTLK 87

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.5 bits (112), Expect = 2e-07
 Identities = 26/96 (27%), Positives = 44/96 (45%), Gaps = 3/96 (3%)

Query: 410 TPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVE 468
           +P +     + +  LPF   + ++  FFS +  V +         GR  G   V+FAS E
Sbjct: 9   SPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQE 68

Query: 469 DAHKAIELNGQMLGNRAIRLDFA--RERGAYTPYSG 502
            A KA++ + + +G+R I +  +   E     P SG
Sbjct: 69  IAEKALKKHKERIGHRYIEIFKSSRAEVRTSGPSSG 104

>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 = 39.8 bits (92), Expect = 1e-04
 Identities = 16/107 (14%), Positives = 36/107 (33%), Gaps = 5/107 (4%)

Query: 506 SNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKG 565
           S S            + ++G      ++++     + F     +           G   G
Sbjct: 3   SGSSGNSPDTANDGFVRLRGLPFGCSKEEIV----QFFSGLEIVPNGMTLPVDFQGRSTG 58

Query: 566 IAYLDFTDADSFNKALEMSGTEIGGYSLVVDEAKQRGDFGSGGGRSG 612
            A++ F   +   KAL+     IG   + + ++ +  +  + G  SG
Sbjct: 59  EAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRA-EVRTSGPSSG 104

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.8 bits (102), Expect = 2e-06
 Identities = 14/75 (18%), Positives = 25/75 (33%), Gaps = 7/75 (9%)

Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI-ELN 477
           + +  LP  V   +V +  S+               ++KG   V   + E A  AI   +
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDYELKYCF------VDKYKGTAFVTLLNGEQAEAAINTFH 54

Query: 478 GQMLGNRAIRLDFAR 492
              L  R + +    
Sbjct: 55  QSRLRERELSVQLQP 69

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.7 bits (94), Expect = 6e-05
 Identities = 17/80 (21%), Positives = 26/80 (32%), Gaps = 6/80 (7%)

Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI- 474
              +   NLP     A++Q  FS    +  V               VEF    +A KA  
Sbjct: 10  KTVILAKNLPAGTLAAEIQETFSRFGSLGRVL-----LPEGGITAIVEFLEPLEARKAFR 64

Query: 475 ELNGQMLGNRAIRLDFARER 494
            L      +  + L++A   
Sbjct: 65  HLAYSKFHHVPLYLEWAPIG 84

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.8 bits (92), Expect = 1e-04
 Identities = 17/83 (20%), Positives = 26/83 (31%), Gaps = 7/83 (8%)

Query: 415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDA--HK 472
           G    F G+L     + D+   FS   E+  +        R    G + F         K
Sbjct: 10  GCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFV-----RGAKEGIILFKEKAKEALGK 64

Query: 473 AIELNGQMLGNRAIRLDFARERG 495
           A + N   L  R   + +    G
Sbjct: 65  AKDANNGNLQLRNKEVTWEVLEG 87

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	675
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.97
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.79
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.78
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.78
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.78
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.78
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.77
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.77
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.77
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.77
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.77
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.77
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.76
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.76
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.76
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.76
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.76
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.76
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.76
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.76
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.76
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.76
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.75
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.75
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.75
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.75
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.75
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.75
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.74
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.74
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.74
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.74
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.74
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.74
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.72
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.72
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.72
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.72
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.72
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.71
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.71
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.71
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.7
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.7
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.7
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.7
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.7
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.69
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.69
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.69
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.69
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.69
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.68
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.68
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.68
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.68
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.67
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.67
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.67
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.67
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.67
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.66
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.66
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.66
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.66
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.66
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.66
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.66
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.66
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.66
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.65
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.65
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.65
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.65
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.65
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.65
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.64
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.64
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.64
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.64
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.64
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.64
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.64
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.64
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.63
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.63
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.63
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.63
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.63
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.63
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.63
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.63
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.63
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.62
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.62
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.62
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.62
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.62
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.61
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.61
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.61
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.61
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.61
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.61
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.6
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.6
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.6
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.6
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.59
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.59
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.59
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.59
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.58
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.58
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.58
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.58
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.57
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.57
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.57
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.56
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.55
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.55
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.55
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.55
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.55
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.55
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.55
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.54
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.53
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.53
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.52
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.52
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.51
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.51
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.5
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.5
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.5
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.49
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.49
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.49
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.48
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.47
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.47
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.47
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.47
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.47
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.47
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.47
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.47
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.46
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.46
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.46
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	99.45
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.44
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.4
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.39
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.37
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.36
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.36
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.34
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.34
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.33
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.33
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.32
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.3
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.29
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	99.22
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.18
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.16
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.1
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.08
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.06
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.8
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.57
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.44
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.11
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	96.53
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	96.04
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	90.46

>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=99.97  E-value=7.5e-30  Score=245.89  Aligned_cols=171  Identities=24%  Similarity=0.432  Sum_probs=152.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEecccc
Q 045516          416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARER  494 (675)
Q Consensus       416 ~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a~~~  494 (675)
                      .|+|||+|||+.+|+++|+++|++||.|..|.|+++. ++.++|||||+|.+.+.|.+|+.+++..++++.|.+......
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~~~~~~~~~   85 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSR   85 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECCCT
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHhcCCcccccchhhhhhhhc
Confidence            4899999999999999999999999999999999987 899999999999999999999998888899999888776543


Q ss_pred             CCCCCCCCCCCCCCccCCCCCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCH
Q 045516          495 GAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDA  574 (675)
Q Consensus       495 ~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~  574 (675)
                      .....            .......++|||+|||+.+++++    |+++|..||.|..|.|+.+..+|.++|||||+|.+.
T Consensus        86 ~~~~~------------~~~~~~~~~i~V~~lp~~~te~~----L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~  149 (183)
T d1u1qa_          86 EDSQR------------PGAHLTVKKIFVGGIKEDTEEHH----LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH  149 (183)
T ss_dssp             TGGGS------------TTTTCCCSEEEEECCCTTCCHHH----HHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCH
T ss_pred             ccccc------------cccccccceeEEccCCCcCCHHH----HhhhhccCCceeeeeeecccccCccceeEEEEECCH
Confidence            32111            11233468999999999999998    778999999999999999999999999999999999


Q ss_pred             HHHHHHHHhCCceeCCeeeEEeccccCC
Q 045516          575 DSFNKALEMSGTEIGGYSLVVDEAKQRG  602 (675)
Q Consensus       575 e~A~~Al~lng~~~~Gr~l~V~~a~~r~  602 (675)
                      +.|.+||.++++.|+|+.|+|.++.++.
T Consensus       150 e~A~~Al~~~~~~~~G~~i~V~~A~~k~  177 (183)
T d1u1qa_         150 DSVDKIVIQKYHTVNGHNCEVRKALSKQ  177 (183)
T ss_dssp             HHHHHHHTSSCEEETTEEEEEEECCCHH
T ss_pred             HHHHHHHHhCCCeECCEEEEEEecCCcc
Confidence            9999999999999999999999997754

>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=99.79  E-value=2.2e-19  Score=150.88  Aligned_cols=82  Identities=28%  Similarity=0.428  Sum_probs=76.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      ..+.++|||+|||+++++++|+++|+.||.|..|+|++++ +|+++|||||+|.+.++|.+||. |||..|.|+.|+|.|
T Consensus         4 s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~   83 (88)
T d1rk8a_           4 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW   83 (88)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            3467899999999999999999999999999999999987 89999999999999999999997 999999999999999


Q ss_pred             cccc
Q 045516          491 ARER  494 (675)
Q Consensus       491 a~~~  494 (675)
                      +..+
T Consensus        84 a~~k   87 (88)
T d1rk8a_          84 CFVK   87 (88)
T ss_dssp             SEEC
T ss_pred             ecCC
Confidence            9765

>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=99.78  E-value=3e-19  Score=148.61  Aligned_cols=78  Identities=23%  Similarity=0.459  Sum_probs=74.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEecc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a~  492 (675)
                      ..++|||+|||+++++++|+++|+.||.|..|+|+++. +|+++|||||+|.+.+.|.+||+++++.|+|+.|+|..|.
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECC
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEeee
Confidence            35799999999999999999999999999999999998 7999999999999999999999999999999999998874

>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=99.78  E-value=7.6e-20  Score=157.70  Aligned_cols=81  Identities=33%  Similarity=0.477  Sum_probs=76.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEecc
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a~  492 (675)
                      .+.++|||+|||+++++++|++||+.||.|.+|+|+++. +|+++|||||+|.+.++|.+||.|||..|+|+.|+|.++.
T Consensus        16 ~~~~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          16 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQ   95 (101)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEEHH
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHHHCCCEECCEEEEEEECC
Confidence            346899999999999999999999999999999999987 7999999999999999999999999999999999999875


Q ss_pred             cc
Q 045516          493 ER  494 (675)
Q Consensus       493 ~~  494 (675)
                      .+
T Consensus        96 ~~   97 (101)
T d2cq4a1          96 AE   97 (101)
T ss_dssp             HH
T ss_pred             CC
Confidence            43

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.78  E-value=5.5e-19  Score=151.83  Aligned_cols=82  Identities=27%  Similarity=0.453  Sum_probs=77.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ...++|||+|||+++++++|++||.+||.|..|+|+++. +++++|||||+|.+.++|..||. ||+..|+|+.|+|.++
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a   85 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            457899999999999999999999999999999999987 89999999999999999999997 9999999999999999


Q ss_pred             cccC
Q 045516          492 RERG  495 (675)
Q Consensus       492 ~~~~  495 (675)
                      ..+.
T Consensus        86 ~~~~   89 (99)
T d1whwa_          86 TIKK   89 (99)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            8754

>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=99.78  E-value=3.8e-19  Score=150.98  Aligned_cols=82  Identities=32%  Similarity=0.490  Sum_probs=77.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ...++|||+|||+++|+++|+++|++||.|..|+|++++ +|.++|||||+|.+.++|.+||. |||+.|+|+.|+|.++
T Consensus         7 ~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A   86 (93)
T d1x5ua1           7 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKA   86 (93)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEET
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            345899999999999999999999999999999999987 89999999999999999999997 9999999999999999


Q ss_pred             cccC
Q 045516          492 RERG  495 (675)
Q Consensus       492 ~~~~  495 (675)
                      ..+.
T Consensus        87 ~~~~   90 (93)
T d1x5ua1          87 SAHN   90 (93)
T ss_dssp             TTTS
T ss_pred             CCCC
Confidence            7653

>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=99.77  E-value=5.3e-19  Score=150.07  Aligned_cols=81  Identities=31%  Similarity=0.492  Sum_probs=76.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ..++||||+|||+++|+++|+++|++||.|.+|+|++++ +++++|||||+|.+.++|..||. |||..|+|+.|+|.|+
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a   84 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD   84 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            357899999999999999999999999999999999997 89999999999999999999997 9999999999999998


Q ss_pred             ccc
Q 045516          492 RER  494 (675)
Q Consensus       492 ~~~  494 (675)
                      ...
T Consensus        85 ~~~   87 (93)
T d1h2vz_          85 AGF   87 (93)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            643

>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=99.77  E-value=2.6e-19  Score=148.32  Aligned_cols=78  Identities=28%  Similarity=0.539  Sum_probs=74.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEeccc
Q 045516          416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       416 ~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~  493 (675)
                      .++|||+|||+++++++|+++|++||.|..|+|+++. +|+++|||||+|.+.++|.+||. |||..|.|+.|+|.++++
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            4689999999999999999999999999999999986 89999999999999999999997 999999999999999864

>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=99.77  E-value=2.5e-19  Score=150.85  Aligned_cols=80  Identities=29%  Similarity=0.514  Sum_probs=75.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~  492 (675)
                      ..++|||+|||+++++++|+++|++||.|..|+|++++ +|+++|||||+|.+.++|.+||. |||..|+|+.|+|.++.
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~   83 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   83 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            35899999999999999999999999999999999988 79999999999999999999997 99999999999999997


Q ss_pred             cc
Q 045516          493 ER  494 (675)
Q Consensus       493 ~~  494 (675)
                      ++
T Consensus        84 p~   85 (89)
T d2cqba1          84 PM   85 (89)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.77  E-value=4.4e-19  Score=149.65  Aligned_cols=82  Identities=24%  Similarity=0.446  Sum_probs=77.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      ..+.++|||+|||+++++++|+++|++||.|..|+|+++. +|+++|||||+|.+.++|.+||+ |||..|+|+.|+|.|
T Consensus         5 ~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~   84 (90)
T d2cq0a1           5 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   84 (90)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            3456899999999999999999999999999999999997 79999999999999999999998 999999999999999


Q ss_pred             cccc
Q 045516          491 ARER  494 (675)
Q Consensus       491 a~~~  494 (675)
                      +.++
T Consensus        85 akp~   88 (90)
T d2cq0a1          85 AKPS   88 (90)
T ss_dssp             SSCC
T ss_pred             eeCC
Confidence            9765

>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=99.77  E-value=6.1e-19  Score=146.04  Aligned_cols=77  Identities=34%  Similarity=0.627  Sum_probs=73.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEeccc
Q 045516          417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       417 ~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~  493 (675)
                      ++|||+|||+++++++|+++|++||.|..|+|+++. +|+++|||||+|.+.++|..||. |||..|+|+.|+|.++++
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            579999999999999999999999999999999987 78999999999999999999997 999999999999999864

>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=99.77  E-value=1.4e-19  Score=148.05  Aligned_cols=75  Identities=23%  Similarity=0.469  Sum_probs=72.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEec
Q 045516          417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFA  491 (675)
Q Consensus       417 ~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a  491 (675)
                      |+|||+|||+++++++|+++|++||.|..|+|++++ +|+++|||||+|.+.++|.+||.+|++.|+||.|.|.+|
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 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            689999999999999999999999999999999998 799999999999999999999999999999999999876

>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=99.76  E-value=5.3e-19  Score=144.96  Aligned_cols=75  Identities=33%  Similarity=0.539  Sum_probs=72.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecc
Q 045516          418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       418 tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~  492 (675)
                      +|||+|||+++++++|+++|++||.|..|+|+++.+|+++|||||+|.+.++|..||+ |||..|+|+.|+|.++.
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 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            6999999999999999999999999999999999999999999999999999999997 99999999999999875

>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=99.76  E-value=4.5e-19  Score=153.31  Aligned_cols=80  Identities=23%  Similarity=0.485  Sum_probs=75.9

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEecccc
Q 045516          416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARER  494 (675)
Q Consensus       416 ~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a~~~  494 (675)
                      .++|||+|||+++++++|++||.+||.|..|+|+++. ++.++|||||+|.+.++|.+||.+|++.|.|+.|.|.++.++
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~~~~~~l~G~~i~V~~a~~k   99 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVAR   99 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECCSSC
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHHhCCCeECCEEEEEEECccc
Confidence            4799999999999999999999999999999999987 789999999999999999999999999999999999998765


Q ss_pred             C
Q 045516          495 G  495 (675)
Q Consensus       495 ~  495 (675)
                      .
T Consensus       100 e  100 (103)
T d1x4ba1         100 E  100 (103)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.76  E-value=6.2e-19  Score=145.33  Aligned_cols=75  Identities=27%  Similarity=0.508  Sum_probs=72.6

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecc
Q 045516          418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       418 tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~  492 (675)
                      +|||+|||+.+|+++|+++|++||.|..|+|++++ +|+++|||||+|.+.++|..||+ |||..|.||+|+|.|+.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            69999999999999999999999999999999998 79999999999999999999997 99999999999999985

>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=99.76  E-value=1e-18  Score=148.64  Aligned_cols=82  Identities=30%  Similarity=0.593  Sum_probs=76.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC--CCCcccEEEEEecCHHHHHHHHH-h-CCcccCCeeEEE
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA--DGRFKGYGHVEFASVEDAHKAIE-L-NGQMLGNRAIRL  488 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~--~g~~kG~afV~F~~~e~A~~Al~-l-~g~~~~gr~i~V  488 (675)
                      ...+++|||+|||+++++++|+.+|..||.|..|+|+++.  +|+++|||||+|.+.++|.+||. | |+..|.|++|+|
T Consensus         5 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V   84 (94)
T d2cpha1           5 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   84 (94)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEE
Confidence            3456899999999999999999999999999999998875  78999999999999999999997 7 899999999999


Q ss_pred             Eecccc
Q 045516          489 DFARER  494 (675)
Q Consensus       489 ~~a~~~  494 (675)
                      .|+...
T Consensus        85 ~~A~~~   90 (94)
T d2cpha1          85 EWADSE   90 (94)
T ss_dssp             EECCCC
T ss_pred             EEcCCC
Confidence            999754

>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=99.76  E-value=1.7e-18  Score=145.88  Aligned_cols=81  Identities=26%  Similarity=0.478  Sum_probs=74.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEecc
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a~  492 (675)
                      ...++|||+|||+++|+++|+++|+.||.|..|+|++++ +|+++|||||+|.+.++|.+||+ ++..|+|+.|.|.++.
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~-~~~~l~Gr~i~v~~a~   84 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS-QRHMIDGRWCDCKLPN   84 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH-SCEEETTEEEEEECCC
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHh-cCCccCCEEeEEEeCC
Confidence            346899999999999999999999999999999999998 79999999999999999999998 3447999999999987


Q ss_pred             ccC
Q 045516          493 ERG  495 (675)
Q Consensus       493 ~~~  495 (675)
                      .+.
T Consensus        85 ~k~   87 (90)
T d2cqga1          85 SKQ   87 (90)
T ss_dssp             TTC
T ss_pred             CCC
Confidence            653

>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=99.76  E-value=1.5e-18  Score=158.64  Aligned_cols=84  Identities=25%  Similarity=0.466  Sum_probs=78.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      ....++|||+|||+++++++|++||+.||.|..|+|+++. +|+++|||||+|.+.++|..||+ |||+.|+||.|+|.+
T Consensus        39 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~  118 (139)
T d1u6fa1          39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3456799999999999999999999999999999999987 79999999999999999999997 999999999999999


Q ss_pred             ccccCC
Q 045516          491 ARERGA  496 (675)
Q Consensus       491 a~~~~~  496 (675)
                      +..+..
T Consensus       119 a~~~~~  124 (139)
T d1u6fa1         119 AASGHQ  124 (139)
T ss_dssp             SSCCCC
T ss_pred             cCCCCC
Confidence            976543

>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=99.76  E-value=5.3e-19  Score=143.84  Aligned_cols=74  Identities=31%  Similarity=0.602  Sum_probs=70.6

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEec
Q 045516          418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFA  491 (675)
Q Consensus       418 tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a  491 (675)
                      +|||+|||+++++++|+++|++||.|..|+|++++ +++++|||||+|.+.++|.+||.+++..|+|+.|.|..|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHHTCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHhcCCCEECCCEEEeeEC
Confidence            59999999999999999999999999999999987 899999999999999999999999999999999999653

>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=99.76  E-value=7.4e-19  Score=146.56  Aligned_cols=78  Identities=27%  Similarity=0.510  Sum_probs=74.7

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecccc
Q 045516          417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARER  494 (675)
Q Consensus       417 ~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~~  494 (675)
                      ++|||+|||+++|+++|+++|++||+|..|+|++++ +|+++|||||+|.+.++|..||. |||..|.|++|.|.++...
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            589999999999999999999999999999999997 79999999999999999999998 9999999999999999654

>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=99.76  E-value=8.9e-19  Score=147.78  Aligned_cols=82  Identities=30%  Similarity=0.603  Sum_probs=76.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      .+.++|||+|||+++++++|++||++||.|..|.++++. +|.++|||||+|.+.++|..||. |||..|+|+.|+|.++
T Consensus         3 ~~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a   82 (90)
T d1x5sa1           3 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA   82 (90)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEE
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            457899999999999999999999999999999998876 89999999999999999999997 9999999999999998


Q ss_pred             cccC
Q 045516          492 RERG  495 (675)
Q Consensus       492 ~~~~  495 (675)
                      .++.
T Consensus        83 ~~~~   86 (90)
T d1x5sa1          83 GKSS   86 (90)
T ss_dssp             ECCC
T ss_pred             CCCC
Confidence            7553

>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=99.76  E-value=1.1e-18  Score=150.63  Aligned_cols=81  Identities=23%  Similarity=0.445  Sum_probs=76.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~  492 (675)
                      .+++|||+|||+++++++|+++|+.||.|..|.|+.+. +|+++|||||+|.+.++|..||. |||..|+|+.|+|.|+.
T Consensus        17 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a~   96 (102)
T d2cpza1          17 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKR   96 (102)
T ss_dssp             TTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEeC
Confidence            45789999999999999999999999999999999987 89999999999999999999997 99999999999999997


Q ss_pred             ccC
Q 045516          493 ERG  495 (675)
Q Consensus       493 ~~~  495 (675)
                      ++.
T Consensus        97 ~k~   99 (102)
T d2cpza1          97 SKN   99 (102)
T ss_dssp             CSC
T ss_pred             CCC
Confidence            664

>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=99.75  E-value=1.3e-18  Score=142.92  Aligned_cols=76  Identities=17%  Similarity=0.396  Sum_probs=73.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEec
Q 045516          416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFA  491 (675)
Q Consensus       416 ~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a  491 (675)
                      .++|||+|||+++|+++|++||++||.|..+.++.+. +++++|||||+|.+.+++.+||.|||+.|+||.|.|..|
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 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHCSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            4799999999999999999999999999999999987 889999999999999999999999999999999999876

>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=99.75  E-value=1.5e-18  Score=144.02  Aligned_cols=74  Identities=32%  Similarity=0.459  Sum_probs=71.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEE
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRL  488 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V  488 (675)
                      ..++|||+|||+.+|+++|+++|++||.|..|+|+++. +++++|||||+|.+.++|..||. |||..|.||.|+|
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 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            46899999999999999999999999999999999997 79999999999999999999997 9999999999987

>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=99.75  E-value=2e-18  Score=143.99  Aligned_cols=76  Identities=30%  Similarity=0.562  Sum_probs=71.4

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCC--eeEEEEec
Q 045516          416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGN--RAIRLDFA  491 (675)
Q Consensus       416 ~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~g--r~i~V~~a  491 (675)
                      .++|||+|||+.+|+++|+++|++||.|..|+|++++ +|+++|||||+|.+.++|..||+ |||..|.|  ++|+|.|+
T Consensus         6 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2           6 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            4789999999999999999999999999999999987 79999999999999999999997 99999998  55888875

>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=99.75  E-value=8e-19  Score=146.70  Aligned_cols=80  Identities=16%  Similarity=0.358  Sum_probs=71.7

Q ss_pred             CCceEEEcCCCCCCC-HHHHHHHhhhCCCeEEEEEeeCC--CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEec
Q 045516          415 GSKTLFVGNLPFSVE-QADVQNFFSEVAEVVDVRLSSDA--DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFA  491 (675)
Q Consensus       415 ~~~tlfV~nLp~~~t-e~~L~~~F~~~G~I~~v~i~~~~--~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a  491 (675)
                      +.++|||+|||++++ ++.|++||++||.|..|+|+.+.  +++++|||||+|.+.++|.+||+||++.|+|+.|+|.++
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~~n~~~~~gr~l~V~~a   82 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISVSLA   82 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGGGTTEEETTEEEEEEEC
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHhcCCCEECCEEEEEEEc
Confidence            578999999999986 56699999999999999997753  789999999999999999999999999999999999998


Q ss_pred             ccc
Q 045516          492 RER  494 (675)
Q Consensus       492 ~~~  494 (675)
                      .++
T Consensus        83 ~~k   85 (86)
T d2ghpa3          83 DKK   85 (86)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            754

>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=99.75  E-value=2.2e-18  Score=143.66  Aligned_cols=77  Identities=25%  Similarity=0.478  Sum_probs=72.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCC--eeEEEEe
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGN--RAIRLDF  490 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~g--r~i~V~~  490 (675)
                      ..++|||+|||+++++++|+++|++||.|..|+|++++ +|+++|||||+|.+.++|.+||+ |||..|.|  ++|+|.|
T Consensus         5 ~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~   84 (85)
T d1b7fa2           5 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRL   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEE
Confidence            35689999999999999999999999999999999987 89999999999999999999997 99999976  8899988


Q ss_pred             c
Q 045516          491 A  491 (675)
Q Consensus       491 a  491 (675)
                      |
T Consensus        85 A   85 (85)
T d1b7fa2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.75  E-value=2.1e-18  Score=143.80  Aligned_cols=77  Identities=21%  Similarity=0.437  Sum_probs=74.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEecc
Q 045516          416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       416 ~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a~  492 (675)
                      .++|||+|||+++|+++|++||+.||.|..|+|+++.+|+++|||||+|.+.++|.+||++++..|.|+.|.|.+..
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 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKD   82 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHTCCCCEETTEECEEEEGG
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHHHCCCEECCEEEEEEEcC
Confidence            57999999999999999999999999999999999999999999999999999999999999999999999998864

>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=99.74  E-value=4.4e-18  Score=144.32  Aligned_cols=82  Identities=32%  Similarity=0.590  Sum_probs=75.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ....++|||+|||+.+++++|++||..||.|..|+|+.+..+ ++|||||+|.+.++|.+||. ||+..|+|+.|+|.++
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~-~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A   86 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   86 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccC-CcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            345679999999999999999999999999999999988644 69999999999999999997 9999999999999999


Q ss_pred             cccC
Q 045516          492 RERG  495 (675)
Q Consensus       492 ~~~~  495 (675)
                      ..+.
T Consensus        87 ~~r~   90 (93)
T d2cq3a1          87 TARV   90 (93)
T ss_dssp             CSSC
T ss_pred             CcCC
Confidence            8764

>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=99.74  E-value=4.4e-18  Score=143.45  Aligned_cols=81  Identities=25%  Similarity=0.471  Sum_probs=74.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ....++|||+|||+++++++|+++|+.||.|..|+|+++..+ .+|||||+|.+.++|..||. |||..|.|+.|+|.|+
T Consensus         5 ~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~-~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a   83 (90)
T d2cqia1           5 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   83 (90)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS-SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCc-cceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            345689999999999999999999999999999999988643 38999999999999999997 9999999999999999


Q ss_pred             ccc
Q 045516          492 RER  494 (675)
Q Consensus       492 ~~~  494 (675)
                      .+.
T Consensus        84 ~~~   86 (90)
T d2cqia1          84 TTP   86 (90)
T ss_dssp             CCT
T ss_pred             CCC
Confidence            754

>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=99.74  E-value=1.1e-18  Score=151.25  Aligned_cols=80  Identities=39%  Similarity=0.696  Sum_probs=75.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~  492 (675)
                      ..++|||+|||+++++++|++||++||.|..|+|++++ +|+++|||||+|.+.++|.+||. |||..|.|+.|+|.++.
T Consensus         7 ~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~   86 (104)
T d1p1ta_           7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            35799999999999999999999999999999999987 79999999999999999999997 99999999999999986


Q ss_pred             cc
Q 045516          493 ER  494 (675)
Q Consensus       493 ~~  494 (675)
                      ..
T Consensus        87 ~~   88 (104)
T d1p1ta_          87 SE   88 (104)
T ss_dssp             CT
T ss_pred             CC
Confidence            43

>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=99.74  E-value=1.4e-18  Score=143.57  Aligned_cols=77  Identities=19%  Similarity=0.278  Sum_probs=67.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEeccc
Q 045516          417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       417 ~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~  493 (675)
                      +||||+|||+++|+++|+++|+.||.|..+.++.+. +|+++|||||+|.+.++|.+||. |||..|.|+.|+|.++.+
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 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            799999999999999999999999999888777665 89999999999999999999997 999999999999999864

>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=99.74  E-value=4.2e-18  Score=147.31  Aligned_cols=80  Identities=24%  Similarity=0.499  Sum_probs=73.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~  492 (675)
                      ..++|||+|||+.+++++|++||+.||.|.+|+|+++. +|+++|||||+|.+.++|.+||+ +|+ .|+||.|+|.++.
T Consensus         9 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a~   87 (103)
T d2cqda1           9 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAY   87 (103)
T ss_dssp             SSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEEST
T ss_pred             CCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEcC
Confidence            45789999999999999999999999999999999997 79999999999999999999998 654 7999999999987


Q ss_pred             ccC
Q 045516          493 ERG  495 (675)
Q Consensus       493 ~~~  495 (675)
                      ...
T Consensus        88 ~~~   90 (103)
T d2cqda1          88 LGA   90 (103)
T ss_dssp             TTC
T ss_pred             CCC
Confidence            543

>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=99.74  E-value=7.6e-19  Score=142.71  Aligned_cols=74  Identities=22%  Similarity=0.421  Sum_probs=70.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEec
Q 045516          418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFA  491 (675)
Q Consensus       418 tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a  491 (675)
                      +|||+|||+++|+++|+++|++||.|..|+|++++ +++++|||||+|.+.++|.+||+++++.|+|+.|.|.+|
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 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTCSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhhCCCEECCEEeEEEEC
Confidence            59999999999999999999999999999999997 899999999999999999999998889999999999864

>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=99.72  E-value=8.8e-18  Score=143.82  Aligned_cols=83  Identities=25%  Similarity=0.432  Sum_probs=75.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hC------CcccCCe
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LN------GQMLGNR  484 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~------g~~~~gr  484 (675)
                      ..+.++|||+|||+++|+++|++||.+||.|..++++.+. +++++|||||+|.+.++|.+||. ||      |..|.||
T Consensus         5 ~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr   84 (98)
T d1x4ha1           5 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   84 (98)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCE
Confidence            4567899999999999999999999999999999999887 78899999999999999999997 75      6778999


Q ss_pred             eEEEEeccccC
Q 045516          485 AIRLDFARERG  495 (675)
Q Consensus       485 ~i~V~~a~~~~  495 (675)
                      .|+|.++.++.
T Consensus        85 ~l~v~~a~~k~   95 (98)
T d1x4ha1          85 QLKVDLAVTRD   95 (98)
T ss_dssp             EEEEECCCCCC
T ss_pred             EEEEEECCCCC
Confidence            99999987653

>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=99.72  E-value=3.8e-18  Score=143.52  Aligned_cols=79  Identities=30%  Similarity=0.570  Sum_probs=73.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEeccc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~  493 (675)
                      ...+|||+|||+++++++|+++|+.||.|..|+|+.+.. .++|||||+|.+.++|.+||+ |||..|+|+.|.|.++..
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~-~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~   85 (89)
T d1cvja2           7 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN-GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   85 (89)
T ss_dssp             TTTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTT-BCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecC-CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            346899999999999999999999999999999998864 368999999999999999997 999999999999999976


Q ss_pred             c
Q 045516          494 R  494 (675)
Q Consensus       494 ~  494 (675)
                      +
T Consensus        86 ~   86 (89)
T d1cvja2          86 R   86 (89)
T ss_dssp             T
T ss_pred             C
Confidence            5

>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=99.72  E-value=2.9e-18  Score=139.29  Aligned_cols=74  Identities=28%  Similarity=0.491  Sum_probs=71.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEec
Q 045516          418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFA  491 (675)
Q Consensus       418 tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a  491 (675)
                      +|||+|||+++|+++|++||+.||.|..|.++++. ++.++|||||+|.+.++|.+||+|||+.|+||.|+|.+|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHHCSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHhcCCCEECCeEEEEEEC
Confidence            59999999999999999999999999999999887 789999999999999999999999999999999999875

>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=99.72  E-value=4.9e-19  Score=149.59  Aligned_cols=81  Identities=30%  Similarity=0.397  Sum_probs=75.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEecc
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a~  492 (675)
                      ....++|||+|||+.+++++|+++|+.||.|..|+|+.+.+|+++|||||+|.+.++|.+||+|||..|+|+.|+|.++.
T Consensus        10 ~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~~~g~~~~g~~i~V~~ak   89 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPK   89 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEECCC
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHhcCCcEECCEEEEEEecC
Confidence            34568999999999999999999999999999999887779999999999999999999999999999999999999986


Q ss_pred             c
Q 045516          493 E  493 (675)
Q Consensus       493 ~  493 (675)
                      .
T Consensus        90 ~   90 (91)
T d1fjeb1          90 G   90 (91)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.72  E-value=3.5e-18  Score=141.78  Aligned_cols=77  Identities=32%  Similarity=0.611  Sum_probs=71.5

Q ss_pred             EEEcCCCCCCCHHHHHHHhhhCCCeEEE-EEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEeccccC
Q 045516          419 LFVGNLPFSVEQADVQNFFSEVAEVVDV-RLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARERG  495 (675)
Q Consensus       419 lfV~nLp~~~te~~L~~~F~~~G~I~~v-~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~~~  495 (675)
                      |||+|||+++++++|+++|++||.|..+ +|+++. +|+++|||||+|.+.++|..||. |||..|+|++|+|.++.++.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            8999999999999999999999999764 778776 79999999999999999999997 99999999999999987653

>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=99.71  E-value=6.7e-18  Score=140.68  Aligned_cols=75  Identities=27%  Similarity=0.526  Sum_probs=69.7

Q ss_pred             EEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CC---CcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEeccc
Q 045516          419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DG---RFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       419 lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g---~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~  493 (675)
                      |||+|||+++|+++|++||++||.|..|.|+++. ++   .++|||||+|.+.++|.+||. |||..|+|+.|+|.++..
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            8999999999999999999999999999999876 32   479999999999999999997 999999999999999854

>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=99.71  E-value=1.2e-17  Score=147.13  Aligned_cols=78  Identities=19%  Similarity=0.414  Sum_probs=72.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEeccc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~  493 (675)
                      .+++|||+|||+++++++|+++|++||.|..|+|..  ++.++|||||+|.+.++|..||. |||+.|.|+.|+|.++..
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~--~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~   83 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN--TPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNA   83 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEC--STTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccc--cCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            468999999999999999999999999999999986  45679999999999999999997 999999999999999864


Q ss_pred             c
Q 045516          494 R  494 (675)
Q Consensus       494 ~  494 (675)
                      .
T Consensus        84 ~   84 (114)
T d2f9da1          84 N   84 (114)
T ss_dssp             H
T ss_pred             C
Confidence            3

>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=99.71  E-value=1.2e-17  Score=144.67  Aligned_cols=80  Identities=35%  Similarity=0.673  Sum_probs=73.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC--CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEecc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA--DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~--~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a~  492 (675)
                      ..++|||+|||+++++++|++||+.|| |+.|+|+.+.  +++++|||||+|.+.++|++|+.||++.|+||.|+|.++.
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~~~~~~~~gr~l~V~~a~   92 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVDVAD   92 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEEEECC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            458999999999999999999999999 8888888775  6889999999999999999888899999999999999987


Q ss_pred             ccC
Q 045516          493 ERG  495 (675)
Q Consensus       493 ~~~  495 (675)
                      .+.
T Consensus        93 ~~~   95 (104)
T d1wi8a_          93 QAQ   95 (104)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.70  E-value=1.5e-17  Score=143.29  Aligned_cols=82  Identities=23%  Similarity=0.423  Sum_probs=74.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCe--------EEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCC
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEV--------VDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGN  483 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I--------~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~g  483 (675)
                      ...++|||+|||+++++++|++||..||.|        ..+.+.++. +|+++|||||+|.+.++|.+||. |||..|+|
T Consensus         6 ~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g   85 (101)
T d2cpea1           6 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQG   85 (101)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEECC
Confidence            456899999999999999999999999987        456677776 78999999999999999999997 99999999


Q ss_pred             eeEEEEeccccC
Q 045516          484 RAIRLDFARERG  495 (675)
Q Consensus       484 r~i~V~~a~~~~  495 (675)
                      |.|+|.++..+.
T Consensus        86 r~i~V~~a~~~~   97 (101)
T d2cpea1          86 SKLKVSLARKKP   97 (101)
T ss_dssp             EECEEECSSCCC
T ss_pred             EEEEEEEcCCCC
Confidence            999999997653

>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=99.70  E-value=7.9e-18  Score=145.30  Aligned_cols=82  Identities=29%  Similarity=0.472  Sum_probs=75.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEecc
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a~  492 (675)
                      ....++|||+||||++|+++|++||..|| |+.|+|+++.+++++|||||+|.+.++|++||+||++.|+||.|+|.++.
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~~~~~~i~gR~I~V~~s~   90 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLNS   90 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESSSSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEEEC
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEecCCcceEEEEEEECCHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            34568999999999999999999999998 56889999989999999999999999999999999999999999999987


Q ss_pred             ccC
Q 045516          493 ERG  495 (675)
Q Consensus       493 ~~~  495 (675)
                      ...
T Consensus        91 ~~~   93 (102)
T d1weza_          91 TAG   93 (102)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>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=99.70  E-value=1.1e-17  Score=143.98  Aligned_cols=80  Identities=21%  Similarity=0.452  Sum_probs=74.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ..+.++|||+|||+++++++|++||+.||.|..++++.+.+++++|||||+|.+.++|.+||. |||..|.|++|.|.++
T Consensus        15 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~   94 (101)
T d1x5oa1          15 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT   94 (101)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCC
Confidence            345689999999999999999999999999999999999899999999999999999999997 9999999999988665


Q ss_pred             c
Q 045516          492 R  492 (675)
Q Consensus       492 ~  492 (675)
                      .
T Consensus        95 ~   95 (101)
T d1x5oa1          95 E   95 (101)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.70  E-value=5e-17  Score=139.39  Aligned_cols=84  Identities=23%  Similarity=0.375  Sum_probs=78.3

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEE
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVV  595 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V  595 (675)
                      ..++|||+|||+.+++++    |+++|..||.|..|+|+++..+|+++|||||+|.+.+.|..||. ||+..|+|+.|+|
T Consensus         7 ~~~~lfV~nL~~~~t~~~----l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V   82 (99)
T d1whwa_           7 GSGRLFVRNLSYTSSEED----LEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHV   82 (99)
T ss_dssp             SCEEEEEECCCTTCCHHH----HHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEE
T ss_pred             CCCEEEEECCCCcCCHHH----HHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            368899999999999998    77888899999999999999999999999999999999999998 9999999999999


Q ss_pred             eccccCCCC
Q 045516          596 DEAKQRGDF  604 (675)
Q Consensus       596 ~~a~~r~~~  604 (675)
                      .++.++...
T Consensus        83 ~~a~~~~~~   91 (99)
T d1whwa_          83 LPSTIKKEA   91 (99)
T ss_dssp             EECCCCSTT
T ss_pred             EECCCCCcc
Confidence            999876544

>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=99.70  E-value=1.7e-17  Score=134.71  Aligned_cols=74  Identities=24%  Similarity=0.411  Sum_probs=69.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEec
Q 045516          417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFA  491 (675)
Q Consensus       417 ~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a  491 (675)
                      .+|||+|||+++++++|++||..||.|..|+|++++.+. ++||||+|.+.++|.+||.||+..|+|++|.|..+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~-~~~afV~F~~~~~a~~Al~~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKN-FRFARIEFARYDGALAAITKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSS-SEEEEEEESSHHHHHHHHTTTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecccc-ceEEEEEEcchHHhHHHHHhcCcEECCEEEEEEEC
Confidence            489999999999999999999999999999999987654 57999999999999999999999999999999864

>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=99.69  E-value=5e-17  Score=136.21  Aligned_cols=82  Identities=29%  Similarity=0.460  Sum_probs=77.2

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEE
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVV  595 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V  595 (675)
                      ..++|||+|||..+++++    |.++|+.||.|..|+|+++..+|.++|||||+|.+.++|.+||. |||..|+|+.|+|
T Consensus         6 ~~~~l~V~nL~~~~t~~~----l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V   81 (88)
T d1rk8a_           6 EGWILFVTSIHEEAQEDE----IQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQV   81 (88)
T ss_dssp             -CEEEEEESCCTTCCHHH----HHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHH----HHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            368999999999999998    77889999999999999999999999999999999999999998 9999999999999


Q ss_pred             eccccCC
Q 045516          596 DEAKQRG  602 (675)
Q Consensus       596 ~~a~~r~  602 (675)
                      .|+.+++
T Consensus        82 ~~a~~kG   88 (88)
T d1rk8a_          82 DWCFVKG   88 (88)
T ss_dssp             EESEECC
T ss_pred             EEecCCC
Confidence            9998764

>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=99.69  E-value=3.4e-17  Score=149.46  Aligned_cols=84  Identities=21%  Similarity=0.323  Sum_probs=77.7

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEE
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVV  595 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V  595 (675)
                      ..++|||+|||+.+++++    |..+|..||.|..|+|+++..+|+++|||||+|.+.++|..||. |||..|+|+.|+|
T Consensus        41 ~~~~l~V~nLp~~~te~~----l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V  116 (139)
T d1u6fa1          41 VLRNLMVNYIPTTVDEVQ----LRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKV  116 (139)
T ss_dssp             TTSEEEEESCSTTCCHHH----HHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHH----HHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            357899999999999998    77889999999999999999999999999999999999999998 9999999999999


Q ss_pred             eccccCCCC
Q 045516          596 DEAKQRGDF  604 (675)
Q Consensus       596 ~~a~~r~~~  604 (675)
                      .|+.++..+
T Consensus       117 ~~a~~~~~~  125 (139)
T d1u6fa1         117 ALAASGHQR  125 (139)
T ss_dssp             EESSCCCCC
T ss_pred             EEcCCCCCC
Confidence            999865543

>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=99.69  E-value=6.6e-17  Score=136.07  Aligned_cols=82  Identities=30%  Similarity=0.439  Sum_probs=78.2

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEE
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVV  595 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V  595 (675)
                      ..++|||+|||..+++++    |+++|..||.|..|+|+++..+|.++|||||+|.+.++|.+||+ |||..|+|+.|+|
T Consensus         7 ~~~~i~V~nLp~~~t~~~----l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v   82 (90)
T d2cq0a1           7 DNATIRVTNLSEDTRETD----LQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNV   82 (90)
T ss_dssp             SSEEEEEESCCTTCCHHH----HHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCEEEEECCCCCCCHHH----HHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            368999999999999998    88999999999999999999999999999999999999999998 9999999999999


Q ss_pred             eccccCC
Q 045516          596 DEAKQRG  602 (675)
Q Consensus       596 ~~a~~r~  602 (675)
                      .|++|+.
T Consensus        83 ~~akp~~   89 (90)
T d2cq0a1          83 EWAKPST   89 (90)
T ss_dssp             EESSCCC
T ss_pred             EeeeCCC
Confidence            9999875

>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=99.69  E-value=3.5e-17  Score=139.30  Aligned_cols=81  Identities=23%  Similarity=0.436  Sum_probs=73.2

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEe
Q 045516          412 QSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF  490 (675)
Q Consensus       412 ~~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~  490 (675)
                      .....++|||+|||+++++++|++||.+||.|..|.+..+  +.++|||||+|.+.++|..||. ||++.|.|+.|+|.|
T Consensus        10 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~--~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~   87 (95)
T d1x4aa1          10 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR--RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF   87 (95)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS--SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc--ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            3456789999999999999999999999999999988654  4568999999999999999997 999999999999999


Q ss_pred             cccc
Q 045516          491 ARER  494 (675)
Q Consensus       491 a~~~  494 (675)
                      ++..
T Consensus        88 a~~~   91 (95)
T d1x4aa1          88 PRSG   91 (95)
T ss_dssp             CCCC
T ss_pred             ccCC
Confidence            8653

>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=99.69  E-value=3.2e-17  Score=141.91  Aligned_cols=83  Identities=27%  Similarity=0.365  Sum_probs=74.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEE-eeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRL-SSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i-~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a  491 (675)
                      .....+|||+||||++|+++|++||..||.|..+.+ +.+.+++++|||||+|.+.++|.+||+||++.|+||.|+|.++
T Consensus        12 ~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~~~~~~i~gR~i~V~~~   91 (104)
T d1wg5a_          12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKS   91 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHhhCCCEEcceEEEEEEC
Confidence            445678999999999999999999999999887544 4445899999999999999999999999999999999999998


Q ss_pred             cccC
Q 045516          492 RERG  495 (675)
Q Consensus       492 ~~~~  495 (675)
                      ....
T Consensus        92 ~~~~   95 (104)
T d1wg5a_          92 SRAE   95 (104)
T ss_dssp             CTTT
T ss_pred             CHHH
Confidence            7654

>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=99.68  E-value=4.1e-17  Score=139.01  Aligned_cols=75  Identities=23%  Similarity=0.483  Sum_probs=70.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecccc
Q 045516          416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARER  494 (675)
Q Consensus       416 ~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~~  494 (675)
                      .++|||+|||+.+++++|+++|++||.|.+|+|+.+     +|||||+|.+.++|.+||. |||..|+|+.|+|.|+..+
T Consensus        18 ~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~-----kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~~   92 (96)
T d1x4ga1          18 NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKES   92 (96)
T ss_dssp             CCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec-----ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            579999999999999999999999999999999975     8999999999999999997 9999999999999998764


Q ss_pred             C
Q 045516          495 G  495 (675)
Q Consensus       495 ~  495 (675)
                      .
T Consensus        93 p   93 (96)
T d1x4ga1          93 P   93 (96)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.68  E-value=5.2e-17  Score=134.24  Aligned_cols=79  Identities=23%  Similarity=0.414  Sum_probs=75.3

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~  596 (675)
                      .++|||+|||..+++++    |+++|++||.|..|+|+++..+|.++|||||+|.+.++|.+||. |||..|+|+.|+|.
T Consensus         2 ~t~l~V~nLp~~~t~~~----l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~   77 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRE----LYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVS   77 (82)
T ss_dssp             CSEEEEECCCTTCCHHH----HHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCEEEEeCCCCCCCHHH----HHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            46899999999999998    77899999999999999999999999999999999999999998 99999999999999


Q ss_pred             cccc
Q 045516          597 EAKQ  600 (675)
Q Consensus       597 ~a~~  600 (675)
                      |++|
T Consensus        78 ~a~p   81 (82)
T d1b7fa1          78 YARP   81 (82)
T ss_dssp             ECCC
T ss_pred             EcCC
Confidence            9976

>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=99.68  E-value=1.5e-17  Score=143.49  Aligned_cols=81  Identities=23%  Similarity=0.426  Sum_probs=76.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~  492 (675)
                      .+++|||+|||+++++++|++||..||.|..+.|+.+. +|+++|||||+|.+.++|..||. |||..|.|+.|+|.|+.
T Consensus        17 ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~ak   96 (102)
T d2cpxa1          17 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGK   96 (102)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeCC
Confidence            46899999999999999999999999999999998876 89999999999999999999997 99999999999999997


Q ss_pred             ccC
Q 045516          493 ERG  495 (675)
Q Consensus       493 ~~~  495 (675)
                      ++.
T Consensus        97 ~k~   99 (102)
T d2cpxa1          97 NKK   99 (102)
T ss_dssp             CCS
T ss_pred             Ccc
Confidence            654

>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=99.68  E-value=5.1e-17  Score=140.15  Aligned_cols=84  Identities=20%  Similarity=0.369  Sum_probs=79.4

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEec
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDE  597 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~~  597 (675)
                      .++|||+|||+.+++++    |+++|.+||.|..|.|+++..++.++|||||+|.+.++|.+||.++++.|+|+.|.|.+
T Consensus        20 ~~~lfVgnLp~~~te~~----L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~~~~~~l~G~~i~V~~   95 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEES----LRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKR   95 (103)
T ss_dssp             HTEEEEECCTTCCCHHH----HHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEEC
T ss_pred             CCEEEEeCCCCcCCHHH----HHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHHhCCCeECCEEEEEEE
Confidence            47899999999999998    78999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCCC
Q 045516          598 AKQRGDFG  605 (675)
Q Consensus       598 a~~r~~~~  605 (675)
                      +.+|...|
T Consensus        96 a~~ke~~g  103 (103)
T d1x4ba1          96 AVAREESG  103 (103)
T ss_dssp             CSSCCCCC
T ss_pred             CcccCCCc
Confidence            99887653

>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=99.67  E-value=1.6e-16  Score=134.57  Aligned_cols=80  Identities=18%  Similarity=0.329  Sum_probs=75.9

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEE
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVV  595 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V  595 (675)
                      .+++|||+|||+.+++++    |+++|..||.|..|+|+++..+|.++|||||+|.+.++|..||. |||..|+|+.|+|
T Consensus         6 ~s~tlfV~nlp~~~te~~----l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   81 (93)
T d1h2vz_           6 KSCTLYVGNLSFYTTEEQ----IYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRT   81 (93)
T ss_dssp             TCCEEEEESCCTTCCHHH----HHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHH----HHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            478999999999999998    78889999999999999999999999999999999999999998 9999999999999


Q ss_pred             ecccc
Q 045516          596 DEAKQ  600 (675)
Q Consensus       596 ~~a~~  600 (675)
                      .|+..
T Consensus        82 ~~a~~   86 (93)
T d1h2vz_          82 DWDAG   86 (93)
T ss_dssp             EEESC
T ss_pred             EEcCC
Confidence            99854

>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=99.67  E-value=5.5e-17  Score=136.27  Aligned_cols=82  Identities=28%  Similarity=0.507  Sum_probs=77.5

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~  596 (675)
                      .++|||+|||+.+++++    |+++|+.||.|..|+|++++.+|.++|||||+|.+.++|..||. |||..|+|+.|+|.
T Consensus         5 ~~tlfV~nLp~~~te~~----l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~   80 (89)
T d2cqba1           5 KRVLYVGGLAEEVDDKV----LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN   80 (89)
T ss_dssp             CSCEEEESCCSSCCHHH----HHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CcEEEEeCCCCcCCHHH----HHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            68999999999999998    78899999999999999999999999999999999999999998 99999999999999


Q ss_pred             ccccCCC
Q 045516          597 EAKQRGD  603 (675)
Q Consensus       597 ~a~~r~~  603 (675)
                      |++++..
T Consensus        81 ~a~p~~~   87 (89)
T d2cqba1          81 LAKPMRI   87 (89)
T ss_dssp             ECCCCCC
T ss_pred             EeCCCCC
Confidence            9987643

>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=99.67  E-value=5.6e-17  Score=135.28  Aligned_cols=76  Identities=26%  Similarity=0.477  Sum_probs=70.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEeccc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~  493 (675)
                      ..++|||+|||+++++++|+++|++||.|.+|+|.++     +|||||+|.+.++|..||. |||..|.|+.|+|.|+..
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~-----k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~   81 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACH   81 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT-----TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            4578999999999999999999999999999999865     7999999999999999998 999999999999999875


Q ss_pred             cC
Q 045516          494 RG  495 (675)
Q Consensus       494 ~~  495 (675)
                      ..
T Consensus        82 ~~   83 (86)
T d2cpja1          82 SA   83 (86)
T ss_dssp             CS
T ss_pred             cC
Confidence            43

>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=99.67  E-value=5.8e-17  Score=135.23  Aligned_cols=76  Identities=28%  Similarity=0.456  Sum_probs=70.7

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhhCCCeEE-EEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVD-VRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       416 ~~tlfV~nLp~~~te~~L~~~F~~~G~I~~-v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      .++|||+|||+++++++|++||..||.|.. ++|..+.+++++|||||+|.+.++|.+||. ||+..|.||+|+|.++
T Consensus         9 ~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           9 PTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             SEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            567999999999999999999999999876 677777799999999999999999999997 9999999999999874

>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=99.67  E-value=5.9e-17  Score=141.89  Aligned_cols=75  Identities=24%  Similarity=0.239  Sum_probs=69.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEeccc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~  493 (675)
                      ..++|||+|||+.+++++|++||+.||.|..|.|..     .+|||||+|.+.++|.+||+ |||..|.|+.|+|.|+..
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~-----~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~   83 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-----GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPI   83 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS-----SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEET
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec-----cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCC
Confidence            457999999999999999999999999999998853     48999999999999999997 999999999999999865


Q ss_pred             c
Q 045516          494 R  494 (675)
Q Consensus       494 ~  494 (675)
                      .
T Consensus        84 ~   84 (111)
T d1whxa_          84 G   84 (111)
T ss_dssp             T
T ss_pred             C
Confidence            4

>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=99.66  E-value=1.3e-16  Score=131.70  Aligned_cols=78  Identities=21%  Similarity=0.426  Sum_probs=74.4

Q ss_pred             eEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEec
Q 045516          519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVDE  597 (675)
Q Consensus       519 ~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~~  597 (675)
                      ++|||+|||..+++++    |+++|+.||.|..|+|+++..+|.++|||||+|.+.++|..|+. |||..|+|+.|+|.|
T Consensus         3 t~l~V~nLp~~~te~~----l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~   78 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEE----FRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSY   78 (82)
T ss_dssp             SEEEEESCCTTCCHHH----HHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CEEEEECCCCCCCHHH----HHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            5799999999999998    77889999999999999999999999999999999999999998 999999999999999


Q ss_pred             ccc
Q 045516          598 AKQ  600 (675)
Q Consensus       598 a~~  600 (675)
                      ++|
T Consensus        79 AkP   81 (82)
T d1fxla1          79 ARP   81 (82)
T ss_dssp             CCC
T ss_pred             eeC
Confidence            976

>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=99.66  E-value=1.8e-16  Score=136.59  Aligned_cols=85  Identities=22%  Similarity=0.345  Sum_probs=79.5

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      ++.++|||+|||+.+++++    |.++|..||.|..|.++.+..+|.++|||||+|.+.++|..||+ |||..|+|+.|+
T Consensus        16 p~~~~l~V~nLp~~~te~~----l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~   91 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQD----LLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLK   91 (102)
T ss_dssp             STTCCEEEESCCSSCCHHH----HHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHH----HHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEE
Confidence            4468899999999999998    77899999999999999999999999999999999999999997 999999999999


Q ss_pred             EeccccCCCC
Q 045516          595 VDEAKQRGDF  604 (675)
Q Consensus       595 V~~a~~r~~~  604 (675)
                      |.|++++..+
T Consensus        92 V~~a~~k~~~  101 (102)
T d2cpza1          92 VQLKRSKNDS  101 (102)
T ss_dssp             EECCCCSCCC
T ss_pred             EEEeCCCCCC
Confidence            9999987654

>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=99.66  E-value=1.3e-16  Score=134.99  Aligned_cols=82  Identities=26%  Similarity=0.454  Sum_probs=77.5

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~  596 (675)
                      .++|||+|||..+++++    |+++|.+||.|..|+|+++..+|.++|||||+|.+.++|..||. |||..|+|+.|+|.
T Consensus         9 ~~tlfV~nLp~~~t~~~----l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   84 (93)
T d1x5ua1           9 DATVYVGGLDEKVSEPL----LWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVN   84 (93)
T ss_dssp             TTEEEEECCCTTCCHHH----HHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEE
T ss_pred             CCEEEEeCCCCcCCHHH----HHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            57999999999999998    77889999999999999999999999999999999999999998 99999999999999


Q ss_pred             ccccCCC
Q 045516          597 EAKQRGD  603 (675)
Q Consensus       597 ~a~~r~~  603 (675)
                      |+.++..
T Consensus        85 ~A~~~~~   91 (93)
T d1x5ua1          85 KASAHNK   91 (93)
T ss_dssp             ETTTTSC
T ss_pred             EcCCCCC
Confidence            9988654

>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=99.66  E-value=1.8e-16  Score=131.57  Aligned_cols=78  Identities=19%  Similarity=0.411  Sum_probs=74.4

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEec
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDE  597 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~~  597 (675)
                      .++|||+|||+++++++    |+++|..||.|..|+|+++..+|.++|||||+|.+.+.|.+||+++++.|+|+.|+|..
T Consensus         6 ~~~lfV~nlp~~~te~~----l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~~~~~~i~Gr~i~V~~   81 (84)
T d1l3ka1           6 LRKLFIGGLSFETTDES----LRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKR   81 (84)
T ss_dssp             GGEEEEESCCTTCCHHH----HHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEE
T ss_pred             CcEEEEECCCCCCCHHH----HHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEe
Confidence            57999999999999998    78999999999999999999999999999999999999999999999999999999988


Q ss_pred             cc
Q 045516          598 AK  599 (675)
Q Consensus       598 a~  599 (675)
                      |.
T Consensus        82 A~   83 (84)
T d1l3ka1          82 AV   83 (84)
T ss_dssp             CC
T ss_pred             ee
Confidence            74

>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=99.66  E-value=4.6e-17  Score=140.67  Aligned_cols=79  Identities=24%  Similarity=0.367  Sum_probs=72.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEE-EEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEeccc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVD-VRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~-v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a~~  493 (675)
                      ...+|||+|||+++|+++|++||..||.|.. |.|+.+.+|+++|||||+|.+.++|.+||.||+..|+||.|.|.++..
T Consensus         7 ~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~~n~~~i~gr~i~V~~~~~   86 (103)
T d2cpya1           7 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHVVTL   86 (103)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEEEECH
T ss_pred             CceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHhcCCCeECCcEEEEEECCH
Confidence            3568999999999999999999999999876 566666799999999999999999999999999999999999988754

>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=99.66  E-value=1.7e-16  Score=138.49  Aligned_cols=76  Identities=25%  Similarity=0.372  Sum_probs=69.9

Q ss_pred             CceEEEcCCCC-CCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEeccc
Q 045516          416 SKTLFVGNLPF-SVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       416 ~~tlfV~nLp~-~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~  493 (675)
                      +++|||+|||+ .+++++|++||+.||.|..|+|+++.    +|||||+|.+.++|.+||+ |||..|.|+.|+|.|+..
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~~   77 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKH   77 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            68999999964 69999999999999999999999864    7999999999999999997 999999999999999865


Q ss_pred             cC
Q 045516          494 RG  495 (675)
Q Consensus       494 ~~  495 (675)
                      ..
T Consensus        78 ~~   79 (109)
T d2adca1          78 QN   79 (109)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.66  E-value=6.4e-17  Score=137.89  Aligned_cols=79  Identities=30%  Similarity=0.554  Sum_probs=71.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ....++|||+|||+++++++|++||..||.|..|++    +++++|||||+|.+.++|..||. |||..|+|+.|+|.|+
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a   88 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT   88 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee----cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            456799999999999999999999999998876653    57889999999999999999997 9999999999999999


Q ss_pred             cccC
Q 045516          492 RERG  495 (675)
Q Consensus       492 ~~~~  495 (675)
                      .++.
T Consensus        89 ~~k~   92 (96)
T d1fjca_          89 GEKG   92 (96)
T ss_dssp             SSSC
T ss_pred             CCCC
Confidence            8764

>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=99.66  E-value=1.9e-16  Score=130.15  Aligned_cols=76  Identities=26%  Similarity=0.398  Sum_probs=72.9

Q ss_pred             EEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEecc
Q 045516          520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVDEA  598 (675)
Q Consensus       520 ~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~~a  598 (675)
                      .|||+|||+.+++++    |.++|..||.|..|+|++++.+|+++|||||+|.+.++|..||+ |||..|+|+.|+|.|+
T Consensus         2 slfV~nL~~~~te~~----l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a   77 (80)
T d1cvja1           2 SLYVGDLHPDVTEAM----LYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWS   77 (80)
T ss_dssp             EEEEESCCTTCCHHH----HHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEEC
T ss_pred             EEEEeCCCCcCCHHH----HHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            599999999999998    77889999999999999999999999999999999999999998 9999999999999998


Q ss_pred             c
Q 045516          599 K  599 (675)
Q Consensus       599 ~  599 (675)
                      +
T Consensus        78 ~   78 (80)
T d1cvja1          78 Q   78 (80)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.66  E-value=1.7e-16  Score=131.47  Aligned_cols=74  Identities=26%  Similarity=0.432  Sum_probs=68.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCccc-CCeeEEEEecc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQML-GNRAIRLDFAR  492 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~-~gr~i~V~~a~  492 (675)
                      .+++|||+|||+++++++|+.+|+.||.|..|+|+++    .+|||||+|.+.++|..||. |||..| +|+.|+|.|++
T Consensus         7 P~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~----~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1           7 PNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN----RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT----TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc----cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEec
Confidence            4689999999999999999999999999999999864    37899999999999999998 999988 57899999985

>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=99.65  E-value=1.4e-16  Score=136.19  Aligned_cols=74  Identities=26%  Similarity=0.574  Sum_probs=68.0

Q ss_pred             CCCceEEEcCCC-CCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          414 GGSKTLFVGNLP-FSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       414 ~~~~tlfV~nLp-~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ...++|||+||| +.+++++|+++|.+||.|..|+|.       +|||||+|.+.++|.+||. |||+.|.|+.|+|.++
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~-------rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a   85 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH-------KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLA   85 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE-------TEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEET
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe-------CCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            445789999996 678999999999999999999994       7999999999999999998 9999999999999999


Q ss_pred             ccc
Q 045516          492 RER  494 (675)
Q Consensus       492 ~~~  494 (675)
                      ...
T Consensus        86 ~~~   88 (98)
T d1wf2a_          86 AEP   88 (98)
T ss_dssp             TSC
T ss_pred             CCC
Confidence            754

>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=99.65  E-value=1.1e-16  Score=133.17  Aligned_cols=80  Identities=29%  Similarity=0.549  Sum_probs=76.0

Q ss_pred             eEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEec
Q 045516          519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVDE  597 (675)
Q Consensus       519 ~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~~  597 (675)
                      ++|||+|||..+++++    |+.+|..||.|..|+|+++..||.++|||||+|.+.++|..|+. |||..|+|+.|+|.|
T Consensus         2 ~rlfV~nlp~~~te~~----l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~   77 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQ----VKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR   77 (85)
T ss_dssp             CCEEEETCCSSCCSHH----HHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEE
T ss_pred             CEEEEECCCCCCCHHH----HHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            5799999999999998    77899999999999999999999999999999999999999998 999999999999999


Q ss_pred             cccCC
Q 045516          598 AKQRG  602 (675)
Q Consensus       598 a~~r~  602 (675)
                      +.+..
T Consensus        78 A~~~~   82 (85)
T d2u2fa_          78 ASVGA   82 (85)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            98654

>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=99.65  E-value=3.7e-17  Score=131.64  Aligned_cols=69  Identities=23%  Similarity=0.415  Sum_probs=66.2

Q ss_pred             EEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEE
Q 045516          419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIR  487 (675)
Q Consensus       419 lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~  487 (675)
                      |||+|||+++|+++|+++|..||.|..+++.++. ++.++|||||+|.+.++|.+||. |||..|.|+.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            8999999999999999999999999999999987 89999999999999999999997 999999999864

>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=99.65  E-value=6.3e-17  Score=139.12  Aligned_cols=81  Identities=23%  Similarity=0.507  Sum_probs=76.4

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEec
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDE  597 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~~  597 (675)
                      .++|||+|||+.+++++    |+++|..||.|..|+|+++..+|+++|||||+|.+.+.|.+||.|||..|+|+.|+|.+
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~~   93 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRD----LEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQA   93 (101)
T ss_dssp             HTEEEEESCCTTCCHHH----HHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCEEEEECCCCCCCHHH----HHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHHHCCCEECCEEEEEEE
Confidence            57899999999999999    77899999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCC
Q 045516          598 AKQRG  602 (675)
Q Consensus       598 a~~r~  602 (675)
                      +.++.
T Consensus        94 a~~~~   98 (101)
T d2cq4a1          94 SQAEK   98 (101)
T ss_dssp             HHHHH
T ss_pred             CCCCC
Confidence            87653

>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=99.65  E-value=2.1e-16  Score=131.75  Aligned_cols=75  Identities=28%  Similarity=0.468  Sum_probs=69.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEeccc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~  493 (675)
                      ..++|||+|||+++++++|+++|+.||.|..+.+..     ++|||||+|.+.++|..||. |||..|.|+.|+|.|+.+
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~-----~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP   81 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK-----IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKP   81 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE-----CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc-----ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccC
Confidence            357999999999999999999999999998888764     48999999999999999997 999999999999999875


Q ss_pred             c
Q 045516          494 R  494 (675)
Q Consensus       494 ~  494 (675)
                      .
T Consensus        82 ~   82 (86)
T d2cpda1          82 V   82 (86)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=3.5e-16  Score=131.41  Aligned_cols=81  Identities=23%  Similarity=0.390  Sum_probs=75.0

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEec
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDE  597 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~~  597 (675)
                      .++|||+|||+++++++    |+++|+.||.|..|+|++++.+|+++|||||.|.+.++|.+||+ +++.|+|+.|.|.+
T Consensus         8 ~~~lfV~nLp~~~te~~----l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~-~~~~l~Gr~i~v~~   82 (90)
T d2cqga1           8 TSDLIVLGLPWKTTEQD----LKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS-QRHMIDGRWCDCKL   82 (90)
T ss_dssp             CCCEEEESCCSSCCHHH----HHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH-SCEEETTEEEEEEC
T ss_pred             CCeEEEECCCCCCCHHH----HHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHh-cCCccCCEEeEEEe
Confidence            68899999999999998    78899999999999999999999999999999999999999998 34589999999999


Q ss_pred             cccCCC
Q 045516          598 AKQRGD  603 (675)
Q Consensus       598 a~~r~~  603 (675)
                      +.++..
T Consensus        83 a~~k~~   88 (90)
T d2cqga1          83 PNSKQS   88 (90)
T ss_dssp             CCTTCC
T ss_pred             CCCCCC
Confidence            987654

>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=99.64  E-value=7.4e-17  Score=132.63  Aligned_cols=74  Identities=24%  Similarity=0.456  Sum_probs=67.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCc-ccCCeeEEEEecccc
Q 045516          417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQ-MLGNRAIRLDFARER  494 (675)
Q Consensus       417 ~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~-~~~gr~i~V~~a~~~  494 (675)
                      ++|||+|||+++++++|+++|.+||.|..+++..     .+|||||+|.+.++|.+||+ |||. .|.|+.|+|.++.++
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~-----~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k   76 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-----KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSK   76 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-----ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec-----ccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCc
Confidence            5899999999999999999999999998877775     38999999999999999997 9986 599999999999865


Q ss_pred             C
Q 045516          495 G  495 (675)
Q Consensus       495 ~  495 (675)
                      .
T Consensus        77 ~   77 (80)
T d2cqha1          77 K   77 (80)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.64  E-value=6.1e-17  Score=135.68  Aligned_cols=77  Identities=22%  Similarity=0.425  Sum_probs=69.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEeccc
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARE  493 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a~~  493 (675)
                      ..+++|||+|||+++|+++|++||++||.|..|+++.    .++|||||+|.+.+.|++||. +++.|+|+.|.|.++.+
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~----~~~gfafV~f~~~~~a~~a~~-~~~~i~g~~l~v~~a~~   77 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK----PFRAFAFVTFADDQIAQSLCG-EDLIIKGISVHISNAEP   77 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS----SCCSCCEEECSCHHHHHHTTT-CEEEETTEEEEEECCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEee----ccCceEEEEECCHHHHHHHHh-CCCEECCEEeEEEeCCC
Confidence            4578999999999999999999999999999998764    468999999999999999996 78899999999999976


Q ss_pred             cC
Q 045516          494 RG  495 (675)
Q Consensus       494 ~~  495 (675)
                      +.
T Consensus        78 k~   79 (88)
T d1wf0a_          78 KH   79 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.64  E-value=1.8e-16  Score=135.00  Aligned_cols=80  Identities=26%  Similarity=0.365  Sum_probs=71.7

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhhCCC-eEEEEEeeCC--CCCcccEEEEEecCHHHHHHHHH-hC--CcccCCeeEEEE
Q 045516          416 SKTLFVGNLPFSVEQADVQNFFSEVAE-VVDVRLSSDA--DGRFKGYGHVEFASVEDAHKAIE-LN--GQMLGNRAIRLD  489 (675)
Q Consensus       416 ~~tlfV~nLp~~~te~~L~~~F~~~G~-I~~v~i~~~~--~g~~kG~afV~F~~~e~A~~Al~-l~--g~~~~gr~i~V~  489 (675)
                      .|+|||+|||+.+++++|+++|+.||. |..|+|+++.  +++++|||||+|.+.++|..||. |+  +..+.|+.|+|.
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~   80 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVD   80 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEE
Confidence            378999999999999999999999996 9999999885  58899999999999999999997 75  455679999999


Q ss_pred             eccccC
Q 045516          490 FARERG  495 (675)
Q Consensus       490 ~a~~~~  495 (675)
                      |+.+..
T Consensus        81 ~A~p~~   86 (96)
T d2disa1          81 WAEPEI   86 (96)
T ss_dssp             ESCSSC
T ss_pred             EcCCCC
Confidence            997654

>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=99.64  E-value=8.7e-17  Score=135.00  Aligned_cols=75  Identities=19%  Similarity=0.348  Sum_probs=68.0

Q ss_pred             CCceEEEcCCCCCCCHHHH---HHHhhhCCCeEEEEEeeCC-CC---CcccEEEEEecCHHHHHHHHH-hCCcccCCeeE
Q 045516          415 GSKTLFVGNLPFSVEQADV---QNFFSEVAEVVDVRLSSDA-DG---RFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAI  486 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L---~~~F~~~G~I~~v~i~~~~-~g---~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i  486 (675)
                      ..++|||+|||+.+++++|   +++|++||.|..|.|++++ ++   .++|||||+|.+.++|.+||+ |||..|.||.|
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~l   86 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   86 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEE
Confidence            4578999999999999999   6789999999999999886 33   356999999999999999997 99999999999


Q ss_pred             EEE
Q 045516          487 RLD  489 (675)
Q Consensus       487 ~V~  489 (675)
                      +|.
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            973

>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=99.64  E-value=1.7e-16  Score=130.05  Aligned_cols=74  Identities=20%  Similarity=0.417  Sum_probs=68.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecc
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~  492 (675)
                      ..+++|||+||+  +|+++|+++|++||.|.+|+|.++     +|||||+|.+.++|..||. |||..|+|+.|+|.|++
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~-----~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~   75 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP-----RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIAR   75 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT-----TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECC
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC-----CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            356899999996  899999999999999999999754     7899999999999999997 99999999999999997


Q ss_pred             cc
Q 045516          493 ER  494 (675)
Q Consensus       493 ~~  494 (675)
                      ++
T Consensus        76 ~~   77 (79)
T d2bz2a1          76 KQ   77 (79)
T ss_dssp             SS
T ss_pred             CC
Confidence            54

>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=99.64  E-value=3.2e-16  Score=131.21  Aligned_cols=76  Identities=29%  Similarity=0.380  Sum_probs=68.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCccc-CCeeEEEEecc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQML-GNRAIRLDFAR  492 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~-~gr~i~V~~a~  492 (675)
                      .+++|||+|||+.+++++|+++|..||.|..+.++.   ++.+|||||+|.+.++|.+||. |||..| .|+.|+|.|++
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~---~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk   85 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF---QKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSK   85 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEEC---SSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEee---ecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCC
Confidence            368999999999999999999999999999888764   3458899999999999999997 999988 58999999986


Q ss_pred             c
Q 045516          493 E  493 (675)
Q Consensus       493 ~  493 (675)
                      .
T Consensus        86 ~   86 (88)
T d2adca2          86 S   86 (88)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.64  E-value=1.9e-16  Score=135.32  Aligned_cols=77  Identities=21%  Similarity=0.296  Sum_probs=70.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ....++|||+|||+.+++++|++||.+||.|..|+|.+      +|||||+|.+.++|.+||+ |||..|.|+.|+|.+.
T Consensus        12 ~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~   85 (98)
T d1wg4a_          12 RRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYI   85 (98)
T ss_dssp             CSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEE
Confidence            34567899999999999999999999999999999874      6899999999999999997 9999999999999998


Q ss_pred             cccC
Q 045516          492 RERG  495 (675)
Q Consensus       492 ~~~~  495 (675)
                      +.+.
T Consensus        86 ~~~~   89 (98)
T d1wg4a_          86 RVYP   89 (98)
T ss_dssp             EEEC
T ss_pred             ecCC
Confidence            7654

>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=99.64  E-value=2.4e-16  Score=127.85  Aligned_cols=75  Identities=21%  Similarity=0.440  Sum_probs=71.2

Q ss_pred             EEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEecc
Q 045516          520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDEA  598 (675)
Q Consensus       520 ~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~~a  598 (675)
                      .|||+|||+.+++++    |.++|.+||.|..|.|+++..+|+++|||||+|.+.++|.+||.++++.|+|+.|+|..|
T Consensus         1 klfV~nl~~~~te~~----l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKD----LKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHH----HHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHHTCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHH----HHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHhcCCCEECCCEEEeeEC
Confidence            489999999999998    778999999999999999999999999999999999999999999999999999999764

>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=99.63  E-value=7.9e-17  Score=134.69  Aligned_cols=72  Identities=24%  Similarity=0.344  Sum_probs=67.0

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecccc
Q 045516          417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARER  494 (675)
Q Consensus       417 ~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~~  494 (675)
                      ++|||+|||+++++++|++||++||.|..|+|+.      .|||||+|.+.++|.+||. |||..|.|+.|.|.++...
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~------~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~   73 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR------DGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECT------TSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhcccccccccc------cceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            4799999999999999999999999999999875      4899999999999999997 9999999999999887654

>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=99.63  E-value=2.2e-16  Score=130.71  Aligned_cols=80  Identities=30%  Similarity=0.502  Sum_probs=73.8

Q ss_pred             EEEecCCCCcCHHHHHHHHHhhhcccCcEEEE-EecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEecc
Q 045516          521 IFIKGFDSSVGEDQVRASLEEHFGSCGEITRI-SVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVDEA  598 (675)
Q Consensus       521 lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v-~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~~a  598 (675)
                      |||+|||+++++++    |+++|.+||.|..+ +|+++..+|+++|||||+|.+.++|..||. |||..|+|+.|+|.|+
T Consensus         1 lfV~nLp~~~te~~----l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a   76 (83)
T d1x5ta1           1 IFIGNLDPEIDEKL----LYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYA   76 (83)
T ss_dssp             EEEECCCTTCCHHH----HHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEES
T ss_pred             CEEcCCCCcCcHHH----HHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEe
Confidence            79999999999998    77899999998664 788999999999999999999999999998 9999999999999999


Q ss_pred             ccCCCC
Q 045516          599 KQRGDF  604 (675)
Q Consensus       599 ~~r~~~  604 (675)
                      .++...
T Consensus        77 ~~k~~k   82 (83)
T d1x5ta1          77 FKKDSK   82 (83)
T ss_dssp             CCCCCC
T ss_pred             cCCCcC
Confidence            877654

>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=99.63  E-value=2.4e-16  Score=131.94  Aligned_cols=75  Identities=19%  Similarity=0.295  Sum_probs=66.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecc
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~  492 (675)
                      ..+++|||+|||+++++++|++||.+|| |..+.+.     +++|||||+|.+.++|.+||. ||++.|.|+.|+|.++.
T Consensus         3 s~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~~-----~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~   76 (88)
T d1wg1a_           3 SGSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVD-----RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEEE-----GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCEEEEeCCCCccChHHHHHHHHhcC-ceeeeee-----ccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            3568999999999999999999999999 3334443     458999999999999999997 99999999999999986


Q ss_pred             cc
Q 045516          493 ER  494 (675)
Q Consensus       493 ~~  494 (675)
                      ..
T Consensus        77 ~~   78 (88)
T d1wg1a_          77 TD   78 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.63  E-value=9.5e-17  Score=130.88  Aligned_cols=76  Identities=26%  Similarity=0.413  Sum_probs=72.8

Q ss_pred             eEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEecc
Q 045516          519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDEA  598 (675)
Q Consensus       519 ~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~~a  598 (675)
                      ++|||+|||+.+++++    |+++|++||.|..|+|+++..+|+++|||||+|.+.++|.+||.+|++.|+|+.|+|.+|
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 CKMFIGGLSWQTTQEG----LREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHH----HHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHH----HHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            4799999999999998    789999999999999999999999999999999999999999999999999999999876

>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=99.63  E-value=2.7e-16  Score=132.57  Aligned_cols=84  Identities=27%  Similarity=0.462  Sum_probs=77.7

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEE
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVV  595 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V  595 (675)
                      |+++|||+|||..+++++|+..|..+|++||.|..|.+...   +.++|||||+|.+.++|..||. |||..|+|+.|+|
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~---~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v   78 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRS---LKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   78 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHH---HHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeee---ccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            47899999999999999999999999999999999998663   6789999999999999999998 9999999999999


Q ss_pred             eccccCCC
Q 045516          596 DEAKQRGD  603 (675)
Q Consensus       596 ~~a~~r~~  603 (675)
                      .|++.+.+
T Consensus        79 ~~ak~~~~   86 (91)
T d1nu4a_          79 QYAKTDSD   86 (91)
T ss_dssp             EECSSCCT
T ss_pred             EEeCCCch
Confidence            99987543

>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=99.63  E-value=1.1e-15  Score=131.69  Aligned_cols=79  Identities=23%  Similarity=0.340  Sum_probs=73.3

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~  596 (675)
                      .++|||+|||+.+++++    |+++|..||.|..|+|+++..+|+++|||||+|.+.++|.+||+ +| ..|+|+.|+|.
T Consensus        10 ~~~lfV~nLp~~~te~~----l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~-~~l~Gr~l~V~   84 (103)
T d2cqda1          10 FTKIFVGGLPYHTTDAS----LRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPN-PIIDGRKANVN   84 (103)
T ss_dssp             SSEEEEECCCSSCCHHH----HHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSS-CEETTEECEEE
T ss_pred             CcEEEEeCCCCcCcHHH----HHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCC-CcCCCEEEEEE
Confidence            57899999999999998    77889999999999999999999999999999999999999999 65 58999999999


Q ss_pred             ccccC
Q 045516          597 EAKQR  601 (675)
Q Consensus       597 ~a~~r  601 (675)
                      ++...
T Consensus        85 ~a~~~   89 (103)
T d2cqda1          85 LAYLG   89 (103)
T ss_dssp             ESTTT
T ss_pred             EcCCC
Confidence            98754

>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=99.63  E-value=8.2e-17  Score=141.22  Aligned_cols=81  Identities=27%  Similarity=0.457  Sum_probs=72.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEE-EEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEecc
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDV-RLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v-~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a~  492 (675)
                      ...++|||+||||++|+++|++||+.||.|..+ .++.+.+|.++|||||+|.+.++|.+||.||+..|+||.|.|.++.
T Consensus        16 ~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~~~~~~i~gR~i~V~~~~   95 (112)
T d1wela1          16 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPIT   95 (112)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEEC
T ss_pred             CCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHHcCCCcCCCEEEEEEEcC
Confidence            456799999999999999999999999998764 4555569999999999999999999999999999999999998875


Q ss_pred             cc
Q 045516          493 ER  494 (675)
Q Consensus       493 ~~  494 (675)
                      ..
T Consensus        96 ~~   97 (112)
T d1wela1          96 KK   97 (112)
T ss_dssp             HH
T ss_pred             hH
Confidence            43

>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=99.63  E-value=1.4e-16  Score=134.25  Aligned_cols=78  Identities=21%  Similarity=0.483  Sum_probs=70.4

Q ss_pred             CCceEEEcCCCCCCCHHHHH----HHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEE
Q 045516          415 GSKTLFVGNLPFSVEQADVQ----NFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLD  489 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~----~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~  489 (675)
                      +++||||+|||+.+++++|+    .+|++||.|..|+|..  +++++|||||+|.+.++|.+||. |||..|.|+.|+|.
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~--~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~   79 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ   79 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH--HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee--eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            46899999999999999886    4689999999998754  56789999999999999999997 99999999999999


Q ss_pred             ecccc
Q 045516          490 FARER  494 (675)
Q Consensus       490 ~a~~~  494 (675)
                      |+...
T Consensus        80 ~ak~~   84 (91)
T d1nu4a_          80 YAKTD   84 (91)
T ss_dssp             ECSSC
T ss_pred             EeCCC
Confidence            99754

>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=99.63  E-value=6.2e-16  Score=131.10  Aligned_cols=82  Identities=23%  Similarity=0.483  Sum_probs=75.3

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccC-CCCCeeeEEEEEeCCHHHHHHHHH-h-CCceeCCeee
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDY-DTGSVKGIAYLDFTDADSFNKALE-M-SGTEIGGYSL  593 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~-~tG~~rG~afV~F~~~e~A~~Al~-l-ng~~~~Gr~l  593 (675)
                      ..++|||+|||+.+++++    |+.+|..||.|..|+|++++ .+|.++|||||+|.+.++|.+||. | |+..|+|+.|
T Consensus         7 ~~~~l~V~nLp~~~~e~~----l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l   82 (94)
T d2cpha1           7 TTSKILVRNIPFQANQRE----IRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRL   82 (94)
T ss_dssp             CCCCEEEESCCTTCCHHH----HHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBC
T ss_pred             CCCEEEEeCCCCCCCHHH----HHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEE
Confidence            368899999999999998    77889999999999999885 489999999999999999999998 7 8999999999


Q ss_pred             EEeccccCC
Q 045516          594 VVDEAKQRG  602 (675)
Q Consensus       594 ~V~~a~~r~  602 (675)
                      +|.|+....
T Consensus        83 ~V~~A~~~~   91 (94)
T d2cpha1          83 VLEWADSEV   91 (94)
T ss_dssp             EEEECCCCC
T ss_pred             EEEEcCCCC
Confidence            999998654

>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=99.62  E-value=7.4e-16  Score=128.07  Aligned_cols=77  Identities=22%  Similarity=0.468  Sum_probs=72.7

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCC--eeeE
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGG--YSLV  594 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~G--r~l~  594 (675)
                      .++|||+|||..+++++    |+++|..||.|..|+|+++..+|.++|||||+|.+.++|..||+ |||..|.|  ++|+
T Consensus         6 ~t~lfV~nlp~~~te~~----l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~   81 (85)
T d1b7fa2           6 DTNLYVTNLPRTITDDQ----LDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLS   81 (85)
T ss_dssp             TCEEEEESCCTTCCHHH----HHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCE
T ss_pred             CCEEEEeCCCCCCCHHH----HHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEE
Confidence            56799999999999998    78899999999999999999999999999999999999999998 99999977  8899


Q ss_pred             Eecc
Q 045516          595 VDEA  598 (675)
Q Consensus       595 V~~a  598 (675)
                      |.||
T Consensus        82 V~~A   85 (85)
T d1b7fa2          82 VRLA   85 (85)
T ss_dssp             EEEC
T ss_pred             EEEC
Confidence            9986

>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=99.62  E-value=8.1e-16  Score=127.24  Aligned_cols=75  Identities=25%  Similarity=0.406  Sum_probs=71.5

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEE
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVV  595 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V  595 (675)
                      +.++|||+|||+.+++++    |+++|+.||.|..|.|+++..+|.++|||||+|.+.++|..||. |||..|+|+.|+|
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 PNCCLGVFGLSLYTTERD----LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             GGGCEEEESCCSSCCHHH----HHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHH----HHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            478999999999999998    77899999999999999999999999999999999999999997 9999999999987

>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=99.62  E-value=5.6e-16  Score=129.11  Aligned_cols=81  Identities=23%  Similarity=0.448  Sum_probs=70.8

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEeccc-CCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKD-YDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d-~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~  596 (675)
                      .++|||+|||++++.++   .|+++|+.||.|..|+|+++ ..+|+++|||||+|.+.++|..||+|||..|+|+.|+|.
T Consensus         4 ~~~l~V~nLp~~~t~ed---~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~~n~~~~~gr~l~V~   80 (86)
T d2ghpa3           4 GREIMIRNLSTELLDEN---LLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISVS   80 (86)
T ss_dssp             TTEEEEEEECTTTCCHH---HHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGGGTTEEETTEEEEEE
T ss_pred             CCEEEEECCCCCcccHH---HHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHhcCCCEECCEEEEEE
Confidence            68999999999987543   27899999999999999875 578999999999999999999999999999999999999


Q ss_pred             ccccC
Q 045516          597 EAKQR  601 (675)
Q Consensus       597 ~a~~r  601 (675)
                      ++.++
T Consensus        81 ~a~~k   85 (86)
T d2ghpa3          81 LADKK   85 (86)
T ss_dssp             ECCCC
T ss_pred             EcCCC
Confidence            99875

>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=99.62  E-value=3.5e-16  Score=131.54  Aligned_cols=83  Identities=28%  Similarity=0.533  Sum_probs=77.2

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~  596 (675)
                      .++|||+|||+.+++.+    |+++|..||.|..|.++++..+|.++|||||.|.+.++|..||. |||..|+|+.|+|.
T Consensus         5 ~~kifV~nLp~~~t~~~----l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~   80 (90)
T d1x5sa1           5 EGKLFVGGLSFDTNEQS----LEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVD   80 (90)
T ss_dssp             CSEEEEESCCTTCCHHH----HHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEE
T ss_pred             CCEEEEECCCCcCCHHH----HHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            57899999999999998    77788889999999999999999999999999999999999997 99999999999999


Q ss_pred             ccccCCCC
Q 045516          597 EAKQRGDF  604 (675)
Q Consensus       597 ~a~~r~~~  604 (675)
                      ++.++...
T Consensus        81 ~a~~~~~~   88 (90)
T d1x5sa1          81 QAGKSSDN   88 (90)
T ss_dssp             EEECCCCC
T ss_pred             EcCCCCCC
Confidence            99876654

>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=99.62  E-value=1.1e-15  Score=125.21  Aligned_cols=77  Identities=27%  Similarity=0.477  Sum_probs=73.6

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEec
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDE  597 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~~  597 (675)
                      .++|||+|||+.+++++    |.++|+.||.|..+.++.+..++.++|||||.|.+.+++.+|+.|||+.|+||.|+|..
T Consensus         2 ~r~lfV~nLp~~~te~~----l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~~~~~~l~Gr~i~V~~   77 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHH----LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRK   77 (79)
T ss_dssp             CSEEEEECCTTTCCHHH----HHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHCSCCEETTEECEEEE
T ss_pred             CCEEEECCCCCcCCHHH----HHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEE
Confidence            57999999999999998    78899999999999999999999999999999999999999999999999999999987


Q ss_pred             c
Q 045516          598 A  598 (675)
Q Consensus       598 a  598 (675)
                      |
T Consensus        78 A   78 (79)
T d1l3ka2          78 A   78 (79)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.61  E-value=2.7e-16  Score=127.36  Aligned_cols=75  Identities=25%  Similarity=0.525  Sum_probs=71.0

Q ss_pred             EEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEecc
Q 045516          520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDEA  598 (675)
Q Consensus       520 ~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~~a  598 (675)
                      .|||+|||+.+++++    |+++|++||.|..|+|++++.+|.++|||||+|.+.+.|.+||+++++.|+|+.|.|..|
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 KIFVGGLSPDTPEEK----IREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHH----HHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTCSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHH----HHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhhCCCEECCEEeEEEEC
Confidence            599999999999998    778888999999999999999999999999999999999999998889999999999865

>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=99.61  E-value=8.6e-16  Score=127.68  Aligned_cols=77  Identities=21%  Similarity=0.443  Sum_probs=71.9

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCC--eeeE
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGG--YSLV  594 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~G--r~l~  594 (675)
                      .++|||+|||..+++++    |+++|++||.|..|+|+++..+|.++|||||+|.+.++|..|++ |||..|.|  ++|+
T Consensus         6 ~~~lfV~nLp~~~te~~----L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~   81 (85)
T d1fxla2           6 DANLYVSGLPKTMTQKE----LEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPIT   81 (85)
T ss_dssp             TCEEEEESCCTTCCHHH----HHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCE
T ss_pred             CCEEEEeCCCCCCCHHH----HHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEE
Confidence            47899999999999998    78899999999999999999999999999999999999999998 99999998  4588


Q ss_pred             Eecc
Q 045516          595 VDEA  598 (675)
Q Consensus       595 V~~a  598 (675)
                      |.||
T Consensus        82 V~~A   85 (85)
T d1fxla2          82 VKFA   85 (85)
T ss_dssp             EEEC
T ss_pred             EEeC
Confidence            8886

>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=99.61  E-value=9e-16  Score=130.87  Aligned_cols=76  Identities=22%  Similarity=0.424  Sum_probs=69.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCC--eeEEEEe
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGN--RAIRLDF  490 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~g--r~i~V~~  490 (675)
                      ..+++|||+|||+++++++|+++|++||.|..|+|.++     ++||||+|.+.++|..||. ||+..|.|  ++|+|.|
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~-----~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~   89 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDF   89 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-----SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc-----ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEe
Confidence            34689999999999999999999999999999999854     7899999999999999997 99999976  5899999


Q ss_pred             cccc
Q 045516          491 ARER  494 (675)
Q Consensus       491 a~~~  494 (675)
                      ++..
T Consensus        90 ak~~   93 (97)
T d1whya_          90 AKSG   93 (97)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8753

>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=99.61  E-value=2.3e-15  Score=130.01  Aligned_cols=84  Identities=27%  Similarity=0.477  Sum_probs=74.1

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccC-CCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEE
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDY-DTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVV  595 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~-~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V  595 (675)
                      +.++|||+|||+.+++++    |+++|..|| |..++|+++. .+|+++|||||+|.+.++|.+|+.||+..|+||.|+|
T Consensus        14 p~~~v~V~nLp~~~te~~----l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~~~~~~~~gr~l~V   88 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEES----IKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRV   88 (104)
T ss_dssp             SCEEEEEESCCSSCCHHH----HHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEE
T ss_pred             CCCEEEEeCCCCcCCHHH----HHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHHcCCCEECCEEEEE
Confidence            468999999999999998    778999999 7777777764 5789999999999999999988889999999999999


Q ss_pred             eccccCCCCC
Q 045516          596 DEAKQRGDFG  605 (675)
Q Consensus       596 ~~a~~r~~~~  605 (675)
                      .++.++....
T Consensus        89 ~~a~~~~~~~   98 (104)
T d1wi8a_          89 DVADQAQDKD   98 (104)
T ss_dssp             EECCCCCCCC
T ss_pred             EECCCCCCCC
Confidence            9998765543

>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=99.61  E-value=3.8e-16  Score=135.03  Aligned_cols=81  Identities=25%  Similarity=0.485  Sum_probs=76.0

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~  596 (675)
                      .++|||+|||+.+++++    |.++|+.||.|..|+|+++..+|+++|||||+|.+.++|..||+ |||..|+|+.|+|.
T Consensus         8 ~rtl~V~nLp~~~te~~----l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~   83 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQ----LKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVD   83 (104)
T ss_dssp             HSCEEEESCCTTSCHHH----HHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEE
T ss_pred             CCEEEEECCCCcCCHHH----HHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            57899999999999998    77889999999999999999999999999999999999999998 99999999999999


Q ss_pred             ccccCC
Q 045516          597 EAKQRG  602 (675)
Q Consensus       597 ~a~~r~  602 (675)
                      ++.+..
T Consensus        84 ~a~~~~   89 (104)
T d1p1ta_          84 NAASEK   89 (104)
T ss_dssp             ETTCTT
T ss_pred             ECCCCC
Confidence            987653

>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=99.61  E-value=4.8e-16  Score=128.01  Aligned_cols=78  Identities=18%  Similarity=0.340  Sum_probs=67.2

Q ss_pred             eEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEec
Q 045516          519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVDE  597 (675)
Q Consensus       519 ~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~~  597 (675)
                      ++|||+|||+.+++++    |+++|+.||.|..+.++.+..+|.++|||||+|.+.++|.+||. |||..|+|+.|+|.+
T Consensus         2 ~tl~v~nLp~~~t~~~----l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~   77 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRN----IRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKV   77 (81)
T ss_dssp             CEEEEECCCTTCCHHH----HHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cEEEEECCCCcCCHHH----HHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            6899999999999998    77888889999999888888899999999999999999999998 999999999999999


Q ss_pred             ccc
Q 045516          598 AKQ  600 (675)
Q Consensus       598 a~~  600 (675)
                      ++|
T Consensus        78 a~P   80 (81)
T d2ghpa1          78 SNP   80 (81)
T ss_dssp             CCC
T ss_pred             ccC
Confidence            876

>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=99.60  E-value=1.1e-15  Score=124.95  Aligned_cols=75  Identities=20%  Similarity=0.395  Sum_probs=70.7

Q ss_pred             EEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEecc
Q 045516          520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVDEA  598 (675)
Q Consensus       520 ~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~~a  598 (675)
                      +|||+|||+.+++++    |+++|..||.|..|+|+++. +|+++|||||+|.+.++|..||+ |||..|+|+.|+|.++
T Consensus         2 rl~V~nLp~~~~~~~----l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a   76 (78)
T d1no8a_           2 KLLVSNLDFGVSDAD----IQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLV   76 (78)
T ss_dssp             EEEEESCCTTCCHHH----HHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             EEEEECCCCCCCHHH----HHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            599999999999999    77889999999999999985 79999999999999999999998 9999999999999987


Q ss_pred             c
Q 045516          599 K  599 (675)
Q Consensus       599 ~  599 (675)
                      .
T Consensus        77 ~   77 (78)
T d1no8a_          77 T   77 (78)
T ss_dssp             C
T ss_pred             e
Confidence            5

>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=99.60  E-value=2.2e-15  Score=130.11  Aligned_cols=80  Identities=16%  Similarity=0.195  Sum_probs=71.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-h--CCcccCCeeEEEEe
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-L--NGQMLGNRAIRLDF  490 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l--~g~~~~gr~i~V~~  490 (675)
                      ..+++|||+|||+.+++++|+.||..||.|..|+|.+.     +|||||+|.+.++|..||. |  ++..+.|++|+|.|
T Consensus        13 ~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~-----k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~   87 (104)
T d1wexa_          13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNY   87 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec-----ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEE
Confidence            45789999999999999999999999999999999854     8999999999999999996 5  66788999999999


Q ss_pred             ccccCCCC
Q 045516          491 ARERGAYT  498 (675)
Q Consensus       491 a~~~~~~~  498 (675)
                      +.......
T Consensus        88 s~~~~~~~   95 (104)
T d1wexa_          88 STSKRITR   95 (104)
T ss_dssp             CSSSSCCC
T ss_pred             cCCCccCC
Confidence            97654433

>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=99.60  E-value=1.6e-15  Score=126.90  Aligned_cols=77  Identities=19%  Similarity=0.287  Sum_probs=70.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH---hCCcccCCeeEEEEe
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE---LNGQMLGNRAIRLDF  490 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~---l~g~~~~gr~i~V~~  490 (675)
                      ..+++|||+|||+.+++++|+++|++||.|..|+|.++     +|||||+|.+.++|..||.   +++..|.|++|+|.|
T Consensus         6 ~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~-----~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~   80 (88)
T d2cq1a1           6 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQY   80 (88)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc-----ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEE
Confidence            46799999999999999999999999999999999854     7899999999999999996   467899999999999


Q ss_pred             ccccC
Q 045516          491 ARERG  495 (675)
Q Consensus       491 a~~~~  495 (675)
                      +..+.
T Consensus        81 sk~~~   85 (88)
T d2cq1a1          81 SNHKE   85 (88)
T ss_dssp             CSCSS
T ss_pred             CCCCC
Confidence            87543

>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=99.60  E-value=1.4e-15  Score=126.33  Aligned_cols=76  Identities=24%  Similarity=0.481  Sum_probs=70.4

Q ss_pred             EEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCC---CeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEe
Q 045516          521 IFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTG---SVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVD  596 (675)
Q Consensus       521 lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG---~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~  596 (675)
                      |||+|||+++++++    |+++|+.||.|..|.|+++..++   .++|||||+|.+.++|.+||. |||..|+|+.|+|.
T Consensus         1 LfV~nLp~~~t~~~----l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~   76 (85)
T d2cpfa1           1 LFIKNLNFSTTEET----LKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVR   76 (85)
T ss_dssp             EEEESCCTTCCHHH----HHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEE
T ss_pred             CEEcCCCCCCCHHH----HHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            89999999999998    77899999999999999887665   579999999999999999998 99999999999999


Q ss_pred             cccc
Q 045516          597 EAKQ  600 (675)
Q Consensus       597 ~a~~  600 (675)
                      |+.+
T Consensus        77 ~a~~   80 (85)
T d2cpfa1          77 ISER   80 (85)
T ss_dssp             CSSC
T ss_pred             ECCC
Confidence            9864

>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=99.59  E-value=1.2e-15  Score=132.83  Aligned_cols=79  Identities=20%  Similarity=0.283  Sum_probs=70.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCccc--CCeeEEEEe
Q 045516          414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQML--GNRAIRLDF  490 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~--~gr~i~V~~  490 (675)
                      ....+|||+|||+.+|+++|+++|++||.|..|.|+++   +.+|||||+|.+.++|..||. |||..|  .|+.|+|.+
T Consensus         5 s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~---~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~   81 (108)
T d2adba1           5 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK---NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF   81 (108)
T ss_dssp             CCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEE---TTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEE
T ss_pred             CCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEee---CCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEe
Confidence            45679999999999999999999999999999999875   358999999999999999997 999988  578889988


Q ss_pred             ccccC
Q 045516          491 ARERG  495 (675)
Q Consensus       491 a~~~~  495 (675)
                      +....
T Consensus        82 s~~~~   86 (108)
T d2adba1          82 SKLTS   86 (108)
T ss_dssp             CSSCS
T ss_pred             cCCcc
Confidence            86544

>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=99.59  E-value=2.1e-15  Score=126.74  Aligned_cols=80  Identities=18%  Similarity=0.291  Sum_probs=72.9

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~  596 (675)
                      .++|||+|||..+++++    |+++|..||.|..|.|+++..++  +|||||+|.+.++|..|+. |||..|.|+.|+|.
T Consensus         8 ~~tl~V~nLp~~~te~~----l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~   81 (90)
T d2cqia1           8 PRTLYVGNLSRDVTEVL----ILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVN   81 (90)
T ss_dssp             CCEEEEESCCTTCCHHH----HHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCEEEEECCCCCCCHHH----HHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            68999999999999998    77888899999999999987654  7899999999999999998 99999999999999


Q ss_pred             ccccCCC
Q 045516          597 EAKQRGD  603 (675)
Q Consensus       597 ~a~~r~~  603 (675)
                      |+.+...
T Consensus        82 ~a~~~~~   88 (90)
T d2cqia1          82 WATTPSS   88 (90)
T ss_dssp             ECCCTTC
T ss_pred             EcCCCCC
Confidence            9986543

>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=99.59  E-value=3.6e-15  Score=126.05  Aligned_cols=80  Identities=20%  Similarity=0.391  Sum_probs=73.9

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~  596 (675)
                      .++|||+|||+.+++++    |+++|..||.|..|.|+.+..  .++|||||+|.+.++|.+||. ||+..|+|+.|+|.
T Consensus        11 ~~~l~v~nLp~~~t~~~----L~~~F~~~G~v~~v~~~~~~~--~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~   84 (93)
T d2cq3a1          11 PKRLHVSNIPFRFRDPD----LRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN   84 (93)
T ss_dssp             CCEEEEESCCTTCCHHH----HHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCEEEEECCCCCCCHHH----HHHHHhhcceeeecccccccc--CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            67899999999999988    889999999999999998853  469999999999999999998 99999999999999


Q ss_pred             ccccCCC
Q 045516          597 EAKQRGD  603 (675)
Q Consensus       597 ~a~~r~~  603 (675)
                      |+++|..
T Consensus        85 ~A~~r~~   91 (93)
T d2cq3a1          85 NATARVM   91 (93)
T ss_dssp             ECCSSCC
T ss_pred             ecCcCCC
Confidence            9998754

>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=99.59  E-value=2e-15  Score=122.20  Aligned_cols=70  Identities=20%  Similarity=0.376  Sum_probs=63.5

Q ss_pred             EEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecccc
Q 045516          419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARER  494 (675)
Q Consensus       419 lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~~~  494 (675)
                      |||+|||+++++++|+++|.+|| |..+++.     +++|||||+|.+.++|.+||. |||..|.|+.|+|.++...
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~~-----~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVD-----KYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEE-----TTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeec-----ccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            89999999999999999999999 5555553     568999999999999999997 9999999999999998643

>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=99.58  E-value=3e-15  Score=128.47  Aligned_cols=84  Identities=29%  Similarity=0.519  Sum_probs=76.0

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEE--------EEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCce
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEIT--------RISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTE  587 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~--------~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~  587 (675)
                      ..++|||+|||+.+++++    |+++|..||.|.        .+.+.++..+|+++|||||+|.+.++|..||. |||..
T Consensus         7 ~~~~i~V~nLp~~~te~~----l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~   82 (101)
T d2cpea1           7 DNSAIYVQGLNDSVTLDD----LADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKD   82 (101)
T ss_dssp             CCCEEEEECCCTTCCHHH----HHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCE
T ss_pred             CCCEEEEECCCCcCCHHH----HHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCE
Confidence            368999999999999998    778889999874        57778888899999999999999999999998 99999


Q ss_pred             eCCeeeEEeccccCCCC
Q 045516          588 IGGYSLVVDEAKQRGDF  604 (675)
Q Consensus       588 ~~Gr~l~V~~a~~r~~~  604 (675)
                      |+|+.|+|.+++++..+
T Consensus        83 ~~gr~i~V~~a~~~~p~   99 (101)
T d2cpea1          83 FQGSKLKVSLARKKPPM   99 (101)
T ss_dssp             ETTEECEEECSSCCCCS
T ss_pred             ECCEEEEEEEcCCCCCC
Confidence            99999999999887654

>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=99.58  E-value=1.6e-15  Score=129.79  Aligned_cols=77  Identities=17%  Similarity=0.287  Sum_probs=69.9

Q ss_pred             CCCCceEEEcCCCCC-CCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH---hCCcccCCeeEEE
Q 045516          413 SGGSKTLFVGNLPFS-VEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE---LNGQMLGNRAIRL  488 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~-~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~---l~g~~~~gr~i~V  488 (675)
                      ...+++|||+|||+. +|+++|+++|+.||.|.+|+|+++     +|||||+|.+.++|..||.   +++..|.|+.|+|
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~-----k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V   89 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM-----KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKV   89 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT-----TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEE
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec-----CCcEEEEecchHHHHHHHHHHhcCCceECCEEEEE
Confidence            456789999999985 899999999999999999999864     7999999999999999985   7899999999999


Q ss_pred             Eecccc
Q 045516          489 DFARER  494 (675)
Q Consensus       489 ~~a~~~  494 (675)
                      .|+...
T Consensus        90 ~~s~~~   95 (99)
T d1x4fa1          90 DLSEKY   95 (99)
T ss_dssp             EEECSC
T ss_pred             EEcCCc
Confidence            999654

>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=99.58  E-value=1.6e-15  Score=127.15  Aligned_cols=80  Identities=28%  Similarity=0.471  Sum_probs=73.1

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~  596 (675)
                      ..+|||+|||+.+++++    |+++|..||.|..|+|+.+.  +.++|||||+|.+.++|..||. |||..|+|+.|+|.
T Consensus         8 ~~~l~V~nLp~~~t~~~----l~~~F~~~G~v~~~~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~   81 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKA----LYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVG   81 (89)
T ss_dssp             TTEEEEESCCSSCCHHH----HHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEE
T ss_pred             CCEEEEeCCCCCCCHHH----HHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            46799999999999998    77889999999999999986  4478999999999999999998 99999999999999


Q ss_pred             ccccCCC
Q 045516          597 EAKQRGD  603 (675)
Q Consensus       597 ~a~~r~~  603 (675)
                      ++.++..
T Consensus        82 ~a~~~~~   88 (89)
T d1cvja2          82 RFKSRKE   88 (89)
T ss_dssp             ECCCTTT
T ss_pred             ECCCCCC
Confidence            9987654

>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=99.58  E-value=1.3e-15  Score=123.42  Aligned_cols=75  Identities=20%  Similarity=0.345  Sum_probs=71.7

Q ss_pred             EEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEecc
Q 045516          520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDEA  598 (675)
Q Consensus       520 ~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~~a  598 (675)
                      +|||+|||+++++++    |+++|+.||.|..+.++++..+|.++|||||+|.+.++|..||+|||+.|+|+.|+|.+|
T Consensus         1 rlfV~nLp~~~te~~----l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVED----VKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHH----HHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHHCSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHH----HHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHhcCCCEECCeEEEEEEC
Confidence            489999999999998    788999999999999999999999999999999999999999999999999999999875

>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=99.57  E-value=6.7e-15  Score=124.88  Aligned_cols=79  Identities=19%  Similarity=0.371  Sum_probs=71.1

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      ...++|||+|||+.+++++    |+++|..||.|..|.+..+   +..+|||||+|.+.++|..||. ||+..|.|+.|+
T Consensus        12 ~~~~~l~V~nLp~~~t~~~----l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~   84 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKD----IEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLR   84 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHH----HHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEECCCCCCCHHH----HHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            3467899999999999998    7789999999999998765   4568999999999999999998 999999999999


Q ss_pred             EeccccC
Q 045516          595 VDEAKQR  601 (675)
Q Consensus       595 V~~a~~r  601 (675)
                      |.|++.+
T Consensus        85 V~~a~~~   91 (95)
T d1x4aa1          85 VEFPRSG   91 (95)
T ss_dssp             EECCCCC
T ss_pred             EEeccCC
Confidence            9998754

>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=99.57  E-value=7.1e-16  Score=132.76  Aligned_cols=86  Identities=22%  Similarity=0.374  Sum_probs=79.1

Q ss_pred             CCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeee
Q 045516          515 GQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSL  593 (675)
Q Consensus       515 ~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l  593 (675)
                      ..++++|||+|||..+++++    |+++|..||.|..+.|+.+..+|.++|||||.|.+.++|..||. |||..|.|+.|
T Consensus        15 ~~ps~tl~V~nLp~~~t~~~----l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l   90 (102)
T d2cpxa1          15 GEPNKVLYLKNLSPRVTERD----LVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKIL   90 (102)
T ss_dssp             CSCCSEEEEECCCTTCCHHH----HHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBC
T ss_pred             CCCCCEEEEeCCCCCCCHHH----HHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEE
Confidence            34578999999999999998    77889999999999999988899999999999999999999998 99999999999


Q ss_pred             EEeccccCCCC
Q 045516          594 VVDEAKQRGDF  604 (675)
Q Consensus       594 ~V~~a~~r~~~  604 (675)
                      +|.|++++..+
T Consensus        91 ~V~~ak~k~~r  101 (102)
T d2cpxa1          91 VIEFGKNKKQR  101 (102)
T ss_dssp             EEEECCCCSCC
T ss_pred             EEEeCCCcccC
Confidence            99999987653

>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=99.57  E-value=5.3e-15  Score=126.17  Aligned_cols=82  Identities=29%  Similarity=0.446  Sum_probs=75.7

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hC------CceeCC
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MS------GTEIGG  590 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-ln------g~~~~G  590 (675)
                      .++|||+|||+.+++++    |+++|..||.|..+.++.+..++.++|||||+|.+.++|.+||. ||      |..|+|
T Consensus         8 ~~tlfV~nLp~~~te~~----l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~g   83 (98)
T d1x4ha1           8 GKTVFIRNLSFDSEEEA----LGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   83 (98)
T ss_dssp             CCCEEEESCCTTCCHHH----HHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             CCEEEEcCCCCcCCHHH----HHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECC
Confidence            68999999999999998    77889999999999999999999999999999999999999998 65      678999


Q ss_pred             eeeEEeccccCCC
Q 045516          591 YSLVVDEAKQRGD  603 (675)
Q Consensus       591 r~l~V~~a~~r~~  603 (675)
                      +.|+|.++.++..
T Consensus        84 r~l~v~~a~~k~~   96 (98)
T d1x4ha1          84 RQLKVDLAVTRDE   96 (98)
T ss_dssp             CEEEEECCCCCCC
T ss_pred             EEEEEEECCCCCc
Confidence            9999999988654

>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=99.56  E-value=1e-14  Score=125.87  Aligned_cols=83  Identities=13%  Similarity=0.161  Sum_probs=75.9

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEec
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDE  597 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~~  597 (675)
                      ..+|||+|||+++++++    |++||..||.|..+.++.+..++.++|||||+|.+.++|.+||.+|++.|+||.|+|.+
T Consensus        15 ~~~v~v~nLP~~~te~d----I~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~~~~~~i~gR~i~V~~   90 (104)
T d1wg5a_          15 DGFVRLRGLPFGCSKEE----IVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFK   90 (104)
T ss_dssp             CCEEEEESCCTTCCHHH----HHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEE
T ss_pred             CcEEEEeCCCCCCCHHH----HHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHhhCCCEEcceEEEEEE
Confidence            56899999999999999    77899999999987777777889999999999999999999999999999999999999


Q ss_pred             cccCCCC
Q 045516          598 AKQRGDF  604 (675)
Q Consensus       598 a~~r~~~  604 (675)
                      +.++...
T Consensus        91 ~~~~~~~   97 (104)
T d1wg5a_          91 SSRAEVR   97 (104)
T ss_dssp             ECTTTSC
T ss_pred             CCHHHhc
Confidence            9876544

>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=99.55  E-value=1.2e-14  Score=123.90  Aligned_cols=74  Identities=24%  Similarity=0.391  Sum_probs=66.2

Q ss_pred             ceEEEEecCC-CCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEE
Q 045516          518 AHTIFIKGFD-SSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVV  595 (675)
Q Consensus       518 ~~~lfV~nLp-~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V  595 (675)
                      ..+|||+||+ ..+++.+    |+++|.+||.|..|+|        ++|||||+|.+.++|.+||. |||..|+|+.|+|
T Consensus        15 ~~~lfV~nL~~~~~~~~~----L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V   82 (98)
T d1wf2a_          15 NSRVFIGNLNTLVVKKSD----VEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDI   82 (98)
T ss_dssp             CCCEEEEEECTTTCCHHH----HHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEE
T ss_pred             CcEEEEeCCCcccCCHHH----HHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            5789999997 5677776    8899999999999998        37899999999999999998 9999999999999


Q ss_pred             eccccCCC
Q 045516          596 DEAKQRGD  603 (675)
Q Consensus       596 ~~a~~r~~  603 (675)
                      .|+.+...
T Consensus        83 ~~a~~~~~   90 (98)
T d1wf2a_          83 NLAAEPKV   90 (98)
T ss_dssp             EETTSCCC
T ss_pred             EECCCCCC
Confidence            99976443

>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=99.55  E-value=7e-15  Score=126.44  Aligned_cols=83  Identities=14%  Similarity=0.232  Sum_probs=72.9

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEE
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVV  595 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V  595 (675)
                      ...++|||+|||+++++++    |++||..|| |..|+++.+. +|.++|||||+|.+.++|.+||+||+..|+||.|+|
T Consensus        13 ~~~~~v~v~nLp~~~te~d----l~~~F~~~~-~~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~~~~~~i~gR~I~V   86 (102)
T d1weza_          13 TTGHCVHMRGLPYRATEND----IYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVEL   86 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHH----HHHSSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEE
T ss_pred             CCCCEEEEeCCCCcCCHHH----HHHHHhccC-cceeeeEEec-CCcceEEEEEEECCHHHHHHHHHcCCCEECCEEEEE
Confidence            3468999999999999999    778999998 5577787774 589999999999999999999999999999999999


Q ss_pred             eccccCCCC
Q 045516          596 DEAKQRGDF  604 (675)
Q Consensus       596 ~~a~~r~~~  604 (675)
                      .++.++...
T Consensus        87 ~~s~~~~~~   95 (102)
T d1weza_          87 FLNSTAGTS   95 (102)
T ss_dssp             EEECCCCCC
T ss_pred             EEcCCCCCC
Confidence            998866543

>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=99.55  E-value=8.2e-15  Score=121.60  Aligned_cols=77  Identities=21%  Similarity=0.390  Sum_probs=71.9

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEec
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDE  597 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~~  597 (675)
                      .++|||+|||..+++++    |.++|..||.|..|+|+++. +|+++|||||+|.+.++|.+||++++..|.|+.|.|.|
T Consensus         6 ~rtvfV~nlp~~~te~~----l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~   80 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDD----IKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILF   80 (85)
T ss_dssp             TTEEEEECCCTTCCHHH----HHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHTCCCCEETTEECEEEE
T ss_pred             cCEEEEECCCCCCCHHH----HHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHHHCCCEECCEEEEEEE
Confidence            57999999999999998    77899999999999998874 79999999999999999999999999999999999998


Q ss_pred             cc
Q 045516          598 AK  599 (675)
Q Consensus       598 a~  599 (675)
                      ..
T Consensus        81 ~~   82 (85)
T d1zh5a2          81 KD   82 (85)
T ss_dssp             GG
T ss_pred             cC
Confidence            64

>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=99.55  E-value=2.3e-15  Score=125.58  Aligned_cols=76  Identities=16%  Similarity=0.280  Sum_probs=68.6

Q ss_pred             eEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEec
Q 045516          519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVDE  597 (675)
Q Consensus       519 ~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~~  597 (675)
                      ++|||+|||+++++++    |+++|+.||.|..|.|+.+       |||||+|.+.++|..||. |||..|.|+.|+|.+
T Consensus         1 nrvfV~nlp~~~~~~~----l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~   69 (87)
T d3begb1           1 NRVVVSGLPPSGSWQD----LKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAY   69 (87)
T ss_dssp             CCEEEEECCSSCCTTH----HHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCB
T ss_pred             CeEEEECCCCcCCHHH----HHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeE
Confidence            4699999999999998    8899999999999998764       899999999999999997 999999999999999


Q ss_pred             cccCCCCC
Q 045516          598 AKQRGDFG  605 (675)
Q Consensus       598 a~~r~~~~  605 (675)
                      ++.+....
T Consensus        70 ~~~~~~~~   77 (87)
T d3begb1          70 IRVKVDGP   77 (87)
T ss_dssp             CEEEECC-
T ss_pred             EecCcCCC
Confidence            87765543

>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=99.55  E-value=8.2e-16  Score=129.47  Aligned_cols=80  Identities=23%  Similarity=0.415  Sum_probs=73.0

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEe
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVD  596 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~  596 (675)
                      ..++|||+|||+.+++++    |+++|..||.|..|.|+.+ .+|+++|||||+|.+.++|.+||+|||..|+|+.|+|.
T Consensus        12 ~~~~ifV~nL~~~~te~~----l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~~~g~~~~g~~i~V~   86 (91)
T d1fjeb1          12 TPFNLFIGNLNPNKSVAE----LKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLE   86 (91)
T ss_dssp             SSEEEEEECCCTTSCHHH----HHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEE
T ss_pred             CCcEEEEeCccCcchHHH----HHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHhcCCcEECCEEEEEE
Confidence            468999999999999999    7778888899999988654 67999999999999999999999999999999999999


Q ss_pred             ccccC
Q 045516          597 EAKQR  601 (675)
Q Consensus       597 ~a~~r  601 (675)
                      +++.|
T Consensus        87 ~ak~k   91 (91)
T d1fjeb1          87 KPKGR   91 (91)
T ss_dssp             CCCCS
T ss_pred             ecCCC
Confidence            99764

>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=99.55  E-value=6e-15  Score=129.56  Aligned_cols=77  Identities=22%  Similarity=0.379  Sum_probs=71.1

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~  596 (675)
                      +++|||+|||+.+++++    |+++|+.||.|..|+|..+   +.++|||||+|.+.++|..||. |||..|+|+.|+|.
T Consensus         7 ~r~l~V~nLp~~~te~~----l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~   79 (114)
T d2f9da1           7 NRILYIRNLPYKITAEE----MYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVL   79 (114)
T ss_dssp             CSEEEEESCCTTCCHHH----HHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCEEEEECCCCCCCHHH----HHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            68999999999999998    7899999999999999865   5679999999999999999998 99999999999999


Q ss_pred             ccccC
Q 045516          597 EAKQR  601 (675)
Q Consensus       597 ~a~~r  601 (675)
                      ++...
T Consensus        80 ~a~~~   84 (114)
T d2f9da1          80 YYNAN   84 (114)
T ss_dssp             ECCHH
T ss_pred             EcCCC
Confidence            98653

>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=99.55  E-value=7.6e-15  Score=124.72  Aligned_cols=76  Identities=25%  Similarity=0.434  Sum_probs=70.6

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~  596 (675)
                      .++|||+|||..+++++    |+++|..||.|..|+|+++      +|||||+|.+.++|..||. |||..|+|+.|+|.
T Consensus        18 ~~~l~v~nL~~~~te~~----L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~   87 (96)
T d1x4ga1          18 NCTVYCGGIASGLTDQL----MRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCY   87 (96)
T ss_dssp             CCEEEEECCSSCCCHHH----HHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCEEEEcCCCCCCCHHH----HHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            57899999999999998    7788999999999999987      7999999999999999998 99999999999999


Q ss_pred             ccccCCC
Q 045516          597 EAKQRGD  603 (675)
Q Consensus       597 ~a~~r~~  603 (675)
                      |+++++.
T Consensus        88 ~ak~~p~   94 (96)
T d1x4ga1          88 WGKESPD   94 (96)
T ss_dssp             CCCCCCS
T ss_pred             EcCCCCC
Confidence            9987654

>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=99.54  E-value=6.2e-15  Score=123.43  Aligned_cols=77  Identities=9%  Similarity=0.194  Sum_probs=69.2

Q ss_pred             CCCCceEEEcCCCCC-CCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-h--CCcccCCeeEEE
Q 045516          413 SGGSKTLFVGNLPFS-VEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-L--NGQMLGNRAIRL  488 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~-~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l--~g~~~~gr~i~V  488 (675)
                      ...+++|||+|||.. +|+++|++||+.||.|.+|+|+.+     ++||||+|.+.++|..||. |  ++..|.|++|+|
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~-----k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V   79 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRV   79 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-----SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc-----ceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEE
Confidence            346799999999986 889999999999999999999865     6899999999999999996 4  788899999999


Q ss_pred             Eecccc
Q 045516          489 DFARER  494 (675)
Q Consensus       489 ~~a~~~  494 (675)
                      .|+...
T Consensus        80 ~~s~~~   85 (89)
T d1x4da1          80 HLSQKY   85 (89)
T ss_dssp             EEECCC
T ss_pred             EECCCc
Confidence            998643

>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=99.53  E-value=6.3e-15  Score=123.18  Aligned_cols=80  Identities=21%  Similarity=0.418  Sum_probs=71.0

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEe
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVD  596 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~  596 (675)
                      ..++|||+|||+.+++++    |+++|.+||.|..|+++.+     ++|||||+|.+.+.|..||. +++.|+|+.|+|.
T Consensus         4 ~s~~lfV~nLp~~~te~~----L~~~F~~~G~v~~v~~~~~-----~~gfafV~f~~~~~a~~a~~-~~~~i~g~~l~v~   73 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDE----LREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCG-EDLIIKGISVHIS   73 (88)
T ss_dssp             CCCEEEEESCCSSSCHHH----HHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTT-CEEEETTEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHH----HHHHHHHcCCceEEEEeec-----cCceEEEEECCHHHHHHHHh-CCCEECCEEeEEE
Confidence            378999999999999998    8899999999999987654     58999999999999999986 7889999999999


Q ss_pred             ccccCCCCCC
Q 045516          597 EAKQRGDFGS  606 (675)
Q Consensus       597 ~a~~r~~~~~  606 (675)
                      ++.++.....
T Consensus        74 ~a~~k~~~~~   83 (88)
T d1wf0a_          74 NAEPKHNSNS   83 (88)
T ss_dssp             CCCCCCCCCS
T ss_pred             eCCCCCCCCC
Confidence            9988766543

>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=99.53  E-value=1.5e-16  Score=133.80  Aligned_cols=75  Identities=20%  Similarity=0.504  Sum_probs=66.7

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEee------CCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEe
Q 045516          417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSS------DADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDF  490 (675)
Q Consensus       417 ~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~------~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~  490 (675)
                      |+|||+|||+++++++|++||+.||.|..+.+..      ..+++++|||||+|.+.++|..||.|||+.|.|+.|+|..
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~l~g~~~~Gr~l~V~r   81 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRR   81 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGGGSSCCSSSSCCCCBC
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHhhCCcEECCEEEEECC
Confidence            7999999999999999999999999887665532      2357889999999999999999999999999999999975


Q ss_pred             c
Q 045516          491 A  491 (675)
Q Consensus       491 a  491 (675)
                      .
T Consensus        82 ~   82 (90)
T d1u2fa_          82 P   82 (90)
T ss_dssp             T
T ss_pred             C
Confidence            4

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.52  E-value=1.1e-14  Score=123.71  Aligned_cols=80  Identities=35%  Similarity=0.517  Sum_probs=71.3

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEE
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVV  595 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V  595 (675)
                      ..++|||+|||+++++++    |.++|..||.|..+.+     ++.++|||||+|.+.+.|..||. |||..|+|+.|+|
T Consensus        15 ~~~~l~V~nL~~~~te~~----l~~~F~~~g~v~~~~~-----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V   85 (96)
T d1fjca_          15 AARTLLAKNLSFNITEDE----LKEVFEDALEIRLVSQ-----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSL   85 (96)
T ss_dssp             GGGEEEEESCCSSCCHHH----HHHHHCSEEEECCEEE-----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHH----HHHHHHhcccceeeee-----cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEE
Confidence            478999999999999998    7788999998876643     57889999999999999999998 9999999999999


Q ss_pred             eccccCCCCC
Q 045516          596 DEAKQRGDFG  605 (675)
Q Consensus       596 ~~a~~r~~~~  605 (675)
                      .|+.+++..+
T Consensus        86 ~~a~~k~~~r   95 (96)
T d1fjca_          86 YYTGEKGGTR   95 (96)
T ss_dssp             EECSSSCCCC
T ss_pred             EEeCCCCCCC
Confidence            9999876643

>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=99.52  E-value=2.1e-14  Score=122.38  Aligned_cols=78  Identities=14%  Similarity=0.288  Sum_probs=71.0

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEE
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVV  595 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V  595 (675)
                      ..++|||+|||+.+++++    |+++|..||.|..|.|.+       +|||||+|.+.++|..||+ |||..|+|+.|+|
T Consensus        14 ~~~~i~V~Nlp~~~~~~~----L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v   82 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQD----LKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGET   82 (98)
T ss_dssp             CSCEEEEECCCSSCCHHH----HHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCE
T ss_pred             CCCEEEEECCCCCCCHHH----HHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEE
Confidence            467899999999999998    788999999999999865       4899999999999999998 9999999999999


Q ss_pred             eccccCCCCC
Q 045516          596 DEAKQRGDFG  605 (675)
Q Consensus       596 ~~a~~r~~~~  605 (675)
                      .+.+.+..+.
T Consensus        83 ~~~~~~~~~~   92 (98)
T d1wg4a_          83 SYIRVYPERS   92 (98)
T ss_dssp             EEEEEECCCS
T ss_pred             EEEecCCCCC
Confidence            9998776544

>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=99.51  E-value=1.8e-14  Score=137.04  Aligned_cols=82  Identities=16%  Similarity=0.347  Sum_probs=76.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHhCCcccCCeeEEEEec
Q 045516          413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAIRLDFA  491 (675)
Q Consensus       413 ~~~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i~V~~a  491 (675)
                      ....++|||+|||+.+++++|+++|..||.|..|.|+.+. +|+++|||||+|.+.++|.+||.+++..|.|+.|.|.++
T Consensus        94 ~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~~~~~~~~G~~i~V~~A  173 (183)
T d1u1qa_          94 HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKA  173 (183)
T ss_dssp             TCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHTSSCEEETTEEEEEEEC
T ss_pred             ccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHHhCCCeECCEEEEEEec
Confidence            3456899999999999999999999999999999999987 799999999999999999999999999999999999998


Q ss_pred             ccc
Q 045516          492 RER  494 (675)
Q Consensus       492 ~~~  494 (675)
                      .++
T Consensus       174 ~~k  176 (183)
T d1u1qa_         174 LSK  176 (183)
T ss_dssp             CCH
T ss_pred             CCc
Confidence            654

>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=99.51  E-value=2.4e-14  Score=118.23  Aligned_cols=76  Identities=20%  Similarity=0.285  Sum_probs=68.7

Q ss_pred             CCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCcee-CCee
Q 045516          515 GQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEI-GGYS  592 (675)
Q Consensus       515 ~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~-~Gr~  592 (675)
                      .+++++|||+|||..+++++    |..+|..||.|..|+|+++.     +|||||+|.+.++|..|+. |||..| +|+.
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~----l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~   75 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMM----LSMLFNQFPGFKEVRLVPNR-----HDIAFVEFTTELQSNAAKEALQGFKITPTHA   75 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHH----HHHHHTTSTTEEEEEECTTT-----CSCEEEEESSHHHHHHHHHHHTTCBSSTTCB
T ss_pred             CCCCCEEEEECCCCCCCHHH----HHhhhccCccEEEeeeeccc-----ceeEEEecCCHHHHHHHHHHhCCcEeCCCcE
Confidence            34579999999999999998    78899999999999998763     6899999999999999998 999988 5789


Q ss_pred             eEEeccc
Q 045516          593 LVVDEAK  599 (675)
Q Consensus       593 l~V~~a~  599 (675)
                      |+|.|++
T Consensus        76 i~v~~ak   82 (83)
T d2b0ga1          76 MKITFAK   82 (83)
T ss_dssp             CEEEECC
T ss_pred             EEEEEec
Confidence            9999986

>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=99.50  E-value=1.2e-14  Score=125.22  Aligned_cols=78  Identities=17%  Similarity=0.132  Sum_probs=69.3

Q ss_pred             CCCceEEEcCCCCCC-C----HHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEE
Q 045516          414 GGSKTLFVGNLPFSV-E----QADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIR  487 (675)
Q Consensus       414 ~~~~tlfV~nLp~~~-t----e~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~  487 (675)
                      ..+++|||+||+..+ +    .++|+.+|++||.|++|++++     ++|||||+|.+.++|.+||. |||..|.|+.|+
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k-----~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~   77 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK-----SFKRVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET-----TTTEEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec-----CCCEEEEEECCHHHHHHHHHHhcccccCCCEeE
Confidence            457899999999886 3    356999999999999999984     48999999999999999998 999999999999


Q ss_pred             EEeccccCC
Q 045516          488 LDFARERGA  496 (675)
Q Consensus       488 V~~a~~~~~  496 (675)
                      |.|+.....
T Consensus        78 v~~a~~~~~   86 (104)
T d1weya_          78 LYFAQTLHI   86 (104)
T ss_dssp             EECCCCSSC
T ss_pred             EeecccCCC
Confidence            999976543

>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=99.50  E-value=1.9e-14  Score=123.52  Aligned_cols=78  Identities=15%  Similarity=0.360  Sum_probs=72.6

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~  596 (675)
                      .++|||+|||+.+++++    |+++|+.||.|..++++.+ .++.++|||||+|.+.++|.+||. |||..|.|++|.|.
T Consensus        18 ~~~lfV~nLp~~~te~~----L~~~F~~~G~i~~~~~~~~-~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~   92 (101)
T d1x5oa1          18 PTNLYISNLPLSMDEQE----LENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSA   92 (101)
T ss_dssp             TTEEEEESCCTTCCHHH----HHHTTTTTSCEEEEEEEEC-SSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCC
T ss_pred             CCEEEEeCCCCCCCHHH----HHHHHhhcccccceeeecc-cccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccC
Confidence            57899999999999998    7899999999999999888 478999999999999999999998 99999999999998


Q ss_pred             cccc
Q 045516          597 EAKQ  600 (675)
Q Consensus       597 ~a~~  600 (675)
                      ++.|
T Consensus        93 ~~~P   96 (101)
T d1x5oa1          93 PTEP   96 (101)
T ss_dssp             CSSC
T ss_pred             CCCC
Confidence            7765

>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=99.50  E-value=3.6e-14  Score=114.72  Aligned_cols=74  Identities=19%  Similarity=0.363  Sum_probs=67.4

Q ss_pred             eEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEecc
Q 045516          519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDEA  598 (675)
Q Consensus       519 ~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~~a  598 (675)
                      .+|||+|||+++++++    |+++|..||.|..|+|+++...  .++||||+|.+.++|.+||.||++.|+|+.|.|..+
T Consensus         1 Ttv~V~nlp~~~t~~~----l~~~F~~~G~I~~v~~~~~~~~--~~~~afV~F~~~~~a~~Al~~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNK----VYKYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAITKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHH----HHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHHTTTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHH----HHHHHhcCCceEEEEEEeeccc--cceEEEEEEcchHHhHHHHHhcCcEECCEEEEEEEC
Confidence            4799999999999998    7788999999999999998653  357999999999999999999999999999999864

>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=99.49  E-value=2.3e-14  Score=119.97  Aligned_cols=78  Identities=17%  Similarity=0.390  Sum_probs=69.8

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCC---eeeEEEEEeCCHHHHHHHHH-hCCceeCCeee
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGS---VKGIAYLDFTDADSFNKALE-MSGTEIGGYSL  593 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~---~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l  593 (675)
                      .++|||+|||+.+++++|+. +.++|++||.|..|.|+++..++.   ++|||||+|.+.++|..||. |||..|+|+.|
T Consensus         8 ~n~vyV~nLp~~~t~~~l~~-~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~l   86 (89)
T d2cpia1           8 KNLVFVVGLSQRLADPEVLK-RPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   86 (89)
T ss_dssp             SSCEEEEEECTTTCCHHHHH-STTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             cCEEEEECCCCccCHHHHHH-HHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEE
Confidence            46899999999999999642 478999999999999999877655   45999999999999999998 99999999999


Q ss_pred             EEe
Q 045516          594 VVD  596 (675)
Q Consensus       594 ~V~  596 (675)
                      +|.
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            984

>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=99.49  E-value=2.2e-14  Score=119.21  Aligned_cols=78  Identities=18%  Similarity=0.200  Sum_probs=69.4

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEE
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVV  595 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V  595 (675)
                      ...+|||+|||+++++++    |+++|..||.|..+.++.+..+|.++|||||+|.+.++|.+||+ ||+..|+||.|+|
T Consensus         8 ~~~~l~v~nLp~~~~~~d----i~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v   83 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDE----ILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKL   83 (86)
T ss_dssp             SSEEEEEESCCTTCCHHH----HHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCEEEEECCCCCCCHHH----HHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEE
Confidence            367899999999999999    77899999998775445555789999999999999999999998 9999999999999


Q ss_pred             ecc
Q 045516          596 DEA  598 (675)
Q Consensus       596 ~~a  598 (675)
                      .++
T Consensus        84 ~l~   86 (86)
T d2cqpa1          84 VLG   86 (86)
T ss_dssp             EES
T ss_pred             EEC
Confidence            875

>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=99.49  E-value=2.6e-14  Score=124.72  Aligned_cols=75  Identities=17%  Similarity=0.239  Sum_probs=68.6

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~  596 (675)
                      .++|||+|||+.+++++    |++||..||.|..|.|..      .+|||||+|.+.++|.+||. |||..|.|+.|+|.
T Consensus        10 ~~~l~V~nLp~~~t~~~----L~~~F~~fG~I~~v~l~~------~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~   79 (111)
T d1whxa_          10 KTVILAKNLPAGTLAAE----IQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLE   79 (111)
T ss_dssp             EEEEEEESCCTTCCHHH----HHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCEEEEECCCCCCCHHH----HHhhhhccCCccEEEeec------cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEE
Confidence            68999999999999998    778999999999999854      37999999999999999998 99999999999999


Q ss_pred             ccccCC
Q 045516          597 EAKQRG  602 (675)
Q Consensus       597 ~a~~r~  602 (675)
                      |+....
T Consensus        80 ~a~~~~   85 (111)
T d1whxa_          80 WAPIGV   85 (111)
T ss_dssp             EEETTT
T ss_pred             ECCCCc
Confidence            986543

>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=99.48  E-value=1.5e-14  Score=116.03  Aligned_cols=70  Identities=19%  Similarity=0.368  Sum_probs=67.1

Q ss_pred             EEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          521 IFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       521 lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      |||+|||..+++++    |+++|..||.|..++++++..++.++|||||+|.+.++|.+|+. |||..|+|+.|+
T Consensus         1 lyV~nLp~~~te~~----l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQD----LVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHH----HHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHH----HHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            79999999999998    78999999999999999999999999999999999999999998 999999999874

>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=99.47  E-value=5e-14  Score=119.60  Aligned_cols=82  Identities=18%  Similarity=0.272  Sum_probs=71.6

Q ss_pred             eEEEEecCCCCcCHHHHHHHHHhhhcccCc-EEEEEecccC-CCCCeeeEEEEEeCCHHHHHHHHH-hCC--ceeCCeee
Q 045516          519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGE-ITRISVPKDY-DTGSVKGIAYLDFTDADSFNKALE-MSG--TEIGGYSL  593 (675)
Q Consensus       519 ~~lfV~nLp~~~te~~i~~~L~~~F~~~G~-I~~v~i~~d~-~tG~~rG~afV~F~~~e~A~~Al~-lng--~~~~Gr~l  593 (675)
                      ++|||+|||..+++++    |+++|..||. |..|.|+++. .+|+++|||||+|.+.+.|..||. |++  ..++|+.|
T Consensus         2 ~rLyV~nLp~~~te~~----l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i   77 (96)
T d2disa1           2 CRLFIGGIPKMKKREE----ILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQI   77 (96)
T ss_dssp             EEEEEECCCTTSCHHH----HHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCC
T ss_pred             CEEEEcCCCCcCCHHH----HHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEE
Confidence            6899999999999998    6778888895 9999999885 578999999999999999999998 754  55689999


Q ss_pred             EEeccccCCCC
Q 045516          594 VVDEAKQRGDF  604 (675)
Q Consensus       594 ~V~~a~~r~~~  604 (675)
                      +|.|+.+....
T Consensus        78 ~V~~A~p~~~~   88 (96)
T d2disa1          78 AVDWAEPEIDV   88 (96)
T ss_dssp             EEEESCSSCST
T ss_pred             EEEEcCCCCCC
Confidence            99999876543

>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=99.47  E-value=9e-14  Score=118.22  Aligned_cols=80  Identities=25%  Similarity=0.425  Sum_probs=70.7

Q ss_pred             CCCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCC--
Q 045516          514 RGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGG--  590 (675)
Q Consensus       514 ~~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~G--  590 (675)
                      ...+.++|||+|||.++++++    |+++|..||.|..|+|.++      ++||||+|.+.++|..|+. ||+..|.|  
T Consensus        13 ~~~Ps~tl~V~nLp~~~t~~~----l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~   82 (97)
T d1whya_          13 KANPTTRLWVGGLGPNTSLAA----LAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPD   82 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHH----HHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSS
T ss_pred             CCCCCCEEEEcCCCCCCCHHH----HHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCc
Confidence            345689999999999999988    7889999999999999876      7899999999999999998 99999987  


Q ss_pred             eeeEEeccccCCC
Q 045516          591 YSLVVDEAKQRGD  603 (675)
Q Consensus       591 r~l~V~~a~~r~~  603 (675)
                      +.|+|.|+++...
T Consensus        83 ~~l~v~~ak~~~~   95 (97)
T d1whya_          83 RRLRVDFAKSGPS   95 (97)
T ss_dssp             CBCEEEECCCCCC
T ss_pred             eEEEEEeCCCCCC
Confidence            5899999986443

>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=99.47  E-value=8.2e-15  Score=126.26  Aligned_cols=79  Identities=13%  Similarity=0.090  Sum_probs=71.2

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEec
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDE  597 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~~  597 (675)
                      ..+|||+|||+.+++++    |.++|..||.|..+.++....+|.++|||||+|.+.++|.+||.||+..|+||.|.|.+
T Consensus         8 ~~~v~v~nLp~~~t~~~----l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~~n~~~i~gr~i~V~~   83 (103)
T d2cpya1           8 KVCAHITNIPFSITKMD----VLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHV   83 (103)
T ss_dssp             CCEEEEESCCTTSCHHH----HHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEEE
T ss_pred             ceEEEEeCCCCCCCHHH----HhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHhcCCCeECCcEEEEEE
Confidence            57899999999999998    77899999999876555665789999999999999999999999999999999999998


Q ss_pred             ccc
Q 045516          598 AKQ  600 (675)
Q Consensus       598 a~~  600 (675)
                      +..
T Consensus        84 ~~~   86 (103)
T d2cpya1          84 VTL   86 (103)
T ss_dssp             ECH
T ss_pred             CCH
Confidence            754

>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=99.47  E-value=6.9e-14  Score=116.17  Aligned_cols=76  Identities=18%  Similarity=0.366  Sum_probs=68.2

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~  596 (675)
                      .++|||+|||+.+++++    |.++|..||.|..+.+..      ++|||||+|.+.++|..||. |||..|+|+.|+|.
T Consensus         8 ~k~l~V~nLp~~~te~~----l~~~F~~~g~i~~~~~~~------~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~   77 (86)
T d2cpda1           8 VKILYVRNLMLSTSEEM----IEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVT   77 (86)
T ss_dssp             CCEEEEESCCTTCCHHH----HHHHHHTTSTTCEEEEEE------CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEE
T ss_pred             CCEEEEcCCCCCCCHHH----HHHhhcccceeeeEEEcc------ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            58999999999999998    678888999988877744      48999999999999999998 99999999999999


Q ss_pred             ccccCCC
Q 045516          597 EAKQRGD  603 (675)
Q Consensus       597 ~a~~r~~  603 (675)
                      |++|+..
T Consensus        78 ~akP~~~   84 (86)
T d2cpda1          78 LAKPVDK   84 (86)
T ss_dssp             CCCCCCC
T ss_pred             eccCCCC
Confidence            9987653

>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=99.47  E-value=3.7e-14  Score=117.87  Aligned_cols=75  Identities=17%  Similarity=0.324  Sum_probs=69.5

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~  596 (675)
                      .++|||+|||..+++++    |.++|..||.|..|+++++      +|||||+|.+.++|..||. |||..|+|+.|+|.
T Consensus         8 ~~~l~V~nLp~~~~~~~----l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~   77 (86)
T d2cpja1           8 RSRLFVGNLPPDITEEE----MRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVR   77 (86)
T ss_dssp             TTEEEEESCCTTCCHHH----HHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEE
T ss_pred             CCEEEEECCCCCCCHHH----HHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            46799999999999998    7889999999999999876      6899999999999999998 99999999999999


Q ss_pred             ccccCC
Q 045516          597 EAKQRG  602 (675)
Q Consensus       597 ~a~~r~  602 (675)
                      |+....
T Consensus        78 ~A~~~~   83 (86)
T d2cpja1          78 FACHSA   83 (86)
T ss_dssp             ESSCCS
T ss_pred             ECCCcC
Confidence            997654

>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=99.47  E-value=9.9e-14  Score=120.53  Aligned_cols=76  Identities=17%  Similarity=0.365  Sum_probs=68.6

Q ss_pred             ceEEEEecCCC-CcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEE
Q 045516          518 AHTIFIKGFDS-SVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVV  595 (675)
Q Consensus       518 ~~~lfV~nLp~-~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V  595 (675)
                      +++|||+||++ .+++++    |.++|..||.|..|.|+++.     +|||||+|.+.++|.+||+ |||..|.|+.|+|
T Consensus         2 ~~~l~V~nL~p~~~te~~----L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v   72 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQS----LFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRI   72 (109)
T ss_dssp             CSEEEEESCCTTTCCHHH----HHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEE
T ss_pred             CCEEEEeCCCcccCCHHH----HHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            58999999964 589988    78999999999999999874     7999999999999999998 9999999999999


Q ss_pred             eccccCC
Q 045516          596 DEAKQRG  602 (675)
Q Consensus       596 ~~a~~r~  602 (675)
                      .|++.+.
T Consensus        73 ~~s~~~~   79 (109)
T d2adca1          73 TLSKHQN   79 (109)
T ss_dssp             ECCSCCC
T ss_pred             EECCCCC
Confidence            9986543

>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=99.47  E-value=4.3e-14  Score=115.48  Aligned_cols=73  Identities=22%  Similarity=0.451  Sum_probs=66.6

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~  596 (675)
                      .++|||+||+  +++++    |+++|++||.|..|.+.++      +|||||+|.+.++|..|+. |||..|+|+.|+|.
T Consensus         5 ~~ti~V~~~~--~te~~----L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~   72 (79)
T d2bz2a1           5 GNTLYVYGED--MTPTL----LRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVN   72 (79)
T ss_dssp             CCEEEEECSS--CCHHH----HHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEE
T ss_pred             CCEEEEECCC--CCHHH----HHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEE
Confidence            6899999996  78877    8899999999999999765      6899999999999999998 99999999999999


Q ss_pred             ccccCC
Q 045516          597 EAKQRG  602 (675)
Q Consensus       597 ~a~~r~  602 (675)
                      |++++.
T Consensus        73 ~a~~~P   78 (79)
T d2bz2a1          73 IARKQP   78 (79)
T ss_dssp             ECCSSC
T ss_pred             EecCCC
Confidence            998653

>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=99.47  E-value=6.3e-14  Score=116.94  Aligned_cols=76  Identities=12%  Similarity=0.220  Sum_probs=65.1

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~  596 (675)
                      .++|||+|||+.+++++    |+++|..|| |..+.+      +..+|||||+|.+.++|..||. ||+..|.|+.|+|.
T Consensus         5 s~~i~V~nLp~~~t~~~----l~~lF~~~G-~~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~   73 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQE----VHDLLKDYD-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQ   73 (88)
T ss_dssp             CCCEEEESCCSSCCHHH----HHHHTCSSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCEEEEeCCCCccChHH----HHHHHHhcC-ceeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            67899999999999999    778999999 333333      3458999999999999999998 99999999999999


Q ss_pred             ccccCCCC
Q 045516          597 EAKQRGDF  604 (675)
Q Consensus       597 ~a~~r~~~  604 (675)
                      |++.+...
T Consensus        74 ~a~~~~~~   81 (88)
T d1wg1a_          74 LQPTDALL   81 (88)
T ss_dssp             ECCCCCCC
T ss_pred             EcCCCCCC
Confidence            99765433

>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=99.46  E-value=7.8e-14  Score=120.02  Aligned_cols=82  Identities=18%  Similarity=0.096  Sum_probs=74.8

Q ss_pred             CceEEEEecCCCCc-CHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeE
Q 045516          517 AAHTIFIKGFDSSV-GEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV  594 (675)
Q Consensus       517 ~~~~lfV~nLp~~~-te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~  594 (675)
                      ..++|||+||+..+ +++++++.|+.+|..||.|..|.+++.      ++||||+|.+.++|.+||. |||..|+|+.|+
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~   77 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT------TTEEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecC------CCEEEEEECCHHHHHHHHHHhcccccCCCEeE
Confidence            36899999999996 788889999999999999999999865      7899999999999999999 999999999999


Q ss_pred             EeccccCCCC
Q 045516          595 VDEAKQRGDF  604 (675)
Q Consensus       595 V~~a~~r~~~  604 (675)
                      |.|++++...
T Consensus        78 v~~a~~~~~~   87 (104)
T d1weya_          78 LYFAQTLHIG   87 (104)
T ss_dssp             EECCCCSSCC
T ss_pred             EeecccCCCC
Confidence            9999766543

>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=99.46  E-value=6.2e-14  Score=116.98  Aligned_cols=78  Identities=18%  Similarity=0.225  Sum_probs=68.9

Q ss_pred             CCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCcee-CCeee
Q 045516          516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEI-GGYSL  593 (675)
Q Consensus       516 ~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~-~Gr~l  593 (675)
                      +++++|||+|||..+++++    |+++|..||.|..+.+...    ..+|||||+|.+.++|..|+. |||..| +|+.|
T Consensus         8 pPs~tL~V~NLp~~~te~~----l~~~F~~~G~v~~~~~~~~----~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l   79 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEED----LKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHL   79 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHH----HHHHHHTTSCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBC
T ss_pred             CCCCEEEEECCCCCCCHHH----HHHHhhccCCEEEEEEeee----cccceeEEEECCHHHHHHHHHhccCCEecCCCEE
Confidence            4588999999999999998    7788999999988877654    347899999999999999997 999988 58999


Q ss_pred             EEeccccC
Q 045516          594 VVDEAKQR  601 (675)
Q Consensus       594 ~V~~a~~r  601 (675)
                      +|.|++++
T Consensus        80 ~v~~sk~~   87 (88)
T d2adca2          80 RVSFSKST   87 (88)
T ss_dssp             EEEECSSC
T ss_pred             EEEeCCCC
Confidence            99998764

>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=99.46  E-value=1.8e-14  Score=118.02  Aligned_cols=76  Identities=25%  Similarity=0.351  Sum_probs=66.9

Q ss_pred             eEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCc-eeCCeeeEEe
Q 045516          519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGT-EIGGYSLVVD  596 (675)
Q Consensus       519 ~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~-~~~Gr~l~V~  596 (675)
                      ++|||+|||.++++++    |+++|.+||.|..+.+..      .+|||||+|.+.++|..||+ |||. .|+|+.|+|.
T Consensus         2 n~l~V~nLp~~~te~~----L~~~F~~~G~i~~~~~~~------~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~   71 (80)
T d2cqha1           2 NKLYIGNLSPAVTADD----LRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVD   71 (80)
T ss_dssp             CCEEEECCCTTCCHHH----HHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CEEEEECCCCCCCHHH----HHHHHHHhCcEEEeEEec------ccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEE
Confidence            5799999999999998    778888999987776655      48999999999999999998 9986 6999999999


Q ss_pred             ccccCCCC
Q 045516          597 EAKQRGDF  604 (675)
Q Consensus       597 ~a~~r~~~  604 (675)
                      |+.++..+
T Consensus        72 ~a~~k~~r   79 (80)
T d2cqha1          72 YSVSKKLR   79 (80)
T ss_dssp             ECCCCCCC
T ss_pred             EcCCcCcC
Confidence            99987653

>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=99.45  E-value=5.8e-15  Score=127.26  Aligned_cols=75  Identities=17%  Similarity=0.211  Sum_probs=71.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEec
Q 045516          417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA  491 (675)
Q Consensus       417 ~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a  491 (675)
                      ..|+|+||+..+++++|+++|++||.|.+|+|+++.+++++|||||+|.+.++|.+||. |||..|+||.|.|.|.
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            46889999999999999999999999999999988899999999999999999999997 9999999999999885

>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=99.44  E-value=4.1e-14  Score=123.68  Aligned_cols=81  Identities=14%  Similarity=0.255  Sum_probs=73.5

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeeeEEe
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVD  596 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l~V~  596 (675)
                      ..++|||+|||+.+++++    |.+||+.||.|..+.++.+..+|.++|||||+|.+.++|.+||.||+..|+||.|.|.
T Consensus        17 ~~~~i~v~nLp~~~t~~d----i~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~~~~~~i~gR~i~V~   92 (112)
T d1wela1          17 AGFCVYLKGLPFEAENKH----VIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVH   92 (112)
T ss_dssp             CCCEEEEECCCTTCCHHH----HHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEE
T ss_pred             CCeEEEEecCCCcCcHHH----HhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHHcCCCcCCCEEEEEE
Confidence            367999999999999999    7789999999988777777788999999999999999999999999999999999998


Q ss_pred             ccccC
Q 045516          597 EAKQR  601 (675)
Q Consensus       597 ~a~~r  601 (675)
                      .+.++
T Consensus        93 ~~~~~   97 (112)
T d1wela1          93 PITKK   97 (112)
T ss_dssp             EECHH
T ss_pred             EcChH
Confidence            87543

>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=99.40  E-value=5.1e-13  Score=111.30  Aligned_cols=78  Identities=14%  Similarity=0.247  Sum_probs=69.8

Q ss_pred             CCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH---hCCceeCCe
Q 045516          515 GQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE---MSGTEIGGY  591 (675)
Q Consensus       515 ~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~---lng~~~~Gr  591 (675)
                      ..++++|||+|||..+++++    |.++|..||.|..|.+.++      ++||||+|.+.++|..|+.   +++..|+|+
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~----L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~   74 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETE----VIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQ   74 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHH----HHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTE
T ss_pred             CCCCCEEEEeCCCCCCCHHH----HHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCC
Confidence            35689999999999999998    7789999999999999876      6899999999999999986   478899999


Q ss_pred             eeEEeccccCC
Q 045516          592 SLVVDEAKQRG  602 (675)
Q Consensus       592 ~l~V~~a~~r~  602 (675)
                      .|+|.|+..+.
T Consensus        75 ~l~v~~sk~~~   85 (88)
T d2cq1a1          75 PIYIQYSNHKE   85 (88)
T ss_dssp             ECEEEECSCSS
T ss_pred             EEEEEECCCCC
Confidence            99999997553

>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=99.39  E-value=1.1e-12  Score=112.96  Aligned_cols=79  Identities=19%  Similarity=0.225  Sum_probs=69.8

Q ss_pred             CCCceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-h--CCceeCCe
Q 045516          515 GQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-M--SGTEIGGY  591 (675)
Q Consensus       515 ~~~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-l--ng~~~~Gr  591 (675)
                      ..++++|||+|||..+++++    |..+|..||.|..|+|.+.      +|||||+|.+.++|..||. |  ++..++|+
T Consensus        12 ~~ps~~l~v~nlp~~~te~~----l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~   81 (104)
T d1wexa_          12 VSVSPVVHVRGLCESVVEAD----LVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQ   81 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHH----HHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSS
T ss_pred             CCCCCEEEEeCCCCCCCHHH----HHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeE
Confidence            34589999999999999998    7899999999999999765      7899999999999999997 5  66788999


Q ss_pred             eeEEeccccCCC
Q 045516          592 SLVVDEAKQRGD  603 (675)
Q Consensus       592 ~l~V~~a~~r~~  603 (675)
                      +|+|.|++....
T Consensus        82 ~l~v~~s~~~~~   93 (104)
T d1wexa_          82 QAFFNYSTSKRI   93 (104)
T ss_dssp             BCEEEECSSSSC
T ss_pred             EEEEEEcCCCcc
Confidence            999999976443

>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=99.37  E-value=6.9e-13  Score=106.98  Aligned_cols=70  Identities=16%  Similarity=0.311  Sum_probs=62.1

Q ss_pred             EEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEeccc
Q 045516          521 IFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVDEAK  599 (675)
Q Consensus       521 lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~~a~  599 (675)
                      |||+|||+++++++    |+++|++|| |..+.+.      +.+|||||.|.+.++|.+|+. |||..|.|+.|+|+|+.
T Consensus         1 i~V~nLp~~~t~~~----l~~~F~~~g-~~~~~~~------~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~   69 (75)
T d1wi6a1           1 ILIRGLPGDVTNQE----VHDLLSDYE-LKYCFVD------KYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQP   69 (75)
T ss_dssp             EEEECCCTTCCHHH----HHHHTTTSC-EEEEEEE------TTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECC
T ss_pred             CEEeCCCCcCCHHH----HHHHHhccc-ccceeec------ccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeC
Confidence            79999999999999    778999999 5555553      458999999999999999998 99999999999999996


Q ss_pred             cC
Q 045516          600 QR  601 (675)
Q Consensus       600 ~r  601 (675)
                      ..
T Consensus        70 ~d   71 (75)
T d1wi6a1          70 TD   71 (75)
T ss_dssp             ST
T ss_pred             CC
Confidence            43

>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=99.36  E-value=5.6e-13  Score=115.55  Aligned_cols=78  Identities=22%  Similarity=0.237  Sum_probs=69.5

Q ss_pred             CceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCcee--CCeee
Q 045516          517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEI--GGYSL  593 (675)
Q Consensus       517 ~~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~--~Gr~l  593 (675)
                      +..+|||+||++.+++++    |+++|+.||.|..|.|+++.    .+|||||+|.+.++|..||. |||..|  .|+.|
T Consensus         6 ~~~~v~V~NL~~~vte~~----L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l   77 (108)
T d2adba1           6 PVLRIIVENLFYPVTLDV----LHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTL   77 (108)
T ss_dssp             CEEEEESCSCCSTTHHHH----HHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCC
T ss_pred             CeEEEEEeCcCCCCCHHH----HHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEE
Confidence            378899999999999998    88999999999999998764    48999999999999999998 999998  57889


Q ss_pred             EEeccccCC
Q 045516          594 VVDEAKQRG  602 (675)
Q Consensus       594 ~V~~a~~r~  602 (675)
                      +|.|++++.
T Consensus        78 ~v~~s~~~~   86 (108)
T d2adba1          78 RIDFSKLTS   86 (108)
T ss_dssp             EEEECSSCS
T ss_pred             EEEecCCcc
Confidence            998887644

>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=99.36  E-value=3.7e-13  Score=110.06  Aligned_cols=72  Identities=17%  Similarity=0.268  Sum_probs=62.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCee-EEEEeccc
Q 045516          416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRA-IRLDFARE  493 (675)
Q Consensus       416 ~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~-i~V~~a~~  493 (675)
                      .+.|||.|||+.++++ |+++|++||.|.++++..     .+|||||.|.+.++|.+||.+||..|+|+. |.|..+..
T Consensus         4 ~~wV~V~G~p~~~~~~-il~~F~~~G~I~~~~~~~-----~~~~~fV~f~~~~~A~~Al~~nG~~~~g~~~vgV~~~~~   76 (81)
T d1wwha1           4 DTWVTVFGFPQASASY-ILLQFAQYGNILKHVMSN-----TGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCID   76 (81)
T ss_dssp             GGEEEEECCCGGGHHH-HHHHHHTTSCEEEEEECS-----SSSEEEEEESSHHHHHHHHTTTTCEETTTEECEEEECCC
T ss_pred             ccEEEEECCChHHHHH-HHHHHHhhhhhheEEecC-----CCCEEEEEEcccHHHHHHHhcCCCeECCcEEEEEEeCCC
Confidence            5789999999999865 556899999999998853     489999999999999999999999999985 56877654

>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=99.34  E-value=1.9e-12  Score=107.92  Aligned_cols=77  Identities=13%  Similarity=0.163  Sum_probs=68.1

Q ss_pred             CCCceEEEEecCCCC-cCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH---hCCceeCC
Q 045516          515 GQAAHTIFIKGFDSS-VGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE---MSGTEIGG  590 (675)
Q Consensus       515 ~~~~~~lfV~nLp~~-~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~---lng~~~~G  590 (675)
                      ..++++|||+|||.. +++.+    |.++|+.||.|..|.|+.+      +++|||+|.+.++|..|+.   +++..|+|
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~e----L~~lF~~fG~I~~i~i~~~------k~~afV~f~~~~~A~~A~~~l~~~~~~~~g   74 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQ----LLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFG   74 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHH----HHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETT
T ss_pred             CCCCcEEEEECCCCCcCCHHH----HHHHHHhhCCeEEEEeecc------ceEEEEEEcchhhHHHHHHHHhhCCCccCC
Confidence            455899999999986 67777    8899999999999999876      5799999999999999986   47889999


Q ss_pred             eeeEEeccccC
Q 045516          591 YSLVVDEAKQR  601 (675)
Q Consensus       591 r~l~V~~a~~r  601 (675)
                      ++|+|.|+...
T Consensus        75 r~l~V~~s~~~   85 (89)
T d1x4da1          75 KPVRVHLSQKY   85 (89)
T ss_dssp             EECEEEEECCC
T ss_pred             ceEEEEECCCc
Confidence            99999998743

>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=99.34  E-value=1.3e-12  Score=111.33  Aligned_cols=80  Identities=20%  Similarity=0.316  Sum_probs=69.0

Q ss_pred             CCCCceEEEcCC--CCCC---------CHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcc
Q 045516          413 SGGSKTLFVGNL--PFSV---------EQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQM  480 (675)
Q Consensus       413 ~~~~~tlfV~nL--p~~~---------te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~  480 (675)
                      ...+++|+|.||  |..+         ..++|++.|++||.|..|.+..+   ..+|||||.|.+.++|.+|+. |||..
T Consensus         5 ~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~---~~~G~~fV~f~~~e~A~~A~~~lng~~   81 (99)
T d2dita1           5 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR---HPDGVASVSFRDPEEADYCIQTLDGRW   81 (99)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT---CTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC---CCccEEEEEECCHHHHHHHHHHhCCcE
Confidence            456899999999  5443         23679999999999999998754   567999999999999999997 99999


Q ss_pred             cCCeeEEEEeccccC
Q 045516          481 LGNRAIRLDFARERG  495 (675)
Q Consensus       481 ~~gr~i~V~~a~~~~  495 (675)
                      |+||.|+|.+...+.
T Consensus        82 ~~gr~i~v~~~~g~~   96 (99)
T d2dita1          82 FGGRQITAQAWDGTT   96 (99)
T ss_dssp             ETTEECEEEECCSCC
T ss_pred             ECCEEEEEEEeCCcC
Confidence            999999999987654

>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=99.33  E-value=5e-13  Score=116.78  Aligned_cols=73  Identities=19%  Similarity=0.218  Sum_probs=63.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCH-HHHHHHHH-hCCcccCCeeEEEEecc
Q 045516          415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASV-EDAHKAIE-LNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       415 ~~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~-e~A~~Al~-l~g~~~~gr~i~V~~a~  492 (675)
                      +...+||+|||+.+|+++|+.+|++||.|..|.|+++     +|||||.|.+. ++|..|+. ||+..|.++.+.|.+..
T Consensus        10 g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~-----kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~   84 (113)
T d1owxa_          10 GCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG-----AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEV   84 (113)
T ss_dssp             CCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT-----CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEE
T ss_pred             CCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC-----CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEee
Confidence            3567799999999999999999999999999999854     89999999995 67888886 99998888777776654

>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=99.33  E-value=8e-13  Score=113.00  Aligned_cols=63  Identities=21%  Similarity=0.354  Sum_probs=57.3

Q ss_pred             CCCceEEEcC--CCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCccc
Q 045516          414 GGSKTLFVGN--LPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQML  481 (675)
Q Consensus       414 ~~~~tlfV~n--Lp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~  481 (675)
                      ..+++|||.|  ||+++|+++|+++|++||.|..|+++.+     +|||||+|.+.++|..|+. |||..|
T Consensus        16 ~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~-----k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT-----CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC-----ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            3468899955  9999999999999999999999998864     7899999999999999997 999876

>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=99.32  E-value=1.6e-12  Score=110.73  Aligned_cols=77  Identities=12%  Similarity=0.179  Sum_probs=68.5

Q ss_pred             CCceEEEEecCCCC-cCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH---hCCceeCCe
Q 045516          516 QAAHTIFIKGFDSS-VGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE---MSGTEIGGY  591 (675)
Q Consensus       516 ~~~~~lfV~nLp~~-~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~---lng~~~~Gr  591 (675)
                      ..+++|||+|||.. +++++    |..+|+.||.|..|.|+++      +|||||+|.+.++|..||.   +++..|+|+
T Consensus        16 ~~~~~l~v~nLp~~~~te~~----l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr   85 (99)
T d1x4fa1          16 ELGRVIHLSNLPHSGYSDSA----VLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGR   85 (99)
T ss_dssp             CCCCEEEEESCCCSSCCSHH----HHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSS
T ss_pred             CCCCEEEEeCCcCCccCHHH----HHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCE
Confidence            34789999999985 88887    8899999999999999876      6899999999999999985   789999999


Q ss_pred             eeEEeccccCC
Q 045516          592 SLVVDEAKQRG  602 (675)
Q Consensus       592 ~l~V~~a~~r~  602 (675)
                      .|+|.|++.+.
T Consensus        86 ~l~V~~s~~~~   96 (99)
T d1x4fa1          86 CVKVDLSEKYK   96 (99)
T ss_dssp             CCEEEEECSCS
T ss_pred             EEEEEEcCCcc
Confidence            99999997543

>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=99.30  E-value=4.1e-12  Score=108.10  Aligned_cols=85  Identities=16%  Similarity=0.362  Sum_probs=72.9

Q ss_pred             CCceEEEEecC--CCCcC-----HHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCce
Q 045516          516 QAAHTIFIKGF--DSSVG-----EDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTE  587 (675)
Q Consensus       516 ~~~~~lfV~nL--p~~~t-----e~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~  587 (675)
                      ..+++|+|.||  |..+.     ..+|.+.|+..|++||.|..|.++.+    .++|||||.|.+.++|.+|+. |||+.
T Consensus         6 ~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng~~   81 (99)
T d2dita1           6 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGRW   81 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCCcE
Confidence            44899999998  43321     45788889999999999999998775    357999999999999999998 99999


Q ss_pred             eCCeeeEEeccccCCCC
Q 045516          588 IGGYSLVVDEAKQRGDF  604 (675)
Q Consensus       588 ~~Gr~l~V~~a~~r~~~  604 (675)
                      |+||.|+|.++.++..+
T Consensus        82 ~~gr~i~v~~~~g~~~~   98 (99)
T d2dita1          82 FGGRQITAQAWDGTTDY   98 (99)
T ss_dssp             ETTEECEEEECCSCCCS
T ss_pred             ECCEEEEEEEeCCcCCC
Confidence            99999999999877654

>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=99.29  E-value=7.2e-14  Score=117.12  Aligned_cols=76  Identities=16%  Similarity=0.334  Sum_probs=65.0

Q ss_pred             eEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEec-----ccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCeee
Q 045516          519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVP-----KDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSL  593 (675)
Q Consensus       519 ~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~-----~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~l  593 (675)
                      ++|||+|||+.+++++    |.++|+.||.|..+.+.     .+..++.++|||||+|.+.++|..|+.|||..|.|+.|
T Consensus         2 RrlyVgNLp~~~te~~----l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~l~g~~~~Gr~l   77 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEA----MMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSL   77 (90)
T ss_dssp             CEEEECSCCTTCCTTH----HHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGGGSSCCSSSSCC
T ss_pred             CEEEEcCCCCccchHH----HHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHhhCCcEECCEEE
Confidence            6899999999999999    66777777877666554     34567888999999999999999999999999999999


Q ss_pred             EEecc
Q 045516          594 VVDEA  598 (675)
Q Consensus       594 ~V~~a  598 (675)
                      +|.++
T Consensus        78 ~V~r~   82 (90)
T d1u2fa_          78 KIRRP   82 (90)
T ss_dssp             CCBCT
T ss_pred             EECCC
Confidence            99753

>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=99.22  E-value=1.3e-12  Score=112.30  Aligned_cols=75  Identities=15%  Similarity=0.219  Sum_probs=64.9

Q ss_pred             eEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEec
Q 045516          519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVDE  597 (675)
Q Consensus       519 ~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~~  597 (675)
                      ..++|.+++..++++.    |.++|++||.|..|+|+++ .+|+++|||||+|.+.++|.+|+. |||++|+||.|+|.|
T Consensus        28 ~~~~v~~~~~~~~ed~----l~e~f~k~G~I~~v~I~~~-~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~  102 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEV----FTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAEL  102 (104)
T ss_dssp             HHHHHHHHHHHHHHHH----HHHHHHHTCCEEEEEECCS-SSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEE
T ss_pred             chHHhhhhhhhhhHHH----HHHHhccCCCEEEEEeecC-CCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEE
Confidence            3466666665555554    7889999999999999877 579999999999999999999998 999999999999987


Q ss_pred             c
Q 045516          598 A  598 (675)
Q Consensus       598 a  598 (675)
                      .
T Consensus       103 s  103 (104)
T d1jmta_         103 S  103 (104)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.18  E-value=9.5e-12  Score=106.80  Aligned_cols=79  Identities=27%  Similarity=0.331  Sum_probs=67.9

Q ss_pred             CCceEEEcCC--CCCC--------CHHHHHHHhhhCCCeEEEEEeeCCC---CCcccEEEEEecCHHHHHHHHH-hCCcc
Q 045516          415 GSKTLFVGNL--PFSV--------EQADVQNFFSEVAEVVDVRLSSDAD---GRFKGYGHVEFASVEDAHKAIE-LNGQM  480 (675)
Q Consensus       415 ~~~tlfV~nL--p~~~--------te~~L~~~F~~~G~I~~v~i~~~~~---g~~kG~afV~F~~~e~A~~Al~-l~g~~  480 (675)
                      .+++|+|.||  +..+        ..++|++.|.+||.|.+|.|+++..   ....||+||+|.+.++|.+|+. |||..
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~   82 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   82 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCC
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCE
Confidence            4789999999  4443        3457899999999999999988763   3457999999999999999997 99999


Q ss_pred             cCCeeEEEEeccc
Q 045516          481 LGNRAIRLDFARE  493 (675)
Q Consensus       481 ~~gr~i~V~~a~~  493 (675)
                      |+||.|.|.|...
T Consensus        83 f~gR~v~v~f~~~   95 (104)
T d1o0pa_          83 FANRVVVTKYCDP   95 (104)
T ss_dssp             SSSSCCEEEEECH
T ss_pred             ECCeEEEEEEcCH
Confidence            9999999999753

>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=99.16  E-value=3.4e-11  Score=103.24  Aligned_cols=85  Identities=13%  Similarity=0.307  Sum_probs=72.6

Q ss_pred             CCceEEEEecC--CCCc----CHHHHHHHHHhhhcccCcEEEEEecccCCCC--CeeeEEEEEeCCHHHHHHHHH-hCCc
Q 045516          516 QAAHTIFIKGF--DSSV----GEDQVRASLEEHFGSCGEITRISVPKDYDTG--SVKGIAYLDFTDADSFNKALE-MSGT  586 (675)
Q Consensus       516 ~~~~~lfV~nL--p~~~----te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG--~~rG~afV~F~~~e~A~~Al~-lng~  586 (675)
                      .|+++|+|.||  +..+    ...+|.+.|+..|.+||.|..|.|+++..+.  ...|++||.|.+.++|.+|+. |||+
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr   81 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   81 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSC
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCC
Confidence            45899999999  4443    3456788899999999999999999876543  356899999999999999998 9999


Q ss_pred             eeCCeeeEEecccc
Q 045516          587 EIGGYSLVVDEAKQ  600 (675)
Q Consensus       587 ~~~Gr~l~V~~a~~  600 (675)
                      .|+||.|.|.|..+
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            99999999999864

>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=99.10  E-value=9.2e-11  Score=102.07  Aligned_cols=73  Identities=14%  Similarity=0.095  Sum_probs=64.3

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCH-HHHHHHHH-hCCceeCCeeeEE
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDA-DSFNKALE-MSGTEIGGYSLVV  595 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~-e~A~~Al~-lng~~~~Gr~l~V  595 (675)
                      ...+||+|||..+++++    |+.+|+.||.|.+|.|+++      +|||||.|.+. ++|..|+. ||+..|.++.+.|
T Consensus        11 ~~~~fvgnL~~~~tee~----Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v   80 (113)
T d1owxa_          11 CLLKFSGDLDDQTCRED----LHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEV   80 (113)
T ss_dssp             CEEEEEESCCSSCCHHH----HHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSE
T ss_pred             CeEEEECCCCCCCCHHH----HHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEE
Confidence            46679999999999998    7899999999999999876      79999999985 67888887 9999999888888


Q ss_pred             ecccc
Q 045516          596 DEAKQ  600 (675)
Q Consensus       596 ~~a~~  600 (675)
                      .+...
T Consensus        81 ~~~~~   85 (113)
T d1owxa_          81 TWEVL   85 (113)
T ss_dssp             EEEEC
T ss_pred             EEeec
Confidence            87754

>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=99.08  E-value=8.6e-11  Score=95.68  Aligned_cols=72  Identities=17%  Similarity=0.198  Sum_probs=61.1

Q ss_pred             ceEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCceeCCee-eEEe
Q 045516          518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYS-LVVD  596 (675)
Q Consensus       518 ~~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~~Gr~-l~V~  596 (675)
                      .+.|+|.|||+..+++.    | .+|..||.|..+++.+.      +|||||+|.+.++|.+||.+||..|+|+. |.|.
T Consensus         4 ~~wV~V~G~p~~~~~~i----l-~~F~~~G~I~~~~~~~~------~~~~fV~f~~~~~A~~Al~~nG~~~~g~~~vgV~   72 (81)
T d1wwha1           4 DTWVTVFGFPQASASYI----L-LQFAQYGNILKHVMSNT------GNWMHIRYQSKLQARKALSKDGRIFGESIMIGVK   72 (81)
T ss_dssp             GGEEEEECCCGGGHHHH----H-HHHHTTSCEEEEEECSS------SSEEEEEESSHHHHHHHHTTTTCEETTTEECEEE
T ss_pred             ccEEEEECCChHHHHHH----H-HHHHhhhhhheEEecCC------CCEEEEEEcccHHHHHHHhcCCCeECCcEEEEEE
Confidence            57899999999887543    4 47999999999988544      79999999999999999999999999985 5677


Q ss_pred             cccc
Q 045516          597 EAKQ  600 (675)
Q Consensus       597 ~a~~  600 (675)
                      .+..
T Consensus        73 ~~~~   76 (81)
T d1wwha1          73 PCID   76 (81)
T ss_dssp             ECCC
T ss_pred             eCCC
Confidence            6654

>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=99.06  E-value=1.2e-10  Score=99.12  Aligned_cols=63  Identities=17%  Similarity=0.446  Sum_probs=56.8

Q ss_pred             CCceEEEEec--CCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCcee
Q 045516          516 QAAHTIFIKG--FDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEI  588 (675)
Q Consensus       516 ~~~~~lfV~n--Lp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~  588 (675)
                      .+.++|||.|  |+..+++++    |+.+|++||.|..|+++++      ++||||+|.+.++|..|+. |||..|
T Consensus        16 ~pt~~l~V~ng~L~~~vte~~----L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          16 YATQSLVVANGGLGNGVSRNQ----LLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             SCCSEEEEETCTGGGTCCHHH----HHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCceEEEECCCCCCCCCHHH----HHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            4478899965  999999998    7889999999999999876      6899999999999999998 999887

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.80  E-value=3e-05  Score=61.77  Aligned_cols=78  Identities=18%  Similarity=0.377  Sum_probs=64.3

Q ss_pred             CCCCceEEEEecCCCCcC-----HHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHHhCCcee
Q 045516          514 RGQAAHTIFIKGFDSSVG-----EDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEI  588 (675)
Q Consensus       514 ~~~~~~~lfV~nLp~~~t-----e~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~lng~~~  588 (675)
                      .+++..||.|.-+.....     .+.+...|-+.|..||+|.-||++.+        ...|+|.+-..|..|+.++|..+
T Consensus        11 qGPpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~l~g~~v   82 (95)
T d1ufwa_          11 QGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLDVDGMKV   82 (95)
T ss_dssp             CCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHHGGGSEE
T ss_pred             cCCCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhccCCeEE
Confidence            456678888876653332     35667778888999999999999887        47999999999999999999999


Q ss_pred             CCeeeEEeccc
Q 045516          589 GGYSLVVDEAK  599 (675)
Q Consensus       589 ~Gr~l~V~~a~  599 (675)
                      +|+.|.|....
T Consensus        83 ~G~~l~It~~~   93 (95)
T d1ufwa_          83 KGRAVKISGPS   93 (95)
T ss_dssp             TTEEEEEECCC
T ss_pred             cceEEEEecCC
Confidence            99999998643

>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=97.57  E-value=0.00014  Score=54.94  Aligned_cols=70  Identities=17%  Similarity=0.290  Sum_probs=62.0

Q ss_pred             CCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCCeeeEEEEEeCCHHHHHHHHH-hCCceeCCeeeEEeccc
Q 045516          527 DSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVVDEAK  599 (675)
Q Consensus       527 p~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~~rG~afV~F~~~e~A~~Al~-lng~~~~Gr~l~V~~a~  599 (675)
                      ++.++..+|++.|...|.++|.|..+.|....+   ..-.|-|...+..+|..|+. ||.+.|++++|.|.++.
T Consensus         1 D~~L~~kelqq~L~~~f~~h~~V~sv~l~~~~d---g~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1           1 DYRLSRKELQQLLQEAFARHGKVKSVELSPHTD---YQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             CTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCS---TTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCcCCHHHHHHHHHHHHHhheeEEEEEEEeccC---CcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            356889999999999999999999999977632   24579999999999999998 99999999999999875

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.44  E-value=0.00013  Score=58.15  Aligned_cols=69  Identities=20%  Similarity=0.333  Sum_probs=57.4

Q ss_pred             CceEEEcCCCCCCCH---------HHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHhCCcccCCeeE
Q 045516          416 SKTLFVGNLPFSVEQ---------ADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNRAI  486 (675)
Q Consensus       416 ~~tlfV~nLp~~~te---------~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~l~g~~~~gr~i  486 (675)
                      ..||.|.=+.+...+         .+|.+.|..||+|+-|||+       .+...|+|.+-..|-+||.++|..+.|+.|
T Consensus        15 DgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv-------~d~mwVTF~dG~SAL~al~l~g~~v~G~~l   87 (95)
T d1ufwa_          15 DATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRIN-------QGQMLVTFADSHSALSVLDVDGMKVKGRAV   87 (95)
T ss_dssp             TCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEE-------TTEEEEECSCSHHHHHHHHGGGSEETTEEE
T ss_pred             CcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEe-------CCeEEEEECCcHHHHHHhccCCeEEcceEE
Confidence            457777555433333         4688899999999999999       457999999999999999999999999999


Q ss_pred             EEEec
Q 045516          487 RLDFA  491 (675)
Q Consensus       487 ~V~~a  491 (675)
                      .|...
T Consensus        88 ~It~~   92 (95)
T d1ufwa_          88 KISGP   92 (95)
T ss_dssp             EEECC
T ss_pred             EEecC
Confidence            99754

>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=97.11  E-value=0.00062  Score=54.94  Aligned_cols=66  Identities=14%  Similarity=0.202  Sum_probs=56.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCC-C-C-CcccEEEEEecCHHHHHHHHH-hCCcccC
Q 045516          417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-D-G-RFKGYGHVEFASVEDAHKAIE-LNGQMLG  482 (675)
Q Consensus       417 ~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~-~-g-~~kG~afV~F~~~e~A~~Al~-l~g~~~~  482 (675)
                      +.|.|++||+++|++++.+.+...|.+....++... + + ..--.|||.|.+.+++....+ ++|+.|.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~   71 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEE
Confidence            579999999999999999999999999888877665 2 2 234679999999999999997 9998883

>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=96.53  E-value=0.0043  Score=46.72  Aligned_cols=60  Identities=25%  Similarity=0.325  Sum_probs=52.0

Q ss_pred             HHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH-hCCcccCCeeEEEEecc
Q 045516          431 ADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFAR  492 (675)
Q Consensus       431 ~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~-l~g~~~~gr~i~V~~a~  492 (675)
                      +-|.+.|..+|.|..|.|....+|.  -.|-|...+..+|..|+. |+...|++++|.|.++.
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~dg~--~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHTDYQ--LKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCCSTT--CCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHhheeEEEEEEEeccCCc--EEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            4466789999999999998765554  468999999999999997 99999999999999875

>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=96.04  E-value=0.0094  Score=47.77  Aligned_cols=68  Identities=13%  Similarity=0.217  Sum_probs=52.8

Q ss_pred             eEEEEecCCCCcCHHHHHHHHHhhhcccCcEEEEEecccCCCCC--eeeEEEEEeCCHHHHHHHHH-hCCceeCC
Q 045516          519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGS--VKGIAYLDFTDADSFNKALE-MSGTEIGG  590 (675)
Q Consensus       519 ~~lfV~nLp~~~te~~i~~~L~~~F~~~G~I~~v~i~~d~~tG~--~rG~afV~F~~~e~A~~Al~-lng~~~~G  590 (675)
                      ..|.|++||++++++++.    +.++..|.+.+........+..  .-.-|||.|.+.+++....+ ++|+.|-+
T Consensus         2 tKvVvRrLPP~Lte~~F~----~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D   72 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQ----EHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLD   72 (91)
T ss_dssp             CEEEEEEECTTCCHHHHH----HHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEEC
T ss_pred             ceEEEecCCCCCCHHHHH----HHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEc
Confidence            578999999999999944    4445678888887776543322  23569999999999999888 99998843

>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=90.46  E-value=0.26  Score=39.29  Aligned_cols=53  Identities=13%  Similarity=0.222  Sum_probs=46.9

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH
Q 045516          416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE  475 (675)
Q Consensus       416 ~~tlfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~~~~g~~kG~afV~F~~~e~A~~Al~  475 (675)
                      ...||.-.+|......+|.++|+.||.|.--+|-       ---|||...+.++|..++.
T Consensus        15 RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswId-------dTSa~V~L~~~e~~~~v~~   67 (100)
T d1whva_          15 RDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWID-------DTSAFVSLSQPEQVQIAVN   67 (100)
T ss_dssp             CCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEEE-------TTEEEEECSCHHHHHHHHH
T ss_pred             cceeEEEeCCcccchhHHHHHhcCCCceEEEEec-------CceEEEEecCHHHHHHHHH
Confidence            4689999999999999999999999998777663       2379999999999999987