Citrus Sinensis ID: 003717

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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-------680-------690-------700-------710-------720-------730-------740-------750-------760-------770-------780-------790-------800
Protein Sequence
MEKKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKEHYLARLKREWAEDDAQLVNPPVTDSVAPDNKDATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPFCGTGKHKYSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPAAGQEEIHDMEELGASVINEEELNLMNSVMNKLFERENVSNAGLSGTELTNYERNSYNFIGDLQIGGNEVDSVADEYNLVINAVSGGNNRMVLSRCQEKTTILPTNKKLTLSEARTSKDRSAQSLPREQKKNDLLRSKKRKSLHNDEILMAASPLDDMNVQTNMNKPSTPLATQHAETDSGVRKSTASHSWSQKMSWKALVGDKDSRAFSVSNILPSDASTEEADNGINSFEELNFDENESDDLMINVVSKKKPKMALSSSQKWETTSTTYRKSVSNEDNNTTKDRPIQQEKSTLPSKKKRKSVIDDESDKNKSVHTVPETDGCAQTYTESQMPTGPQLVEPESVVEQSISDHSESKKPSQRVVIGSKGNDESSVSNVLPDNSAKEEQRVFDCPDEPLGSTDSKNQNSLARNENLEGKLAETESVEVPAKAQPSKSNTAPNKSGKGSSWFQKSPWTQLVNEDNSSFSITQISPGITFKKHDVPKTQLGKEVANPNDKKSSKSVGQAGSKPITCASTALEDGKKGEIVSQIIPEKNQPTDVGDNEASASMVADKHDLTPRQTTNVDGTIGETCSFMRSAASIKEWSTAKAALSGSQSHKRKSHK
Secondary Structure (PSIPRED)
ccHHHHHHccccccEEEEccccccccHHHHHHHHHccccccEEEEcccccccEEEEEEccccHHHHHHHHHHHcccEEcccEEEEcccccHHHHHHHcccHHHHHHcccccccccccccccccccccccccccccccHHHHcccccccEEEcccccccccccccccccccccccccccccccHHHHHHHcccccccccccccccHHHHHHcccccHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccHHHHHHHHHccccccccccccccccccccccccccHHHHHHHHccccccccccHHHHHHHHHHHHHHccccHHHHHHccccccccccccccccccccccccccccccccccccccccccccHHHHHHHccccccccccccccccccccHHccccccccccccccccccHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHcccccccEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccEEccccccccccccccccccccccccccccccccEEccccccccccccccccHHHHHHHHHHHHHHcccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHccccccEEEEEEEccccccccHHHHHHHHHccccEcEEEEEEEcccEEEEEEEEcccHHHHHHHHHHHccccccccEEEEHcccHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccHHHccccccEEEEccccccccEcccccccccEEEEEEEEcccccccccccHHccccccccccccccccccccccHcHHHHHHcccccHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccEEEEEccccccccEEccccccccccHHHHHccHHHHHcccccccccccHHcccccccccccccccccccEEccccccccccccccccccccccccccccccccccccccccccccccHHHHHHcccccccEEHHHcccccccccccccccccHHHcccccccccccEcccccccccccccccccccccccccHHHHHcccccccccccccccHHccccccccccHccccccccccEEEEccccccccccccccccccccccccccccHHHccccccccccccHHHHHcccccccccHHHcccccccccHHcccccccccccccccccccccccccccccccccccHEcccccccccccccccccccccHHHHHHHHHHHHHccccccEEEEEccccccccccccccccccccccccccccccccccccccccEEEcccEEcccccccEEcccccccccccEccccccccccccccccEcEEEccccEEEEcccccccccHHHHHHHHHHHHHHHcccHccccccc
Coil and Loop (DISEMBL)
MEKKEAEAEVEEQTRIYVgglgekvtddDLAKVFSSLGEVKAVDIVRtkgrsfgyvdffpsshksLSKLFSTYngcvwkggrlRLERAKEHYLARLKREwaeddaqlvnppvtdsvapdnkdatrldtpkklldkdkklniffprlrkvktlpfcgtgkhkysfqrveapplpkyfcdceehSAAFHAaegkqihhpaagqeEIHDMEELGASVINEEELNLMNSVMNKLFerenvsnaglsgteltnyernsynfigdlqiggnevdsVADEYNLVINAVSGGNNRMVLSRCQekttilptnkkltlseartskdrsaqslpreqkknDLLRSKkrkslhndeilmaasplddmnvqtnmnkpstplatqhaetdsgvrkstashswsQKMSWKALvgdkdsrafsvsnilpsdasteeadnginsfeelnfdenesddLMINVVSkkkpkmalsssqkwetTSTTYRksvsnednnttkdrpiqqekstlpskkkrksviddesdknksvhtvpetdgcaqtytesqmptgpqlvepesvvEQSIsdhseskkpsqrvvigskgndessvsnvlpdnsakeeqrvfdcpdeplgstdsknqnslarnenlegklaetesvevpakaqpsksntapnksgkgsswfqkspwtqlvnednssfsitqispgitfkkhdvpktqlgkevanpndkkssksvgqagskpitcastaledgkkgeivsqiipeknqptdvgdneasasmvadkhdltprqttnvdgtigETCSFMRSAASIKEWSTAKAAlsgsqshkrkshk
Flexible Loop (DISEMBL)
mekkeaeaeveeqtriyvgglgekvtDDDLAKVFSslgevkavdivrtKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKEHYLARLKrewaeddaqlvnppvtdsvapdnkdatrldtpkklldkdkklniffprlrkvktlpfcgtgkhKYSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPAAGQEEIHDMEELGASVINEEELNLMNSVMNKLFERENVSNAGLSGTELTNYERNSYNFIGDLQIGGNEVDSVADEYNLVINavsggnnrMVLSRCQEkttilptnkkltlseartskdrsaqslpreqkkndllrskkrkslhndeILMAASPLDDMNVQTNMNKPSTPLATQHAETDSGVRkstashswsqkMSWKALVGDKDSRAFSVSnilpsdasteeadNGINSFEelnfdenesDDLMINVVSKKkpkmalsssqkwettsttyrksvsnednnttkdrpiqqekstlpskkkrksviddesdknksvhtvpetdgcaQTYTESQMPTGPQLVEPESVVEQSIsdhseskkpsqrvvigskgndessvsnvlpdnsakeeqrvfdcpdeplgstdsknqnsLARNENLegklaetesvevpakaqpsksntapnksgkgsswFQKSPWTQLVNEDNSSFSITQISPGITFKKHDVPKTqlgkevanpndkkssksvgqagskpitcastaledgkkgeivsqiipeknqptdvgDNEASASmvadkhdltprqttnvdgtigETCSFMRSAASIKEWSTAkaalsgsqshkrkshk
Low Complexity Region (SEG)
MekkeaeaeveeQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKEHYLARLKREWAEDDAQLVNPPVTDSVAPDNKDATRLDTPkklldkdkklNIFFPRLRKVKTLPFCGTGKHKYSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPAAGQEEIHDMEELGASVINEEELNLMNSVMNKLFERENVSNAGLSGTELTNYERNSYNFIGDLQIGGNEVDSVADEYNLVINAVSGGNNRMVLSRCQEKTTILPTNKKLTLSEARTSKDRSAQSLPREQKKNDLLRSKKRKSLHNDEILMAASPLDDMNVQTNMNKPSTPLATQHAETDSGVRKSTASHSWSQKMSWKALVGDKDSRAFSVSNILPSDASTEEADNGINSFEELNFDENESDDLMINVVSKKKPKMALSSSQKWETTSTTYRKSVSNEDNNTTKDRPIQQEKSTLPSKKKRKSVIDDESDKNKSVHTVPETDGCAQTYTESQMPTGPQLVEPESVVEQSISDHSESKKPSQRVVIGSKGNDESSVSNVLPDNSAKEEQRVFDCPDEPLGSTDSKNQNSLARNENLEGKLAETESVEVPAKAQPSKSNTAPNKSGKGSSWFQKSPWTQLVNEDNSSFSITQISPGITFKKHDVPKTQLGKEVANPNDKKSSKSVGQAGSKPITCASTALEDGKKGEIVSQIIPEKNQPTDVGDNEASASMVADKHDLTPRQTTNVDGTIGETCSFMRSAASIKEWSTAKAALSGSQSHKRKSHK
Disordered region (IsUnstruct)
**************RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKEHYLARLKREWAE*********************************DKKLNIFFPRLRKVKTLPFCGTGKHKYSFQRVEAPPLPKYFCDCEEHSAAFHAA******************************LNLMNSVMNKLFERENVSNAGLSGTELTNYERNSYNFIGDLQIGGNEVDSVADEYNLVINAVSGGNNRMVLSRCQEKTTI************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************TCSF*****************************
Disordered Region (DISOPRED)
***************IYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERA******************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************FQ**PW**************************************************************************************************************GTIGETCSFMRSAAS*K**S******************
Disordered Region (DISEMBL)
***********EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKEHYLARLKREWAEDDAQLVNPPVTDSVAPDNKDATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPFCGTGKHKYSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPAAGQEEIHDMEELGASVINEEELNLMNSVMNKLFERENVSNAGLSGTELTNYERNSYNFIGDLQIGGNEVDSVADEYNLVINAVSGGNNRMVLSRCQEKTTILPTNKKLTL******************KKNDLLRSKKRKSLHNDEILMAASPLDDMNVQTNMNKPST*************************MSWKALVGDKDSRAFSVSNILPSDASTEEADNGINSFEELNFDENESDDLMINVVSKK******************************************************************PETDGCAQTYTESQMPTGP****************************************VLPDNSAKEEQRVFDCPDEPLGSTDSKNQNSLARNENLEGKL******************************FQKSPWTQLVNEDNSSFSITQISPGITFKKHDVPKTQLGK*******************KPITCASTALEDGKKGEIVSQIIPEKNQPTDVGDNEASASMVADKHDLTPRQTTNVDGTIGETCSFMRSAASIK*********************
Disordered Region (DISPRO)
*********VEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKEHYLARLKREWAEDDA*****************************KDKKLNIFFPRLRKVKTLPFCGTGKHKYSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPAAGQEEIHDMEELGASVINEEELNLMNSVMNKLFERENVS**********************************DEYNLVINAVSGGNNRM*******KTTI**********************************************************************************************W*A**G*KDSRAFSVSNILP**************************************************************************************************************************************************************************************************************************************SSWFQKSPWTQLVNEDNSSFSITQISPGITFKKH******************************ITCASTALEDGKKGEIVSQIIP**********************DLTPRQTTNVDGTIGETCSFMRSAA*IKEWSTAKA*LS***********
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
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Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEKKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKEHYLARLKREWAEDDAQLVNPPVTDSVAPDNKDATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPFCGTGKHKYSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPAAGQEEIHDMEELGASVINEEELNLMNSVMNKLFERENVSNAGLSGTELTNYERNSYNFIGDLQIGGNEVDSVADEYNLVINAVSGGNNRMVLSRCQEKTTILPTNKKLTLSEARTSKDRSAQSLPREQKKNDLLRSKKRKSLHNDEILMAASPLDDMNVQTNMNKPSTPLATQHAETDSGVRKSTASHSWSQKMSWKALVGDKDSRAFSVSNILPSDASTEEADNGINSFEELNFDENESDDLMINVVSKKKPKMALSSSQKWETTSTTYRKSVSNEDNNTTKDRPIQQEKSTLPSKKKRKSVIDDESDKNKSVHTVPETDGCAQTYTESQMPTGPQLVEPESVVEQSISDHSESKKPSQRVVIGSKGNDESSVSNVLPDNSAKEEQRVFDCPDEPLGSTDSKxxxxxxxxxxxxxxxxxxxxxEVPAKAQPSKSNTAPNKSGKGSSWFQKSPWTQLVNEDNSSFSITQISPGITFKKHDVPKTQLGKEVANPNDKKSSKSVGQAGSKPITCASTALEDGKKGEIVSQIIPEKNQPTDVGDNEASASMVADKHDLTPRQTTNVDGTIGETCSFMRSAASIKEWSTAKAALSGSQSHKRKSHK
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	800	2.2.26 [Sep-21-2011]
Q3UHX0	1147	Nucleolar protein 8 OS=Mu	yes	no	0.108	0.075	0.372	8e-10
Q76FK4	1167	Nucleolar protein 8 OS=Ho	yes	no	0.108	0.074	0.372	1e-09
Q9HFE6	478	Uncharacterized RNA-bindi	yes	no	0.123	0.207	0.323	4e-06
Q7S6N6	764	Polyadenylate-binding pro	N/A	no	0.112	0.117	0.282	0.0003
Q04047	700	Protein no-on-transient A	yes	no	0.107	0.122	0.3	0.0005
Q4WK03	753	Polyadenylate-binding pro	yes	no	0.142	0.151	0.276	0.0008
A1D4K4	751	Polyadenylate-binding pro	N/A	no	0.142	0.151	0.276	0.0008

>sp|Q3UHX0|NOL8_MOUSE Nucleolar protein 8 OS=Mus musculus GN=Nol8 PE=1 SV=2

 Score = 66.6 bits (161), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 35/94 (37%), Positives = 51/94 (54%), Gaps = 7/94 (7%)

Query: 12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKG------RSFGYVDFFPSSHKS 65
          E  R++VGGLG+ +++ DL   F   GEV  V+I+  K       + F YV+    +   
Sbjct: 6  EMKRLFVGGLGQGISETDLQNQFGRFGEVSDVEIITRKDDQGNSQKVFAYVN-IQITEAD 64

Query: 66 LSKLFSTYNGCVWKGGRLRLERAKEHYLARLKRE 99
          L K  S  N   WKGG L+++ AKE +L RL +E
Sbjct: 65 LKKCMSILNKTKWKGGTLQIQLAKESFLHRLAQE 98

Plays an essential role in the survival of diffuse-type gastric cancer cells. Acts as a nucleolar anchoring protein for DDX47. May be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells.
Mus musculus (taxid: 10090)

>sp|Q76FK4|NOL8_HUMAN Nucleolar protein 8 OS=Homo sapiens GN=NOL8 PE=1 SV=1

 Score = 65.9 bits (159), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 35/94 (37%), Positives = 51/94 (54%), Gaps = 7/94 (7%)

Query: 12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKG------RSFGYVDFFPSSHKS 65
          E  R+YVGGL + +++ DL   FS  GEV  V+I+  K       + F Y++    +   
Sbjct: 6  ETKRLYVGGLSQDISEADLQNQFSRFGEVSDVEIITRKDDQGNPQKVFAYIN-ISVAEAD 64

Query: 66 LSKLFSTYNGCVWKGGRLRLERAKEHYLARLKRE 99
          L K  S  N   WKGG L+++ AKE +L RL +E
Sbjct: 65 LKKCMSVLNKTKWKGGTLQIQLAKESFLHRLAQE 98

Plays an essential role in the survival of diffuse-type gastric cancer cells. Acts as a nucleolar anchoring protein for DDX47. May be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells.

Homo sapiens (taxid: 9606)

>sp|Q9HFE6|YNW6_SCHPO Uncharacterized RNA-binding protein P16F5.06 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPBP16F5.06 PE=1 SV=1

 Score = 54.3 bits (129), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 34/105 (32%), Positives = 52/105 (49%), Gaps = 6/105 (5%)

Query: 10  VEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKG-----RSFGYVDFFPSSHK 64
           +E + RIYVGGL   +   DL   FS  G V  ++I+         + F Y++F     K
Sbjct: 1   MELEKRIYVGGLSSSIESSDLESRFSRFGSVSNLEIINKSTPVGTIQRFAYLNFRTDEDK 60

Query: 65  SLSKLFSTYNGCVWKGGRLRLERAKEHYLARLKREWAEDDAQLVN 109
              K  S  +   +KG +LR+E A+ +YL +L++E    D Q  N
Sbjct: 61  -WQKCKSYLSNATFKGSKLRIEEARPYYLVKLQQEKKIADLQSTN 104

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

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

 Score = 48.1 bits (113), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 28/99 (28%), Positives = 57/99 (57%), Gaps = 9/99 (9%)

Query: 1   MEKKEAEAEVEEQ----TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVR---TKGRSF 53
           + KK+ +++ EE     T +YV  +  +VTD++  ++F+  GEV +  + R    K R F
Sbjct: 224 IPKKDRQSKFEEMKANFTNVYVKNINNEVTDEEFRELFAKFGEVTSSSLARDQEGKSRGF 283

Query: 54  GYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKEHY 92
           G+V+F  ++H++ ++     NG  ++G  L + RA++ +
Sbjct: 284 GFVNF--TTHEAAAQAVDELNGKDFRGQDLYVGRAQKKH 320

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

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

>sp|Q04047|NONA_DROME Protein no-on-transient A OS=Drosophila melanogaster GN=nonA PE=1 SV=2

 Score = 47.0 bits (110), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 27/90 (30%), Positives = 47/90 (52%), Gaps = 4/90 (4%)

Query: 7   EAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSL 66
           E +   + R+YVG L   +TDD+L ++F   GE+  +     K  +F  VD+ P++ K+ 
Sbjct: 295 ETKFSGRNRLYVGNLTNDITDDELREMFKPYGEISEIFSNLDKNFTFLKVDYHPNAEKAK 354

Query: 67  SKLFSTYNGCVWKGGRLRLERAKEHYLARL 96
             L    +G + KG +LR+  A    + R+
Sbjct: 355 RAL----DGSMRKGRQLRVRFAPNATILRV 380

Required for normal vision and courtship behavior in Drosophila.

Drosophila melanogaster (taxid: 7227)

>sp|Q4WK03|PABP_ASPFU Polyadenylate-binding protein, cytoplasmic and nuclear OS=Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) GN=pab1 PE=3 SV=1

 Score = 46.6 bits (109), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 37/134 (27%), Positives = 63/134 (47%), Gaps = 20/134 (14%)

Query: 1   MEKKEAEAEVEEQ----TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVR---TKGRSF 53
           + KK+ +++ EE     T +Y+  + ++VTD++  K+F   GE+ +  + R    K R F
Sbjct: 216 ISKKDRQSKFEEMKANFTNVYIKNIDQEVTDEEFRKMFEKFGEITSATLSRDQEGKSRGF 275

Query: 54  GYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERA-----------KEHYLARLKREWAE 102
           G+V+F  S+H S        N    KG +L + RA           K++  ARL++    
Sbjct: 276 GFVNF--STHDSAQAAVDEMNDKEIKGQKLYVGRAQKKHEREEELRKQYEAARLEKASKY 333

Query: 103 DDAQLVNPPVTDSV 116
               L    +TD V
Sbjct: 334 QGVNLYVKNLTDDV 347

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

Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (taxid: 330879)

>sp|A1D4K4|PABP_NEOFI Polyadenylate-binding protein, cytoplasmic and nuclear OS=Neosartorya fischeri (strain ATCC 1020 / DSM 3700 / FGSC A1164 / NRRL 181) GN=pab1 PE=3 SV=1

 Score = 46.6 bits (109), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 37/134 (27%), Positives = 63/134 (47%), Gaps = 20/134 (14%)

Query: 1   MEKKEAEAEVEEQ----TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVR---TKGRSF 53
           + KK+ +++ EE     T +Y+  + ++VTD++  K+F   GE+ +  + R    K R F
Sbjct: 216 ISKKDRQSKFEEMKANFTNVYIKNIDQEVTDEEFRKMFEKFGEITSATLSRDQEGKSRGF 275

Query: 54  GYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERA-----------KEHYLARLKREWAE 102
           G+V+F  S+H S        N    KG +L + RA           K++  ARL++    
Sbjct: 276 GFVNF--STHDSAQAAVDEMNDKEIKGQKLYVGRAQKKHEREEELRKQYEAARLEKASKY 333

Query: 103 DDAQLVNPPVTDSV 116
               L    +TD V
Sbjct: 334 QGVNLYVKNLTDDV 347

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

Neosartorya fischeri (strain ATCC 1020 / DSM 3700 / FGSC A1164 / NRRL 181) (taxid: 331117)

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	800
296081053	847	unnamed protein product [Vitis vinifera]	0.455	0.429	0.481	7e-92
255563870	636	conserved hypothetical protein [Ricinus	0.465	0.584	0.472	3e-89
147769592	654	hypothetical protein VITISV_001744 [Viti	0.47	0.574	0.459	1e-85
356530527	615	PREDICTED: uncharacterized protein LOC10	0.465	0.604	0.435	8e-74
357450429	660	hypothetical protein MTR_2g048340 [Medic	0.506	0.613	0.390	7e-72
356558554	607	PREDICTED: uncharacterized protein LOC10	0.467	0.616	0.423	4e-71
449476201	657	PREDICTED: uncharacterized protein LOC10	0.472	0.575	0.415	3e-70
449442775	649	PREDICTED: uncharacterized protein LOC10	0.472	0.582	0.413	2e-69
297796733	728	hypothetical protein ARALYDRAFT_495917 [	0.351	0.385	0.468	2e-65
224118684	583	predicted protein [Populus trichocarpa]	0.477	0.655	0.419	6e-65

>gi|296081053|emb|CBI18334.3| unnamed protein product [Vitis vinifera]

 Score =  345 bits (884), Expect = 7e-92,   Method: Compositional matrix adjust.
 Identities = 199/413 (48%), Positives = 260/413 (62%), Gaps = 49/413 (11%)

Query: 14  TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTY 73
           TRI+VGGLGE VT DD+ K+ SSLG VK VDI+RTKGRSF Y+DF PSS KSLSKLFSTY
Sbjct: 184 TRIFVGGLGETVTSDDINKMLSSLGTVKVVDIMRTKGRSFAYLDFLPSSAKSLSKLFSTY 243

Query: 74  NGCVWKGGRLRLERAKEHYLARLKREWAEDDAQLVNPPVTDSVAPDNKDATRLDTPKKLL 133
           NGC WKGGRL+LE+AKEHYL RL REWAED    ++ P ++S+   N +    D  KK +
Sbjct: 244 NGCFWKGGRLKLEKAKEHYLVRLSREWAEDGELAISQP-SNSI-DKNTNIVASDKLKKTV 301

Query: 134 DKDK-KLNIFFPRLRKVKTLPFCGTGKHKYSFQRVEAPPLPKYFCDCEEHSAAFHAAEGK 192
           +++K +L IFFP+LRK+K+LPF GTGKHKYSFQR+E P LP +FCDCEEHS   H A+ +
Sbjct: 302 NQEKSQLRIFFPKLRKMKSLPFSGTGKHKYSFQRIEVPSLPTHFCDCEEHSGPPHIAQKQ 361

Query: 193 QIHHPAAGQEEIHDMEELGASVINEEELNLMNSVMNKLFERENVSNAGLSGTELTNYERN 252
               P           E  +  +N++ELN+MNSVMNK+FERE         T+L +    
Sbjct: 362 YFCDP-----------ESQSGGMNKDELNVMNSVMNKIFERE---------TDLKD---- 397

Query: 253 SYNFIGDLQIGGNEVDSVADEYNLVINAVSGGNNRMVLSRCQEKTTILPTNKKLTLSEAR 312
                 +L++ GNE D V DE NLVIN  + G +RM L   QE+  I   N+K   ++  
Sbjct: 398 ------ELRVDGNESDLVEDEDNLVINMFT-GRHRMALLGSQEQEAI-SMNQKSRFNDTW 449

Query: 313 TSKDRSAQ-SLPREQKKNDLLRSKKRKSLHNDEI----LMAASPLDDMNVQTNMNKPSTP 367
           TS D  A  +LP          +KKRKSLH DE      ++A P    ++QT+ N     
Sbjct: 450 TSTDGPAPITLP---------STKKRKSLHIDESDGNEFLSAIPGKKPSLQTHSNDSGVQ 500

Query: 368 LATQHAETDSGVRKSTASHSWSQKMSWKALVGDKDSRAFSVSNILPSDASTEE 420
              Q +E   G++K+TA+ SWSQK SW+ LVGDK +  F +S++LP   S ++
Sbjct: 501 SGAQTSELRPGIQKTTANLSWSQKSSWRELVGDKGNNPFIISDMLPGVGSRKQ 553

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255563870|ref|XP_002522935.1| conserved hypothetical protein [Ricinus communis] gi|223537829|gb|EEF39446.1| conserved hypothetical protein [Ricinus communis]

 Score =  336 bits (862), Expect = 3e-89,   Method: Compositional matrix adjust.
 Identities = 196/415 (47%), Positives = 269/415 (64%), Gaps = 43/415 (10%)

Query: 13  QTRIYVGGLGEKVTDDDLAKVFSSLG-EVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFS 71
           + RI+VGGLGE VT DDL  + S +G   ++VDI+RTKGRSF Y+DF PSS  +L KLF+
Sbjct: 13  RVRIHVGGLGENVTRDDLCNLLSKVGIGFQSVDIIRTKGRSFAYIDFLPSSVSALPKLFN 72

Query: 72  TYNGCVWKGGRLRLERAKEHYLARLKREWAEDDAQLVNPPVTDSVAPDNKDATR-LDTPK 130
           TYNGCVWKGGRL+L++AKEHYL RLKREWAE DAQL N   +D V   N DA + +++P+
Sbjct: 73  TYNGCVWKGGRLKLDKAKEHYLDRLKREWAE-DAQLANSTCSDDV---NNDADKQMESPR 128

Query: 131 KL-----LDKDKKLNIFFPRLRKVKTLPFCGTGKHKYSFQRVEAPPLPKYFCDCEEHSAA 185
           K      LDK K+L +FFPRL+K+K++PF GTGKHKYSF+RVE P LP +FCDCEEHS +
Sbjct: 129 KTKKDLSLDK-KQLRLFFPRLQKLKSIPFSGTGKHKYSFRRVEVPSLPLHFCDCEEHSGS 187

Query: 186 FHAAEGKQIHHPAAGQEEIHDMEELGASVINEEELNLMNSVMNKLFERENVSNAGLSGTE 245
            HA +GKQI  P         +EE G  V N+EEL+LM SVMN+LFE ENVS A  S  E
Sbjct: 188 LHAPKGKQI--PV--------LEEQGGGV-NQEELDLMISVMNRLFEIENVSGAPHSDNE 236

Query: 246 LTNYERNSYNFIGDLQIGGNEVDSVADEYNLVINAVSGGNNRMVLSRCQEKTTILPTNKK 305
           LT  E  + N   + Q+  +E  S ADE +L+IN VS           + K T   +N++
Sbjct: 237 LTKEEDYNTNATDNPQLDESEGYSTADEDDLIINVVS-----------RRKETAF-SNQE 284

Query: 306 LTLSEARTSKDRSAQSLPREQKKNDLLRSKKRKSLHNDEILMAASPLDDMNVQTNMNKPS 365
             L++ + S+DR AQ + R++ +ND      +++  N+ + +A+      ++Q   N P 
Sbjct: 285 SKLNKRQASEDRPAQEVLRKRTRND------KENDTNNYVSVASQ--GKGSLQAPSNGPG 336

Query: 366 TPLATQHAETDSGVRKSTASHSWSQKMSWKALVGDKDSRAFSVSNILPSDASTEE 420
                Q  E+ S V++S    SWSQK SW+ LVG++++ A S+S+ILP  ++ +E
Sbjct: 337 MLSGDQLIESQSIVKQSAPGVSWSQKSSWRELVGNRNNNAISISDILPGISANKE 391

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147769592|emb|CAN65705.1| hypothetical protein VITISV_001744 [Vitis vinifera]

 Score =  324 bits (830), Expect = 1e-85,   Method: Compositional matrix adjust.
 Identities = 197/429 (45%), Positives = 256/429 (59%), Gaps = 53/429 (12%)

Query: 14  TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTY 73
           TRI+VGGLGE VT DD+ K+ SSLG VK VDIVRTKGRSF Y+DF PSS KSLSKLFST 
Sbjct: 21  TRIFVGGLGETVTSDDINKMLSSLGTVKVVDIVRTKGRSFAYLDFLPSSAKSLSKLFST- 79

Query: 74  NGCVWKGGRLRLERAKEHYLARLKREWAEDDAQLVNPPVTDSVAPDNKDATRLDTPKKLL 133
                 GGRL+LE+AKEHYL RL REWAED    ++ P ++S+   N +    D  KK +
Sbjct: 80  ------GGRLKLEKAKEHYLVRLSREWAEDGELAISQP-SNSI-DKNTNIVSSDKLKKTV 131

Query: 134 DKDK-KLNIFFPRLRKVKTLPFCGTGKHKYSFQRVEAPPLPKYFCDCEEHSAAFHAAEGK 192
           +++K +L IFFP+LRK+K+LPF GTGKHKYSFQR+E P LP +FCDCEEHS   H A+ +
Sbjct: 132 NQEKSQLRIFFPKLRKMKSLPFSGTGKHKYSFQRIEVPSLPTHFCDCEEHSGPPHIAQKQ 191

Query: 193 QIHHPAAGQEEIHDMEELGASVINEEELNLMNSVMNKLFERENVSNAGLSGTELTNYERN 252
               P           E  +  +N++ELN+MNSVMNK+FERE       + T LT    +
Sbjct: 192 YFCDP-----------EPQSGGMNKDELNMMNSVMNKIFERETDLKVAYNVTGLTKGGHD 240

Query: 253 SY-----NFIGD-----------LQIGGNEVDSVADEYNLVINAVSGGNNRMVLSRCQEK 296
           S        I D           L++ GNE D   DE NLVIN  + G +RM L   QE+
Sbjct: 241 SLKSTNERLIDDNESDHAADEDELRVDGNESDLAEDEDNLVINMFT-GRHRMALLGSQEQ 299

Query: 297 TTILPTNKKLTLSEARTSKDRSAQ-SLPREQKKNDLLRSKKRKSLHNDEI----LMAASP 351
             I   N+K   ++  TS D  A  +LP          +KKRKSLH DE      ++A P
Sbjct: 300 EAI-SMNQKSRFNDTWTSTDGPAPITLP---------STKKRKSLHIDESDGNEFLSAIP 349

Query: 352 LDDMNVQTNMNKPSTPLATQHAETDSGVRKSTASHSWSQKMSWKALVGDKDSRAFSVSNI 411
               ++QT+ N        Q +E   G++K+TA+ SWSQK SW+ LVGDK +  F +S++
Sbjct: 350 GKKPSLQTHSNDSGVQSGAQTSELRPGIQKTTANLSWSQKSSWRELVGDKGNNPFIISDM 409

Query: 412 LPSDASTEE 420
           LP   S ++
Sbjct: 410 LPGVGSRKQ 418

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356530527|ref|XP_003533832.1| PREDICTED: uncharacterized protein LOC100778779 [Glycine max]

 Score =  285 bits (729), Expect = 8e-74,   Method: Compositional matrix adjust.
 Identities = 181/416 (43%), Positives = 247/416 (59%), Gaps = 44/416 (10%)

Query: 5   EAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHK 64
           EAE E +   RI+VGGL E V+ +DL  +F+SLG V++V  +RTKGRSF Y+DF  S  K
Sbjct: 4   EAE-ETKSAARIFVGGLAEAVSAEDLRSLFASLGSVQSVQTIRTKGRSFAYLDFL-SDPK 61

Query: 65  SLSKLFSTYNGCVWKGGRLRLERAKEHYLARLKREWAE---DDAQLVNPP--VTDSVAPD 119
           SLSKLFS YNGC+WKGGRLRLE+AKE YL RLKREW +   DDA    PP   ++   P+
Sbjct: 62  SLSKLFSKYNGCLWKGGRLRLEKAKEDYLVRLKREWEQGTLDDA-TQKPPTAASEEEMPN 120

Query: 120 NKDATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPFCGTGKHKYSFQRVEAPPLPKYFCDC 179
              +++ +T        K LNIFFPRLRKVK++PF GTGKHKYSFQ ++ PPLP +FCDC
Sbjct: 121 TAQSSKSNT--------KHLNIFFPRLRKVKSIPFSGTGKHKYSFQNIKVPPLPVHFCDC 172

Query: 180 EEHSAAFHAAEGKQIHHPAAGQEEIHDMEELGASVINEEELNLMNSVMNKLFERENVSNA 239
           EEH   F          P   +  I    E G   IN+EE+++MN+VMNKLFE+E VSNA
Sbjct: 173 EEHCKPF---------VPEREKLSIDRTAESGG--INDEEISIMNAVMNKLFEKEQVSNA 221

Query: 240 GLSGTELTNYERNSYNFIGDLQIGGNEVDSVADEYNLVINAVSGGNNRMVLSRCQEKTTI 299
              G E  ++E        + +      DS  DE +L+IN V    N+  L+  +E   I
Sbjct: 222 KNLGEEKDSFESPDALHSDECE------DSATDEDDLIIN-VETKKNKTSLTEDKELQRI 274

Query: 300 LPTNKKLTLSEARTSKDRSAQSLPREQKKNDLL--RSKKRKSLHNDEILMAASPLDDMNV 357
           L  N++   ++ + +K+   +S    QK+++    ++KKRKSL   E+  + +P    N+
Sbjct: 275 L-ENQESWFNKRKIAKEEPNKSTLLVQKRSNSNPDKNKKRKSLPKLEV--STTPGSKSNM 331

Query: 358 QTNMNKPSTPLATQHAETDSGVRKSTASHSWSQKMSWKALVGDKDSRAFSVSNILP 413
           QT  ++  +       E D G +      SWSQK SW+ L+GDK + +FS S ILP
Sbjct: 332 QTLPDEVGSDAQPTELEDDFGEKV-----SWSQKSSWRELLGDKGNTSFSASLILP 382

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357450429|ref|XP_003595491.1| hypothetical protein MTR_2g048340 [Medicago truncatula] gi|124360045|gb|ABN08061.1| RNA-binding region RNP-1 (RNA recognition motif); Pyridoxal-dependent decarboxylase [Medicago truncatula] gi|355484539|gb|AES65742.1| hypothetical protein MTR_2g048340 [Medicago truncatula]

 Score =  278 bits (712), Expect = 7e-72,   Method: Compositional matrix adjust.
 Identities = 171/438 (39%), Positives = 253/438 (57%), Gaps = 33/438 (7%)

Query: 1   MEKKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFP 60
           ME++E+E       RI+VGG+GE VT DD+ ++F SLG V++++ +RTKGRS  Y+DF  
Sbjct: 1   MEEEESEKRT---VRIFVGGIGEAVTSDDIRRLFESLGSVQSLETIRTKGRSLAYLDFLA 57

Query: 61  SSHKSLSKLFSTYNGCVWKGGRLRLERAKEHYLARLKREWAEDDAQLVNPPVTDSVAPDN 120
            S KSLSKLFS YNGCVWKGG+L+LE+AKEHYL RLK+EW ED    + PP +D V+   
Sbjct: 58  DS-KSLSKLFSKYNGCVWKGGKLKLEKAKEHYLDRLKKEWEEDAILSIEPPASD-VSTHK 115

Query: 121 KDATRLDTP--KKLLDKDKK-LNIFFPRLRKVKTLPFCGTGKHKYSFQRVEAPPLPKYFC 177
           +D  + + P  ++++D D K LNI+FPRLR VK++PF GTGKHKYSFQ ++  PLP +FC
Sbjct: 116 EDLVK-EKPNARRIVDPDAKPLNIYFPRLRTVKSIPFSGTGKHKYSFQNIKVGPLPVHFC 174

Query: 178 DCEEHSAAFHAAEGKQIHHPAAGQEEIHDMEELGASVINEEELNLMNSVMNKLFERENVS 237
           DCEEH + F   + K     +   E   +  E+G   IN+EE+N+MN+VMNKL E+E VS
Sbjct: 175 DCEEHCSPFITKKEKL----SMNGETEREKSEIGG--INDEEINIMNAVMNKLLEKEKVS 228

Query: 238 NAGLSGTELTNYERNSYNFIGDLQIGGNEVDSVADEYNLVINAVSGGNNRMVLSRCQEKT 297
           N    G +  ++E  S     + ++     D   D+ +L+ N ++   N+  L+  +E  
Sbjct: 229 NTKHLGKKHDSFESLSVIHSNECEVDSATDDGDDDDDDLITN-IATKKNKAALTGTEELE 287

Query: 298 TILPTNKKLTLSEARTSKDRSAQSLPREQKKNDLLRSKKRKSLHNDEI-------LMAAS 350
            I+        S+  ++K   A+  P E +K     S K K   +          + +++
Sbjct: 288 RIME-------SQEWSNKTNIAEEEPVEAQKRSKSNSNKVKKRKSLSKSESESNGVASST 340

Query: 351 PLDDMNVQTNMNKPSTPLATQHAETDSGVRKSTASHSWSQKMSWKALVGDKDSRAFSVSN 410
           P+    +QT +++  +       E D G    +A  SWSQK SW+ LVG   + +FS S 
Sbjct: 341 PVGKSKMQTLLDEVGSGAKPTEPEYDFG---ESAKVSWSQKSSWRELVGKGGNASFSASL 397

Query: 411 ILPSDASTEEADNGINSF 428
           I P   S ++  N   S+
Sbjct: 398 ISPKFDSADDQQNSDGSY 415

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356558554|ref|XP_003547570.1| PREDICTED: uncharacterized protein LOC100808161 [Glycine max]

 Score =  276 bits (705), Expect = 4e-71,   Method: Compositional matrix adjust.
 Identities = 177/418 (42%), Positives = 246/418 (58%), Gaps = 44/418 (10%)

Query: 3   KKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSS 62
           ++EAE E +   RI+VGGL   V+ +DL  +F+SLG V++V  +RTKGRSF Y+DF  S 
Sbjct: 2   EEEAE-ETKSAVRIFVGGLAGAVSAEDLRSLFASLGSVQSVQTIRTKGRSFAYLDFL-SD 59

Query: 63  HKSLSKLFSTYNGCVWKGGRLRLERAKEHYLARLKREW---AEDDAQLVNPPVT--DSVA 117
            KSLSKLFS YNGC+WKGGRLRLE+AKE YL RLKREW   A DDA    PP    +   
Sbjct: 60  PKSLSKLFSKYNGCLWKGGRLRLEKAKEDYLVRLKREWEQGALDDATQ-KPPAAAIEEEI 118

Query: 118 PDNKDATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPFCGTGKHKYSFQRVEAPPLPKYFC 177
           P    ++  +T        K LNIFFPRLRKVK++PF GTGKHKYSFQ ++ P LP +FC
Sbjct: 119 PSTAHSSESNT--------KHLNIFFPRLRKVKSIPFSGTGKHKYSFQNIKVPLLPVHFC 170

Query: 178 DCEEHSAAFHAAEGKQIHHPAAGQEEIHDMEELGASVINEEELNLMNSVMNKLFERENVS 237
           DCEEH + F          P   +  I    + GA  +N+EE+++MN+VMNKL  ++ VS
Sbjct: 171 DCEEHCSPF---------VPEREKLSIDRAADSGA--MNDEEISIMNAVMNKLLGKQKVS 219

Query: 238 NAGLSGTELTNYERNSYNFIGDLQIGGNEVDSVADEYNLVINAVSGGNNRMVLSRCQEKT 297
           NA   G E  ++E        + +      DS  DE +L+IN V    N+  L+  +E  
Sbjct: 220 NAKKLGEEKGSFESPDALHSDECE------DSATDEDDLIIN-VETKKNKTALTGDEELQ 272

Query: 298 TILPTNKKLTLSEARTSKDRSAQSLPREQKK--NDLLRSKKRKSLHNDEILMAASPLDDM 355
            IL  N++  L++ + +K+   +S+P  QK+  ++  ++KKRKSL   E+  + +P    
Sbjct: 273 RIL-ENQESWLNKTKIAKEEPNKSMPPVQKRSNSNHDKNKKRKSLPKLEV--STTPGSKS 329

Query: 356 NVQTNMNKPSTPLATQHAETDSGVRKSTASHSWSQKMSWKALVGDKDSRAFSVSNILP 413
           N+Q   ++  +       E D G +      SWSQK SW+ L+GDK + +FS S ILP
Sbjct: 330 NMQMLPDEVGSGAQPTELEDDFGEKV-----SWSQKSSWRELLGDKGNTSFSASLILP 382

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449476201|ref|XP_004154670.1| PREDICTED: uncharacterized protein LOC101231362 [Cucumis sativus]

 Score =  273 bits (698), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 177/426 (41%), Positives = 237/426 (55%), Gaps = 48/426 (11%)

Query: 1   MEKKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEV-KAVDIVRTKGRSFGYVDFF 59
           MEK ++ +E     RIYVGGLG  +T+DDL KVF S+G V +AVD VRTK RSF YVDFF
Sbjct: 1   MEKGQSASE---NMRIYVGGLGAAMTEDDLRKVFHSVGGVVEAVDFVRTKSRSFAYVDFF 57

Query: 60  PSSHKSLSKLFSTYNGCVWKGGRLRLERAKEHYLARLKREWAEDDAQLVNPPV---TDSV 116
           PSS  SLSKLFSTYNGC WKGG+LRLE+AKE+YLARLKREW E+DAQ+ +  V    + V
Sbjct: 58  PSSQSSLSKLFSTYNGCAWKGGKLRLEKAKENYLARLKREW-EEDAQIRDSNVGADMELV 116

Query: 117 APDNKDATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPFCGTGKHKYSFQRVEAPPLPKYF 176
           AP++ +          + K + +NIFFP L +VK LP  GTG HKY F  VE PP P +F
Sbjct: 117 APESTEH---------VTKSEHINIFFPSLGEVKPLPISGTGTHKYDFPHVEVPPFPVHF 167

Query: 177 CDCEEHSAAFHAAEGKQIHHPAAGQEEIHDMEELGA--SVINEEELNLMNSVMNKLFERE 234
           CDCEEH+A+              G  +     +L A    ++E+E+ +MN+V++KLFER+
Sbjct: 168 CDCEEHNAS-----------SPIGNSKYTKTRDLNAENGGMDEDEIKMMNAVLSKLFERK 216

Query: 235 NVSNAGLSGTELTNYERNSYNFIGDLQIGGNEVDSVADEYNLVINAVSGGNNRMVLSRCQ 294
             S +  + +   N + NS     +  +  N+VDS  DE NLV+N ++        S C 
Sbjct: 217 EASQSNCNDSMALNDKHNSTTSTDNQLLEDNKVDS--DEDNLVLNVMA--------SNCN 266

Query: 295 EKTTILPTNKKLTLSEARTSKDRSAQSLPREQKKNDLLRSKKRKSLHNDEILMAASPLDD 354
            KT  L    K+  +    SKD       R+QK N  ++SKKRKS  ++E     S    
Sbjct: 267 SKTMALNRGNKIFKAHG-NSKDAV-----RDQKNNCRVQSKKRKSFISEEFDGNESVPSI 320

Query: 355 MNVQTNMNKPSTPLATQHAETDSGVRKSTASHSWSQKMSWKALVGDKDSRAFSVSNILPS 414
                  +    P  +   +     R        SQK SWK L+ DK + +F +S+IL S
Sbjct: 321 FTSNRGTDPSYDPARSSRPQAPD--RGPPVQSLRSQKSSWKTLIRDKSNVSFCISDILSS 378

Query: 415 DASTEE 420
             S  E
Sbjct: 379 VPSANE 384

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449442775|ref|XP_004139156.1| PREDICTED: uncharacterized protein LOC101203716 [Cucumis sativus]

 Score =  270 bits (691), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 176/426 (41%), Positives = 236/426 (55%), Gaps = 48/426 (11%)

Query: 1   MEKKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEV-KAVDIVRTKGRSFGYVDFF 59
           MEK ++ +E     RIYVGGLG  +T+DDL KVF S+G V +AVD VRTK RSF YVDFF
Sbjct: 1   MEKGQSASE---NMRIYVGGLGAAMTEDDLRKVFHSVGGVVEAVDFVRTKSRSFAYVDFF 57

Query: 60  PSSHKSLSKLFSTYNGCVWKGGRLRLERAKEHYLARLKREWAEDDAQLVNPPV---TDSV 116
           PSS  SLSKLFSTYNGC WKGG+LRLE+AKE+YLARL REW E+DAQ+ +  V    + V
Sbjct: 58  PSSQSSLSKLFSTYNGCAWKGGKLRLEKAKENYLARLNREW-EEDAQIRDNNVGADMELV 116

Query: 117 APDNKDATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPFCGTGKHKYSFQRVEAPPLPKYF 176
           AP++ +          + K + +NIFFP L +VK LP  GTG HKY F  VE PP P +F
Sbjct: 117 APESTEH---------VTKSEHINIFFPSLGEVKPLPISGTGTHKYDFPHVEVPPFPVHF 167

Query: 177 CDCEEHSAAFHAAEGKQIHHPAAGQEEIHDMEELGA--SVINEEELNLMNSVMNKLFERE 234
           CDCEEH+A+              G  +     +L A    ++E+E+ +MN+V++KLFER+
Sbjct: 168 CDCEEHNAS-----------SPIGNSKYTKTRDLNAENGGMDEDEIKMMNAVLSKLFERK 216

Query: 235 NVSNAGLSGTELTNYERNSYNFIGDLQIGGNEVDSVADEYNLVINAVSGGNNRMVLSRCQ 294
             S +  + +   N + NS     +  +  N+VDS  DE NLV+N ++        S C 
Sbjct: 217 EASQSNCNDSMALNDKHNSTTSTDNQLLEDNKVDS--DEDNLVLNVMA--------SNCN 266

Query: 295 EKTTILPTNKKLTLSEARTSKDRSAQSLPREQKKNDLLRSKKRKSLHNDEILMAASPLDD 354
            KT  L    K+  +    SKD       R+QK N  ++SKKRKS  ++E     S    
Sbjct: 267 SKTMALNRGNKIFKAHG-NSKDAV-----RDQKNNCRVQSKKRKSFISEEFDGNESVPSI 320

Query: 355 MNVQTNMNKPSTPLATQHAETDSGVRKSTASHSWSQKMSWKALVGDKDSRAFSVSNILPS 414
                  +    P  +   +     R        SQK SWK L+ DK + +F +S+IL S
Sbjct: 321 FTSNRGTDPSYDPARSSRPQAPD--RGPPVQSLRSQKSSWKTLIRDKSNVSFCISDILSS 378

Query: 415 DASTEE 420
             S  E
Sbjct: 379 VPSANE 384

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297796733|ref|XP_002866251.1| hypothetical protein ARALYDRAFT_495917 [Arabidopsis lyrata subsp. lyrata] gi|297312086|gb|EFH42510.1| hypothetical protein ARALYDRAFT_495917 [Arabidopsis lyrata subsp. lyrata]

 Score =  257 bits (656), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 150/320 (46%), Positives = 192/320 (60%), Gaps = 39/320 (12%)

Query: 14  TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTY 73
            R++VGGLGE V  DDL K+FS +G V AV+ VRTKGRSF YVDF PSS  SL+KLFSTY
Sbjct: 11  VRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKGRSFAYVDFSPSSTNSLTKLFSTY 70

Query: 74  NGCVWKGGRLRLERAKEHYLARLKREWAEDDAQLVNPPVTDSVAPDNKDATRLDTPKKLL 133
           NGCVWKGGRLRLE+AKEHYLARLKREW              S + +   A    TP    
Sbjct: 71  NGCVWKGGRLRLEKAKEHYLARLKREWE----------AASSTSDNTIKAPSDSTPS--- 117

Query: 134 DKDKKLNIFFPRLRKVKTLPFCGTGKHKYSFQRVE-APPLPKYFCDCEEHSAAFHAAEGK 192
                LNIFFPRLRKVK +P  GTGKHKYSFQRV  +  LPK FCDCEEHS   ++   +
Sbjct: 118 ---THLNIFFPRLRKVKAMPLTGTGKHKYSFQRVPLSSSLPKSFCDCEEHSN--NSLTPR 172

Query: 193 QIHHPAAGQEEIHDMEELGASVINEEELNLMNSVMNKLFERENVSNAGLSGTELTNYERN 252
           + H        + D+E L     NE+E+N+MNSVMNKLFE+ N+  A     E    E +
Sbjct: 173 ETH--------LQDLESLNVGR-NEDEVNVMNSVMNKLFEKNNIPIA----EEDNEIEAD 219

Query: 253 SYNFIGDLQIGGNEVDSVADEYNL----VINAVSGGNNRMVLSRCQEKTTILPTNKKLTL 308
             N I ++   GN++DS  D+ +     ++N  +        S  ++   I P+ K+ T+
Sbjct: 220 QDNLIINVASSGNDMDSELDKLSRKRKSILNETTPSGEG--YSEGRKGNHIHPSKKRQTI 277

Query: 309 SEARTSKDRSAQSLPREQKK 328
           S   + +  S+QS+ RE+KK
Sbjct: 278 SLEESGRQESSQSI-REKKK 296

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224118684|ref|XP_002331422.1| predicted protein [Populus trichocarpa] gi|222873636|gb|EEF10767.1| predicted protein [Populus trichocarpa]

 Score =  255 bits (652), Expect = 6e-65,   Method: Compositional matrix adjust.
 Identities = 188/448 (41%), Positives = 247/448 (55%), Gaps = 66/448 (14%)

Query: 15  RIYVGGLGEKVTDDDLAKVFSS-----LGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKL 69
           RI+VGGLGE V+ +DL  +FSS     LG +++V+I+R+KGRSF Y+DFF SS+ SLSKL
Sbjct: 27  RIFVGGLGESVSSEDLRNIFSSNKSLGLG-IQSVEIIRSKGRSFAYIDFFSSSNNSLSKL 85

Query: 70  FSTYNGCVWKGGRLRLERAKEHYLARLKREWA----EDDAQLVNPPVTDSVA--PDNKDA 123
           F+TYNGC WKGG+LRLE+AKEHYLARL  EWA    ED   L+  P  D     P NK  
Sbjct: 86  FNTYNGCAWKGGKLRLEKAKEHYLARLTCEWAQDQDEDQHPLLPTPNLDHAQDDPTNKKL 145

Query: 124 TRLDTP--KKLLDKDKKLNIFFPRLRKVKTLPFCGTGKHKYSFQRVEAPPLPKYFCDCEE 181
           +    P  K+LL ++K+L +FFP L K+K++PF GTGKH+YSF+RVE PPLPK+FCDCEE
Sbjct: 146 SISSKPSNKELLSENKQLRLFFPGLGKIKSIPFRGTGKHRYSFRRVEVPPLPKHFCDCEE 205

Query: 182 HSAAFHAAEGKQIHHPAAGQEEIHDMEELGASVINEEELNLMNSVMNKLFERENVSNAGL 241
           HS    AA  K  H P         MEE GA  +++EEL LMNSVMNKLF+ ENVS+   
Sbjct: 206 HSEP-PAAAAKCRHIPI--------MEEQGAG-MDKEELTLMNSVMNKLFQMENVSDNAC 255

Query: 242 SGTELTNYERNSYNFIGDLQIGGNEVDSVADEYNLVINAVSGGNNRM---------VLSR 292
              EL     +S        +  NE D   D+ NL+IN     N R          VL +
Sbjct: 256 CEIELDKKVDDSMKTTDKPPLEENEGDIDEDDDNLIINMRRRFNVRQTSTDEPTQKVLQK 315

Query: 293 CQEKTTILPTNK--KLTLSEARTSKDRSAQSLPREQKKNDLLRSKKRKSLHNDEIL---- 346
            +  TT  P+NK  K+ L+E    +  +++ +P     N  L  ++ KS +  E L    
Sbjct: 316 QKRNTT--PSNKKRKIVLNE----ESNTSEGMPAMPGGNGSLLEQQSKSDNASETLPGHS 369

Query: 347 ----------MAASPLDDMN----VQTNMNKPSTPL--ATQHAET-----DSGVRKSTAS 385
                       A   D  N     Q N N+  + +     H E      DS   K    
Sbjct: 370 SSKEEQPKCDKVADSRDSENNKSWKQENQNEHFSRIKEVGGHKEALSTKLDSASNKPGRG 429

Query: 386 HSWSQKMSWKALVGDKDSRAFSVSNILP 413
           ++W  K SW  LV   +S AFS+++ILP
Sbjct: 430 YAWLNKSSWTQLVSGNNSNAFSITHILP 457

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	800
TAIR|locus:2155811	748	ROS3 "REPRESSOR OF SILENCING 3	0.67	0.716	0.306	5.6e-48
ZFIN|ZDB-GENE-050208-491	1230	nol8 "nucleolar protein 8" [Da	0.127	0.082	0.353	1.3e-13
FB|FBgn0037836	2743	CG14692 [Drosophila melanogast	0.555	0.161	0.259	4.8e-11
GENEDB_PFALCIPARUM|PF14_0758	1263	PF14_0758 "hypothetical protei	0.652	0.413	0.202	1.8e-10
UNIPROTKB|Q8IK49	1263	PF14_0758 "Putative uncharacte	0.652	0.413	0.202	1.8e-10
MGI|MGI:1918180	1147	Nol8 "nucleolar protein 8" [Mu	0.111	0.077	0.387	1.8e-10
UNIPROTKB|F8WE42	970	NOL8 "Nucleolar protein 8" [Ho	0.105	0.086	0.373	6.6e-10
UNIPROTKB|E1BT63	1165	NOL8 "Uncharacterized protein"	0.123	0.084	0.367	7.1e-10
UNIPROTKB|F5H101	1085	NOL8 "Nucleolar protein 8" [Ho	0.105	0.077	0.373	8.6e-10
UNIPROTKB|Q76FK4	1167	NOL8 "Nucleolar protein 8" [Ho	0.105	0.071	0.373	1e-09

TAIR|locus:2155811 ROS3 "REPRESSOR OF SILENCING 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 520 (188.1 bits), Expect = 5.6e-48, P = 5.6e-48
 Identities = 180/588 (30%), Positives = 280/588 (47%)

Query:    15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYN 74
             R++VGGLGE V  DDL K+FS +G V AV+ VRTKGRSF Y+DF PSS  SL+KLFSTYN
Sbjct:    11 RLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKGRSFAYIDFSPSSTNSLTKLFSTYN 70

Query:    75 GCVWKGGRLRLERAKEHYLARLKREWAEDDAQLVNPPVTDSVAPDNKDATRLDTPXXXXX 134
             GCVWKGGRLRLE+AKEHYLARLKREW    +   N   T     D+  AT L        
Sbjct:    71 GCVWKGGRLRLEKAKEHYLARLKREWEAASSTSDN---TIKAPSDSPPATHL-------- 119

Query:   135 XXXXXNIFFPRLRKVKTLPFCGTGKHKYSFQRVE-APPLPKYFCDCEEHSAAFHAAEGKQ 193
                  NIFFPRLRKVK +P  GTGKHKYSFQRV  +  LP+ FCDCEEHS +        
Sbjct:   120 -----NIFFPRLRKVKPMPLSGTGKHKYSFQRVPVSSSLPRSFCDCEEHSNSSLTPREIH 174

Query:   194 IHHPAA---GQEEIHDMEELGASVINE--EELNLMNSVMNKL-FEREN-VSNAGLSGTEL 246
             +H   A   G++E  ++  +  SV+N+  E+ N+     N++  +++N + N   SG ++
Sbjct:   175 LHDLEAVNVGRQEA-EVNVMN-SVMNKLFEKNNVDPEEDNEIEADQDNLIINVASSGNDM 232

Query:   247 TN----YERNSYNFIGDLQIGGNEVDSVADEYNLVINAVSGGNNRMVLSRCQEKTTILPT 302
              +      R   + +   +    E  S   + NL   + +     +  +  QE +  +  
Sbjct:   233 DSALDMLSRKRKSILNK-KTPSEEGYSEGRKGNLTHPSKNRQTISLEETGRQESSQAIRG 291

Query:   303 NKKLTLSEARTSKDRSAQSLPREQKKNDLLRSKKRKSLHNDEILMAASPLDDMNVQTNMN 362
              KK +      S D  +++   EQ  +++  S+K       + LMA    +D +V + + 
Sbjct:   292 KKKPSEVVPDKSSDEPSRTKDLEQSIDNISWSQKSSW----KSLMANGNSNDFSVSSFLP 347

Query:   363 KPSTPLATQHAETDSGVRKSTASHSWSQKMSWKALVGDKDSRAFSVSNILPSDASTEEAD 422
                +  A Q A  ++ +    +  +  +K   K +     +    VS+ +  D S   AD
Sbjct:   348 GVGSSKAVQPAPRNTDLAGLPSRENLKKKTKRKRVTSTIMAEDLPVSDDIKRDDSDTMAD 407

Query:   423 N----GINSFEELNFDENESDDLMINVVSKKKPKMALSSSQKWETTSTTYRK-SVSNEDN 477
             +      ++ E     E+ +DD   + V+++    A+      ++ +      SV+  D+
Sbjct:   408 DIERDDSDAVEYYTACESMADDTASDSVAERDDSDAVEDDTAIDSMADDPASDSVAESDD 467

Query:   478 NTTKDRPIQQEKSTLPSKKKRKSVIDDESDKNKSVHTVPETDG-CAQTYTESQMPTGPQL 536
                 +     +  ++       S+   ESD   +V      D  C  T  +     G   
Sbjct:   468 GDAVENDTAID--SMADDTVSNSMA--ESDDGDNVEDDTAIDSMCDDTANDD---VGSD- 519

Query:   537 VEPESVVEQSISDHSESKKPSQRVVIGSKGNDESSVSNVLPDNSAKEE 584
              +  S+ + ++SD S    P +  V  ++G+     SNV    +  E+
Sbjct:   520 -DSGSLAD-TVSDTSVEAVPLE-FVANTEGDSVDGKSNVEKHENVAED 564

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0003723 "RNA binding" evidence=IDA

GO:0016458 "gene silencing" evidence=IMP

GO:0080111 "DNA demethylation" evidence=IMP

GO:0051604 "protein maturation" evidence=RCA

ZFIN|ZDB-GENE-050208-491 nol8 "nucleolar protein 8" [Danio rerio (taxid:7955)]

 Score = 158 (60.7 bits), Expect = 1.3e-13, Sum P(2) = 1.3e-13
 Identities = 40/113 (35%), Positives = 57/113 (50%)

Query:    15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKG------RSFGYVDFFPSSHKSLSK 68
             R+Y+GGLG  VT+ DL   F   G+VK V+I+  K       ++FGY++    +     +
Sbjct:     3 RLYIGGLGHTVTEKDLKDRFGKFGDVKDVEIITRKDDQGAPLKTFGYINI-NITDAEFKR 61

Query:    69 LFSTYNGCVWKGGRLRLERAKEHYLARLKREWAEDDAQLVNPPVTDSVAPDNK 121
                  N   WKGG L ++ AKE +L RL    AE+  Q V    T  +AP  K
Sbjct:    62 CVGILNKSTWKGGTLLIQLAKESFLHRL----AEEREQQVEKIKTPKIAPQEK 110

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

FB|FBgn0037836 CG14692 [Drosophila melanogaster (taxid:7227)]

 Score = 196 (74.1 bits), Expect = 4.8e-11, P = 4.8e-11
 Identities = 128/494 (25%), Positives = 207/494 (41%)

Query:   284 GNNRMVLSRCQEKTTILPTNKKLTLSEARTSKDRSAQSLPREQKKNDLLRSKKRKSLHND 343
             G  + V  + +EKT+  PT  +   +E R    +S +SL  +  +ND  RS   ++L + 
Sbjct:  1013 GQLKTVFEQSEEKTS--PTKSESLHAEDRKISGKSKESL-EDAGEND--RSTLLENLPSS 1067

Query:   344 EILMAASPLDDMNVQTNMNKPSTPLATQHAETDSGVRKSTASHSWSQKMSWKAL-VGDKD 402
             E   + S LD+  +     K ST L     +  SG  KST+    S     K+  + +K 
Sbjct:  1068 EKENSTS-LDENPLP---EKESTSL---DEKPSSGTEKSTSLDEKSSSEKEKSTSLDEKP 1120

Query:   403 SRAFSVSNILPSDASTEEADNGINSFEELNFDENESDDLMINVVSKKKPKMAL---SSSQ 459
             S     S  L    S+E+ ++   S +E    E ES  L     S  +   +L   SSS+
Sbjct:  1121 SSEKEKSTSLDETPSSEKENS--TSLDEKPSPEKESTSLDEKPSSGTEKSTSLDEKSSSE 1178

Query:   460 KWETTSTTYRKSVSNEDNNTTKDRPI-QQEKSTL----PSKKKRKSVIDDE----SDKNK 510
             K ++TS   + S   E + +  +RP  ++E ST     PS +K  + +D++    ++K+ 
Sbjct:  1179 KEKSTSLDEKPSSEKEKSTSLNERPSSEKENSTSLVENPSPEKESTSLDEKPSSGTEKST 1238

Query:   511 SVHTVPETDGCAQTY------TESQMPTGPQLVEPESVVEQSIS-DHSESKKPSQRVVIG 563
             S+   P ++    T       +E +  T  Q  +P S  E+S S D   S +  +   + 
Sbjct:  1239 SLDENPSSEKEKSTSLNERPSSEKENSTS-QDEKPSSETEKSTSLDEKPSSEKEKSTSLD 1297

Query:   564 SKGNDESSVSNVLPDNSAKEEQRVFDCPDEPLGSTDSKNQNSLARNENLEGKLAETESVE 623
              K + E   S  L +N + E+++     + P  S++ +N  SL  N +      E ES  
Sbjct:  1298 GKPSSEKEKSTSLDENPSSEKEKSTSLNERP--SSEKENSTSLVENPS-----PEKESTS 1350

Query:   624 VPAKAQPSKSNTAPNKSGKGSSWFQKSPWTQLVNEDNSSFSITQISPGITFKKHDVPKTQ 683
             +  K  PS S T  + S   +   +K   T L NE  SS      S            T 
Sbjct:  1351 LDEK--PS-SGTEKSTSLDENPSSEKEKSTSL-NERPSSEKENSTSQDEKPSSEKEKSTL 1406

Query:   684 LGKEVANPNDK-KSSKSVGQAGSK-PITCASTALEDGKKGEIVSQIIPEKNQPTDVGDNE 741
             L K      D  + S+ V +  SK     A   L D  KGE V+  + +K    ++ D +
Sbjct:  1407 LDKNTDLMRDLIQVSQKVDEEMSKGKAAIAVVDLPDINKGESVNSPLEKKPSSQELEDIQ 1466

Query:   742 ASASMVADKHDLTP 755
             A  S   DK    P
Sbjct:  1467 AELS--TDKETGEP 1478

GO:0008603 "cAMP-dependent protein kinase regulator activity" evidence=IEA

GO:0007165 "signal transduction" evidence=IEA

GO:0032027 "myosin light chain binding" evidence=RCA

GENEDB_PFALCIPARUM|PF14_0758 PF14_0758 "hypothetical protein" [Plasmodium falciparum (taxid:5833)]

 Score = 187 (70.9 bits), Expect = 1.8e-10, P = 1.8e-10
 Identities = 118/584 (20%), Positives = 231/584 (39%)

Query:   207 MEELGASVINEEELNLMNSVMNKLFERENVSNAGLSGTELTNYERNSYNFIGDLQIGGNE 266
             +E+   +V N+E  N    + N L ++++       G ++T  + N  N +G+      +
Sbjct:   376 LEKPSNTVENKEGKNPF--IDNDLSDKKSNMQDNNKGLKVTTNKTNLKNKLGN---NTKQ 430

Query:   267 VDSVADEYNLVINAVSGGNNRMVLSRCQEKTTILPTNKKLTLSEARTSKDRSAQSLPREQ 326
             +   A+ +  + N VS   + +  S      T   TN K  L +      +       E 
Sbjct:   431 IKQGANPF--IENDVSDKKDNLQDSNKGLNVTTNKTNDKTKLEDNTKQIKKGTNPFMDED 488

Query:   327 KKNDLLRSKKRKSLHNDEILMAASPLDDMNVQTNMNKPSTPLATQHAETDSGVRKSTASH 386
             +  +LLR ++ + + N++           N   N NK S        + + G++ +T   
Sbjct:   489 ELEELLRLEREEKIKNEK---------KKNEDDNQNKKSNM-----QDNNKGLKVTTNKT 534

Query:   387 SWSQKMSWKALVGDKDSRAFSVSNILPSDASTEEADNGINSFEELNFDENESDDLMINVV 446
             +   K+        + +  F  +++     + ++++ G+N       D+ + +D    + 
Sbjct:   535 NLKNKLGNNTKQIKQGANPFIENDVSDKKDNLQDSNKGLNVTTNKTNDKTKLEDNTKQIK 594

Query:   447 SKKKPKM---ALSSSQKWETTSTTYRKSVSNEDNNTTK-DRPIQQEKSTLPSKKK----- 497
                 P M    L    + E       +   NED+N  K   P  Q K+   +K+      
Sbjct:   595 KGTNPFMDEDELEELLRLEREEKIKNEKKKNEDDNQNKKSNPSSQNKTNSQNKQNSQDKT 654

Query:   498 -RKSVIDDESDKN-KSVHTVPETDGCAQTYTESQMPTGPQLVEPESVVEQSISDHSESKK 555
              ++S +D ++ KN K+  ++P          E    + P  ++ ++   +       +K 
Sbjct:   655 NKQSKLDTQNGKNEKNEKSIPNKLDSQNGKNEKNEKSIPNKLDSQNGKNEKNEKSIPNKL 714

Query:   556 PSQRVVIGSKGNDESSVSNVLPDNSAKEEQRVFDCPDEPLGSTDSKNQ-NSLARNENLEG 614
              SQ    G    +E S+ N L   + K E+     P++ L S + KN+ N  +    L+ 
Sbjct:   715 DSQN---GKNEKNEKSIPNKLDSQNGKNEKNEKSIPNK-LDSQNGKNEKNEKSIPNKLDS 770

Query:   615 KLAETESVEVPAKAQ----PSKSNTAPNKSGKGSSWFQKSPWTQLVNEDNSSFSITQISP 670
             +  + E   +P K      P+K N  PNK    +   +K    +L NE+  +   TQ + 
Sbjct:   771 QNGKNEK-NIPNKLDSQNVPNKQNI-PNKLDSQNVKNEKDTPNKLDNENKEN---TQSNK 825

Query:   671 GITFKKHDVP-------KTQLGKEVANPNDKKSSKSVGQAGSKPITCASTALEDGKKGEI 723
              +  KK D+        +T   K++   N+ ++  +V  +  K      T  +D + G  
Sbjct:   826 NLNAKKSDIGTNGKSNIETSQDKQLTTKNNDENKNTVKNSKFKDALLEVT--KDIEHG-- 881

Query:   724 VSQIIPEKNQPTDVGDNEASASMVADKHDLTPRQTTNVDGTIGE 767
             +S  +  KNQ    G    S S+   K++L  + T N+DG   E
Sbjct:   882 ISSDMLNKNQK---GKQLKSESL--KKNELENKNTKNMDGNKNE 920

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|Q8IK49 PF14_0758 "Putative uncharacterized protein" [Plasmodium falciparum 3D7 (taxid:36329)]

 Score = 187 (70.9 bits), Expect = 1.8e-10, P = 1.8e-10
 Identities = 118/584 (20%), Positives = 231/584 (39%)

Query:   207 MEELGASVINEEELNLMNSVMNKLFERENVSNAGLSGTELTNYERNSYNFIGDLQIGGNE 266
             +E+   +V N+E  N    + N L ++++       G ++T  + N  N +G+      +
Sbjct:   376 LEKPSNTVENKEGKNPF--IDNDLSDKKSNMQDNNKGLKVTTNKTNLKNKLGN---NTKQ 430

Query:   267 VDSVADEYNLVINAVSGGNNRMVLSRCQEKTTILPTNKKLTLSEARTSKDRSAQSLPREQ 326
             +   A+ +  + N VS   + +  S      T   TN K  L +      +       E 
Sbjct:   431 IKQGANPF--IENDVSDKKDNLQDSNKGLNVTTNKTNDKTKLEDNTKQIKKGTNPFMDED 488

Query:   327 KKNDLLRSKKRKSLHNDEILMAASPLDDMNVQTNMNKPSTPLATQHAETDSGVRKSTASH 386
             +  +LLR ++ + + N++           N   N NK S        + + G++ +T   
Sbjct:   489 ELEELLRLEREEKIKNEK---------KKNEDDNQNKKSNM-----QDNNKGLKVTTNKT 534

Query:   387 SWSQKMSWKALVGDKDSRAFSVSNILPSDASTEEADNGINSFEELNFDENESDDLMINVV 446
             +   K+        + +  F  +++     + ++++ G+N       D+ + +D    + 
Sbjct:   535 NLKNKLGNNTKQIKQGANPFIENDVSDKKDNLQDSNKGLNVTTNKTNDKTKLEDNTKQIK 594

Query:   447 SKKKPKM---ALSSSQKWETTSTTYRKSVSNEDNNTTK-DRPIQQEKSTLPSKKK----- 497
                 P M    L    + E       +   NED+N  K   P  Q K+   +K+      
Sbjct:   595 KGTNPFMDEDELEELLRLEREEKIKNEKKKNEDDNQNKKSNPSSQNKTNSQNKQNSQDKT 654

Query:   498 -RKSVIDDESDKN-KSVHTVPETDGCAQTYTESQMPTGPQLVEPESVVEQSISDHSESKK 555
              ++S +D ++ KN K+  ++P          E    + P  ++ ++   +       +K 
Sbjct:   655 NKQSKLDTQNGKNEKNEKSIPNKLDSQNGKNEKNEKSIPNKLDSQNGKNEKNEKSIPNKL 714

Query:   556 PSQRVVIGSKGNDESSVSNVLPDNSAKEEQRVFDCPDEPLGSTDSKNQ-NSLARNENLEG 614
              SQ    G    +E S+ N L   + K E+     P++ L S + KN+ N  +    L+ 
Sbjct:   715 DSQN---GKNEKNEKSIPNKLDSQNGKNEKNEKSIPNK-LDSQNGKNEKNEKSIPNKLDS 770

Query:   615 KLAETESVEVPAKAQ----PSKSNTAPNKSGKGSSWFQKSPWTQLVNEDNSSFSITQISP 670
             +  + E   +P K      P+K N  PNK    +   +K    +L NE+  +   TQ + 
Sbjct:   771 QNGKNEK-NIPNKLDSQNVPNKQNI-PNKLDSQNVKNEKDTPNKLDNENKEN---TQSNK 825

Query:   671 GITFKKHDVP-------KTQLGKEVANPNDKKSSKSVGQAGSKPITCASTALEDGKKGEI 723
              +  KK D+        +T   K++   N+ ++  +V  +  K      T  +D + G  
Sbjct:   826 NLNAKKSDIGTNGKSNIETSQDKQLTTKNNDENKNTVKNSKFKDALLEVT--KDIEHG-- 881

Query:   724 VSQIIPEKNQPTDVGDNEASASMVADKHDLTPRQTTNVDGTIGE 767
             +S  +  KNQ    G    S S+   K++L  + T N+DG   E
Sbjct:   882 ISSDMLNKNQK---GKQLKSESL--KKNELENKNTKNMDGNKNE 920

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

MGI|MGI:1918180 Nol8 "nucleolar protein 8" [Mus musculus (taxid:10090)]

 Score = 151 (58.2 bits), Expect = 1.8e-10, Sum P(2) = 1.8e-10
 Identities = 38/98 (38%), Positives = 55/98 (56%)

Query:    15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK---GRS---FGYVDFFPSSHKSLSK 68
             R++VGGLG+ +++ DL   F   GEV  V+I+  K   G S   F YV+    +   L K
Sbjct:     9 RLFVGGLGQGISETDLQNQFGRFGEVSDVEIITRKDDQGNSQKVFAYVNI-QITEADLKK 67

Query:    69 LFSTYNGCVWKGGRLRLERAKEHYLARLKREWAEDDAQ 106
               S  N   WKGG L+++ AKE +L RL +E   +DA+
Sbjct:    68 CMSILNKTKWKGGTLQIQLAKESFLHRLAQE--REDAK 103

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003674 "molecular_function" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005730 "nucleolus" evidence=ISO

GO:0006260 "DNA replication" evidence=ISO

GO:0006364 "rRNA processing" evidence=ISO

GO:0030307 "positive regulation of cell growth" evidence=ISO

UNIPROTKB|F8WE42 NOL8 "Nucleolar protein 8" [Homo sapiens (taxid:9606)]

 Score = 147 (56.8 bits), Expect = 6.6e-10, Sum P(2) = 6.6e-10
 Identities = 34/91 (37%), Positives = 50/91 (54%)

Query:    15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKG------RSFGYVDFFPSSHKSLSK 68
             R+YVGGL + +++ DL   FS  GEV  V+I+  K       + F Y++    +   L K
Sbjct:     9 RLYVGGLSQDISEADLQNQFSRFGEVSDVEIITRKDDQGNPQKVFAYINI-SVAEADLKK 67

Query:    69 LFSTYNGCVWKGGRLRLERAKEHYLARLKRE 99
               S  N   WKGG L+++ AKE +L RL +E
Sbjct:    68 CMSVLNKTKWKGGTLQIQLAKESFLHRLAQE 98

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|E1BT63 NOL8 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 132 (51.5 bits), Expect = 7.1e-10, Sum P(2) = 7.1e-10
 Identities = 39/106 (36%), Positives = 50/106 (47%)

Query:    15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKG------RSFGYVDFFPSSHKSLSK 68
             R+YVGGLG  V+  +L + F   G V  V+I+  K       ++F YV    SS   L K
Sbjct:     9 RLYVGGLGHTVSKAELQERFGKFGRVLDVEIITRKDEQGNPTKTFAYVTV-SSSEADLRK 67

Query:    69 LFSTYNGCVWKGGRLRLERAKEHYLARLKREWAEDDAQLVNPPVTD 114
               S  N   W G  L++E AKE +L RL  E  E   Q   P   D
Sbjct:    68 CISILNKTKWGGKTLQIEFAKESFLHRLAVEREEAKLQKEKPRRND 113

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

GO:0030307 "positive regulation of cell growth" evidence=IEA

UNIPROTKB|F5H101 NOL8 "Nucleolar protein 8" [Homo sapiens (taxid:9606)]

 Score = 147 (56.8 bits), Expect = 8.6e-10, Sum P(2) = 8.6e-10
 Identities = 34/91 (37%), Positives = 50/91 (54%)

Query:    15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKG------RSFGYVDFFPSSHKSLSK 68
             R+YVGGL + +++ DL   FS  GEV  V+I+  K       + F Y++    +   L K
Sbjct:     9 RLYVGGLSQDISEADLQNQFSRFGEVSDVEIITRKDDQGNPQKVFAYINI-SVAEADLKK 67

Query:    69 LFSTYNGCVWKGGRLRLERAKEHYLARLKRE 99
               S  N   WKGG L+++ AKE +L RL +E
Sbjct:    68 CMSVLNKTKWKGGTLQIQLAKESFLHRLAQE 98

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|Q76FK4 NOL8 "Nucleolar protein 8" [Homo sapiens (taxid:9606)]

 Score = 147 (56.8 bits), Expect = 1.0e-09, Sum P(2) = 1.0e-09
 Identities = 34/91 (37%), Positives = 50/91 (54%)

Query:    15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKG------RSFGYVDFFPSSHKSLSK 68
             R+YVGGL + +++ DL   FS  GEV  V+I+  K       + F Y++    +   L K
Sbjct:     9 RLYVGGLSQDISEADLQNQFSRFGEVSDVEIITRKDDQGNPQKVFAYINI-SVAEADLKK 67

Query:    69 LFSTYNGCVWKGGRLRLERAKEHYLARLKRE 99
               S  N   WKGG L+++ AKE +L RL +E
Sbjct:    68 CMSVLNKTKWKGGTLQIQLAKESFLHRLAQE 98

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005730 "nucleolus" evidence=IDA

GO:0006364 "rRNA processing" evidence=IMP

GO:0030307 "positive regulation of cell growth" evidence=IMP

GO:0006260 "DNA replication" evidence=IMP

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	800
PLN03213	759	PLN03213, PLN03213, repressor of silencing 3; Prov	5e-77
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	2e-23
smart00360	73	smart00360, RRM, RNA recognition motif	2e-10
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	6e-10
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	3e-09
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	5e-07
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	6e-07
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	7e-07
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	1e-06
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	2e-06
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	4e-06
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	4e-06
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	5e-06
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	7e-06
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	1e-05
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	2e-05
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	3e-05
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	3e-05
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	4e-05
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	5e-05
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	7e-05
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	9e-05
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	1e-04
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	1e-04
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	1e-04
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	1e-04
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	2e-04
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	2e-04
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	2e-04
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	2e-04
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	2e-04
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	2e-04
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	2e-04
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	2e-04
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	2e-04
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	3e-04
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	3e-04
cd12558	76	cd12558, RRM3_RBM15B, RNA recognition motif 3 in p	4e-04
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	5e-04
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	5e-04
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	5e-04
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	0.001
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	0.001
cd12620	73	cd12620, RRM3_TIAR, RNA recognition motif 3 in nuc	0.002
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	0.002
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	0.002
cd12681	69	cd12681, RRM_SKAR, RNA recognition motif in S6K1 A	0.002
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	0.002
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	0.003
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	0.003
cd12597	73	cd12597, RRM1_SRSF1, RNA recognition motif 1 in se	0.003
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	0.003
cd12644	90	cd12644, RRM_CFIm59, RNA recognition motif of pre-	0.003
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	0.004
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	0.004
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	0.004
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	0.004

>gnl|CDD|178752 PLN03213, PLN03213, repressor of silencing 3; Provisional

 Score =  264 bits (675), Expect = 5e-77
 Identities = 263/841 (31%), Positives = 384/841 (45%), Gaps = 157/841 (18%)

Query: 15  RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYN 74
           R++VGGLGE V  DDL K+FS +G V AV+ VRTKGRSF Y+DF PSS  SL+KLFSTYN
Sbjct: 12  RLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKGRSFAYIDFSPSSTNSLTKLFSTYN 71

Query: 75  GCVWKGGRLRLERAKEHYLARLKREWAEDDAQLVNPPVTDSVAPDNKDATRLDTPKKLLD 134
           GCVWKGGRLRLE+AKEHYLARLKREW              S   DN      D+P     
Sbjct: 72  GCVWKGGRLRLEKAKEHYLARLKREWE-----------AASSTSDNTIKAPSDSPPA--- 117

Query: 135 KDKKLNIFFPRLRKVKTLPFCGTGKHKYSFQRVE-APPLPKYFCDCEEHSAAFHAAEGKQ 193
               LNIFFPRLRKVK +P  GTGKHKYSFQRV  +  LPK FCDCEEHS    +   ++
Sbjct: 118 --THLNIFFPRLRKVKAMPLSGTGKHKYSFQRVPLSSSLPKSFCDCEEHSNN--SLTPRE 173

Query: 194 IHHPAAGQEEIHDMEELGASVINEEELNLMNSVMNKLFERENVSNAGLSGTELTNYERNS 253
           IH        +HD+E L     NE E+N+MNSVMNKLFE+ N+  A     E    E + 
Sbjct: 174 IH--------LHDLEALNVGR-NEAEVNVMNSVMNKLFEKNNIDIA----EEDNEIEADQ 220

Query: 254 YNFIGDLQIGGNEVDSVADEYNLVINAVSGGN--NRMVLSRCQEKTTILPTNKKLTLSEA 311
            N I ++   GN++DS  D+ +    ++      +    S  ++   I P+ K+ T+S  
Sbjct: 221 DNLIINVASSGNDMDSALDKLSRKRKSILNEKTPSEEGYSEGRKGNHIHPSKKRQTISLE 280

Query: 312 RTSKDRSAQSLPREQKKNDLLRSKKRKSLHNDEILMAASPLDDMNVQTNMNKPSTPLATQ 371
            + +  S+Q++  ++K ++++  K                        ++++PS      
Sbjct: 281 ESGRQESSQAIREKKKPSEVVPDK------------------------SLDEPSR----- 311

Query: 372 HAETDSGVRKSTASHSWSQKMSWKALVGDKDSRAFSVSNILPSDASTEEADNGINSFEEL 431
                  + +S  + SWSQK SWK+L+ + +S  FSVS+ LP   S++       + +  
Sbjct: 312 ----TKDLEQSIDNISWSQKSSWKSLMANGNSNDFSVSSFLPGVGSSKAVQPAPRNTDLA 367

Query: 432 NFDENESDDLMINVVSKKKPKMALSSSQKWETTSTTYRKSVSNEDNNTTKDRPIQQEKST 491
                E      N+  K K K   S+    +         +  +D++T  D   + + + 
Sbjct: 368 ELPSRE------NLKEKTKRKRVTSTIMAEDLPVP---DDIKRDDSDTMADDIERDDSAA 418

Query: 492 LPSKKKRKSVIDD-------ESDKNKSVHTVPETDGCAQTYTESQMPTGPQLVEPESVVE 544
           +      +S+ DD       E D + +V      D  A       M         ++V E
Sbjct: 419 VEYYTACESMADDAANDSVAERDDSDAVECDTAIDSMADDTAIDSMADDAA---SDAVAE 475

Query: 545 QSISDHSESKKPSQRVVIGSKGNDESSVSNVLPDNSAKEEQRVF------DCPDEPLGST 598
               D  E+        I S  +D +S S    D+    E          D  ++ +GS 
Sbjct: 476 SDDGDAVEND-----TAIDSMADDTASNSMAESDDGDNVEDDTAIDSMADDTANDDVGSD 530

Query: 599 DSKNQNSLARNENLEGK----LAETESVEVPAKAQPSKSNT------------------- 635
           DS++      + +++      +A TE      K+   K                      
Sbjct: 531 DSESLADTVIDTSVDAVPLDFVANTEGDSGDGKSNVEKHENGAEDLNAEKESLVVKENVV 590

Query: 636 -----------APNKSGKGSSWFQKSPWTQLVNEDN-SSFSITQISPGITFKKHDVPKTQ 683
                      A NKS  GSSW QK+ WTQLV++ N SSFSITQ+ P ++  K +     
Sbjct: 591 DEEEAGKEPLKACNKSTGGSSWLQKASWTQLVSDKNTSSFSITQLFPDLSSDKGEAAGVI 650

Query: 684 LGKEVANPNDKKSSKSVGQAGSKPITCASTALEDGKKGEIVSQIIPEKNQPTDV------ 737
              E    N  K++ ++ Q       C+S        G  V+  +P  + P         
Sbjct: 651 NNVENQFSNSHKTASAMKQTD---YACSS--------GGFVAAGVPVASTPVRSLDENRH 699

Query: 738 ---GDNEASASMVADKHDLTPRQTTNVDGTIGETCSFMRSAASIKEWSTAKAALSGSQSH 794
              G N +  + +  K  +  R+  +     G+TC+FMRS+ S+KEW+ AK ALS  +  
Sbjct: 700 HLNGKNLSEGAKLGAKKKIIKRKVGS-----GDTCTFMRSSTSLKEWAKAKKALSEPRRK 754

Query: 795 K 795
           K
Sbjct: 755 K 755

Length = 759

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

 Score = 94.2 bits (235), Expect = 2e-23
 Identities = 34/79 (43%), Positives = 44/79 (55%), Gaps = 5/79 (6%)

Query: 15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKG----RSFGYVDFFPSSHKSLSKLF 70
          R++VGGL   VT+ DL + FS  G V  V+I++ K     R F Y+D   S    L K  
Sbjct: 1  RLFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSE-AQLKKCK 59

Query: 71 STYNGCVWKGGRLRLERAK 89
          ST NG  WKG  L++E AK
Sbjct: 60 STLNGTKWKGSVLKIEEAK 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|214636 smart00360, RRM, RNA recognition motif

 Score = 56.8 bits (138), Expect = 2e-10
 Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 6/75 (8%)

Query: 15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK--GRS--FGYVDFFPSSHKSLSKLF 70
           ++VG L    T+++L ++FS  G+V++V +VR K  G+S  F +V+F   S +   K  
Sbjct: 1  TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEF--ESEEDAEKAL 58

Query: 71 STYNGCVWKGGRLRL 85
             NG    G  L++
Sbjct: 59 EALNGKELDGRPLKV 73

Length = 73

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

 Score = 55.8 bits (135), Expect = 6e-10
 Identities = 24/74 (32%), Positives = 40/74 (54%), Gaps = 5/74 (6%)

Query: 16 IYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT---KGRSFGYVDFFPSSHKSLSKLFST 72
          ++VG L    T++DL ++FS  GE+++V IVR    K + F +V+F   S +   K    
Sbjct: 1  LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEF--ESPEDAEKALEA 58

Query: 73 YNGCVWKGGRLRLE 86
           NG    G +L++ 
Sbjct: 59 LNGKELDGRKLKVS 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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 53.7 bits (130), Expect = 3e-09
 Identities = 25/71 (35%), Positives = 37/71 (52%), Gaps = 4/71 (5%)

Query: 16 IYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVR--TKGRSFGYVDFFPSSHKSLSKLFSTY 73
          +YV  L   VT++DL + FS  G+V+ V +VR   + R F +V+F  +S +         
Sbjct: 1  LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEF--ASPEDAEAALKKL 58

Query: 74 NGCVWKGGRLR 84
          NG V  G  LR
Sbjct: 59 NGLVLDGRTLR 69

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

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

 Score = 47.2 bits (113), Expect = 5e-07
 Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 5/63 (7%)

Query: 16 IYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT-KGRS--FGYVDFFPSSHKSLSKLFST 72
          ++VG L    T++DL  +FS  G ++++ IVR   GRS  F +V+F     +   K    
Sbjct: 1  LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFE--DEEDAEKALEA 58

Query: 73 YNG 75
           NG
Sbjct: 59 LNG 61

(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 = 47.2 bits (113), Expect = 6e-07
 Identities = 23/79 (29%), Positives = 39/79 (49%), Gaps = 6/79 (7%)

Query: 15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK--GRS--FGYVDFFPSSHKSLSKLF 70
           +YVG L   VT++DL  +F   GEV +  ++  +  GRS  FG+V+    + +  +   
Sbjct: 1  NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEM--ETAEEANAAI 58

Query: 71 STYNGCVWKGGRLRLERAK 89
             NG  + G  L +  A+
Sbjct: 59 EKLNGTDFGGRTLTVNEAR 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|240841 cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 46.8 bits (112), Expect = 7e-07
 Identities = 26/77 (33%), Positives = 40/77 (51%), Gaps = 11/77 (14%)

Query: 16 IYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVR----TKGRSFGYVDF--FPSSHKSLSKL 69
          ++VG L   + +++L K F   G+V+AV IVR      G+ FGYV F    S   +L   
Sbjct: 2  VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKL- 60

Query: 70 FSTYNGCVWKGGRLRLE 86
              NG   KG ++R++
Sbjct: 61 ----NGIKLKGRKIRVK 73

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

>gnl|CDD|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins

 Score = 46.5 bits (111), Expect = 1e-06
 Identities = 27/74 (36%), Positives = 43/74 (58%), Gaps = 7/74 (9%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFF--PSSHKSLSKLFS 71
          T +YVGGLGE+VT+ DL   F   GE++++ +V  +  +F  V F    ++ K+  +LF 
Sbjct: 2  TTLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQQCAF--VTFTTREAAEKAAERLF- 58

Query: 72 TYNGCVWKGGRLRL 85
            N  +  G RL+L
Sbjct: 59 --NKLIINGRRLKL 70

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

 Score = 46.1 bits (110), Expect = 2e-06
 Identities = 20/79 (25%), Positives = 41/79 (51%), Gaps = 6/79 (7%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGEVK----AVDIVRTKGRSFGYVDFFPSSHKSLSKL 69
           RIYV  +   +++DD+  VF + G++K    A D    K + +G++++   + +S    
Sbjct: 1  NRIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEY--ENPQSAQDA 58

Query: 70 FSTYNGCVWKGGRLRLERA 88
           ++ N     G +LR+ +A
Sbjct: 59 IASMNLFDLGGQQLRVGKA 77

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

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

 Score = 44.9 bits (107), Expect = 4e-06
 Identities = 17/47 (36%), Positives = 25/47 (53%), Gaps = 4/47 (8%)

Query: 16 IYVGGLGEKVTDDDLAKVFSSLGEVKAVDI----VRTKGRSFGYVDF 58
          +YVGGL E+V +  L   F   G++K + I       K R F +V+F
Sbjct: 1  LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEF 47

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|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 = 44.9 bits (107), Expect = 4e-06
 Identities = 22/80 (27%), Positives = 40/80 (50%), Gaps = 6/80 (7%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK----GRSFGYVDFFPSSHKSLSKL 69
           +++V GL  + T+ +L  +FS  G V+ V +++       R FG+V F   S +     
Sbjct: 2  NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTF--ESVEDADAA 59

Query: 70 FSTYNGCVWKGGRLRLERAK 89
              NG   +G  +++E+AK
Sbjct: 60 IRDLNGKELEGRVIKVEKAK 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|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 44.9 bits (107), Expect = 5e-06
 Identities = 24/81 (29%), Positives = 40/81 (49%), Gaps = 10/81 (12%)

Query: 16 IYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKG----RSFGYVDFFPSSH--KSLSKL 69
          ++V  L    TD+ L + FS +G +K   +V+ KG    R FGYV F       ++L + 
Sbjct: 2  LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 70 FSTYNGCVWKGGRLRLERAKE 90
            T     + G ++ +E AK+
Sbjct: 62 KKT----KFGGRKIHVEFAKK 78

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

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

 Score = 44.2 bits (105), Expect = 7e-06
 Identities = 21/60 (35%), Positives = 34/60 (56%), Gaps = 6/60 (10%)

Query: 16 IYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVR--TKGRS--FGYVDFF--PSSHKSLSKL 69
          +YVG L   +T+DDL  +F   GE++ V + R    GRS  +G++ F     + K+L +L
Sbjct: 1  LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

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

 Score = 43.8 bits (104), Expect = 1e-05
 Identities = 21/48 (43%), Positives = 31/48 (64%), Gaps = 4/48 (8%)

Query: 15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKG----RSFGYVDF 58
          +++VGGL E VT++DL + FS  G V++V+IV  K     R F +V F
Sbjct: 1  KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTF 48

This subfamily corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 73

>gnl|CDD|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 = 42.7 bits (101), Expect = 2e-05
 Identities = 24/74 (32%), Positives = 39/74 (52%), Gaps = 8/74 (10%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFF--PSSHKSLSKLFS 71
          T ++VGGL   VT+D+L  +F   GE+  V I    G+  G+V F    ++  ++ +L  
Sbjct: 2  TTVFVGGLDPAVTEDELRSLFGPFGEIVYVKI--PPGKGCGFVQFVHRAAAEAAIQQL-- 57

Query: 72 TYNGCVWKGGRLRL 85
             G +  G R+RL
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|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins

 Score = 42.4 bits (100), Expect = 3e-05
 Identities = 19/48 (39%), Positives = 24/48 (50%), Gaps = 4/48 (8%)

Query: 15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RTKGRS--FGYVDF 58
           ++VG L   V D+ L   F   G V    ++  R  GRS  FGYVDF
Sbjct: 1  TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDF 48

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

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

 Score = 46.5 bits (109), Expect = 3e-05
 Identities = 35/149 (23%), Positives = 63/149 (42%), Gaps = 6/149 (4%)

Query: 1   MEKKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKG----RSFGYV 56
              K  +   EE   ++VG L   VT++DL ++F   G VK V +VR +     R F +V
Sbjct: 103 ESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFV 162

Query: 57  DFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKEHYLARLKREWAEDDAQLVNPPVTDSV 116
           +F   S +S  K     NG   +G  LR+++A+     R +     D +         ++
Sbjct: 163 EF--ESEESAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKAL 220

Query: 117 APDNKDATRLDTPKKLLDKDKKLNIFFPR 145
             +  D   +        +++  ++F  R
Sbjct: 221 LLEKSDNLYVGNLPLKTAEEELADLFKSR 249

Length = 306

>gnl|CDD|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic activator RIM4 and similar proteins

 Score = 42.3 bits (100), Expect = 4e-05
 Identities = 15/74 (20%), Positives = 37/74 (50%), Gaps = 4/74 (5%)

Query: 16 IYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVR--TKGRSFGYVDFFPSSHKSLSKLFSTY 73
          I+VG L   VT ++L + FS  G++  V++++      +F ++ F     ++ ++   + 
Sbjct: 6  IFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFIKF--EREQAAARAVESE 63

Query: 74 NGCVWKGGRLRLER 87
          N  + K   + ++ 
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|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 41.9 bits (99), Expect = 5e-05
 Identities = 19/61 (31%), Positives = 35/61 (57%), Gaps = 3/61 (4%)

Query: 16 IYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGR-SFGYVDFFPSSHKSLSKLFSTYN 74
          +YVG L   VT+D LA++FS +G +K+  ++R  G   + +V+++     + +    T N
Sbjct: 1  LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDPYAFVEYYDHRSAAAA--LQTMN 58

Query: 75 G 75
          G
Sbjct: 59 G 59

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

 Score = 41.8 bits (99), Expect = 7e-05
 Identities = 19/48 (39%), Positives = 28/48 (58%), Gaps = 4/48 (8%)

Query: 15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVR----TKGRSFGYVDF 58
          RI+VG LG +VTD+ LA+ FS     +   +VR     K + +G+V F
Sbjct: 8  RIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSF 55

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

 Score = 41.1 bits (97), Expect = 9e-05
 Identities = 14/44 (31%), Positives = 24/44 (54%), Gaps = 1/44 (2%)

Query: 15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDF 58
          ++YVG LG + T  +L   F   G +++V + R     F +V+F
Sbjct: 1  KVYVGNLGPRATKRELEDEFEKYGPLRSVWVAR-NPPGFAFVEF 43

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

>gnl|CDD|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 = 41.1 bits (97), Expect = 1e-04
 Identities = 16/52 (30%), Positives = 31/52 (59%), Gaps = 4/52 (7%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKS 65
          T +YVG L   +T+++L + FS  G ++ V + + KG  + +V F   +H++
Sbjct: 1  TTVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDKG--YAFVRF--DTHEA 48

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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 40.2 bits (95), Expect = 1e-04
 Identities = 17/57 (29%), Positives = 32/57 (56%), Gaps = 3/57 (5%)

Query: 30 LAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLE 86
          L K+FS  G V+ + +++ K   F +V+F  S+ ++  K     NG ++ G  LR++
Sbjct: 1  LYKLFSPFGNVEKIKLLKKKPG-FAFVEF--STEEAAEKAVQYLNGVLFGGRPLRVD 54

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

 Score = 40.7 bits (96), Expect = 1e-04
 Identities = 14/44 (31%), Positives = 27/44 (61%), Gaps = 2/44 (4%)

Query: 13 QTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYV 56
          + R++VG L   +T+++  ++FS  GEV  V +   K + FG++
Sbjct: 1  RCRLFVGNLPNDITEEEFKELFSKYGEVSEVFL--NKEKGFGFI 42

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

 Score = 40.8 bits (96), Expect = 1e-04
 Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 7/75 (9%)

Query: 16 IYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT---KGRSFGYVDFFPSSHK-SLSKLFS 71
          ++VG L  +VT++ L ++F   G ++ V I +    K +SF +V F    H+ S+     
Sbjct: 4  LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTF---KHEVSVPYAIQ 60

Query: 72 TYNGCVWKGGRLRLE 86
            NG    G  LR++
Sbjct: 61 LLNGIRLFGRELRIK 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|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins

 Score = 40.3 bits (95), Expect = 2e-04
 Identities = 23/49 (46%), Positives = 29/49 (59%), Gaps = 4/49 (8%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGEV-KAV---DIVRTKGRSFGYVDF 58
          T+I+VGGL    TDD L K FS  GE+ +AV   D    K R +G+V F
Sbjct: 1  TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTF 49

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|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 40.7 bits (96), Expect = 2e-04
 Identities = 18/42 (42%), Positives = 29/42 (69%), Gaps = 2/42 (4%)

Query: 16 IYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK--GRSFGY 55
          IY+GGL  ++T+ D+  VFS  GE+  +++VR K  G+S G+
Sbjct: 12 IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGF 53

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|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 = 40.4 bits (95), Expect = 2e-04
 Identities = 24/78 (30%), Positives = 41/78 (52%), Gaps = 9/78 (11%)

Query: 16 IYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RTKGRSFGYVDF--FPSSHKSLSKLFS 71
          I+VGG+   +++DDL + FS+ GEV  V +   R     F +V+F    S+  +L+    
Sbjct: 3  IHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSARFAFVEFADAESALSALNL--- 59

Query: 72 TYNGCVWKGGRLRLERAK 89
            +G +  G  LR+  +K
Sbjct: 60 --SGTLLGGHPLRVSPSK 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|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 40.3 bits (95), Expect = 2e-04
 Identities = 22/48 (45%), Positives = 31/48 (64%), Gaps = 3/48 (6%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK-GRS--FGYVDF 58
          +RI V  L + VT+D L + F S GEV  V ++RT+ G+S  FG+V F
Sbjct: 1  SRIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGF 48

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

 Score = 40.1 bits (94), Expect = 2e-04
 Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 3/73 (4%)

Query: 15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDI-VRTKGRSFGYVDFFPSSHKSLSKLFSTY 73
          RIYVG L   + + D+  +F   G +KA+D+  R +G  F +V+F     +         
Sbjct: 1  RIYVGNLPGDIRERDIEDLFYKYGPIKAIDLKNRRRGPPFAFVEF--EDPRDAEDAVRGR 58

Query: 74 NGCVWKGGRLRLE 86
          +G  + G RLR+E
Sbjct: 59 DGYDFDGYRLRVE 71

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|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 40.2 bits (94), Expect = 2e-04
 Identities = 20/47 (42%), Positives = 28/47 (59%), Gaps = 3/47 (6%)

Query: 15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKG---RSFGYVDF 58
          RI+VGG+  K  ++DL K FS  G VK V IV  +    + +G+V F
Sbjct: 4  RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAGVSKGYGFVTF 50

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

 Score = 40.3 bits (95), Expect = 2e-04
 Identities = 23/83 (27%), Positives = 37/83 (44%), Gaps = 9/83 (10%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV-------RTKGRSFGYVDFFPSSHKSL 66
          T +YVG L  KVT++ L + F   G + +V I+       R + R+ G+V F   +    
Sbjct: 2  TNLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFM--NRADA 59

Query: 67 SKLFSTYNGCVWKGGRLRLERAK 89
           +     +G    G  L+L   K
Sbjct: 60 ERALDELDGKDVMGYELKLGWGK 82

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

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

 Score = 40.0 bits (94), Expect = 2e-04
 Identities = 15/51 (29%), Positives = 27/51 (52%), Gaps = 7/51 (13%)

Query: 15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK-------GRSFGYVDF 58
          R+++G L  ++T+  L K+FS  G++K  D +  K        R + +V F
Sbjct: 1  RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTF 51

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

 Score = 39.9 bits (94), Expect = 2e-04
 Identities = 18/46 (39%), Positives = 29/46 (63%), Gaps = 3/46 (6%)

Query: 16 IYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT-KGRS--FGYVDF 58
          ++V  L   V +D+L K+FS  GE+  V +V+  KG+S  + YV+F
Sbjct: 2  VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEF 47

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

 Score = 39.9 bits (94), Expect = 3e-04
 Identities = 18/42 (42%), Positives = 25/42 (59%), Gaps = 1/42 (2%)

Query: 15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK-GRSFGY 55
          RI+VGG+    T+++L   FS  G VK V I+  + G S GY
Sbjct: 4  RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGY 45

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

 Score = 39.5 bits (93), Expect = 3e-04
 Identities = 23/78 (29%), Positives = 42/78 (53%), Gaps = 5/78 (6%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT---KGRSFGYVDFFPSSHKSLSKLF 70
          T +YV  LGE + D+ L ++F   G++ +  +++    K + FG+V+F   +H++  K  
Sbjct: 2  TNVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNF--ENHEAAQKAV 59

Query: 71 STYNGCVWKGGRLRLERA 88
             NG    G +L + RA
Sbjct: 60 EELNGKEVNGKKLYVGRA 77

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|241002 cd12558, RRM3_RBM15B, RNA recognition motif 3 in putative RNA-binding protein 15B (RBM15B) from vertebrate

 Score = 39.2 bits (91), Expect = 4e-04
 Identities = 18/45 (40%), Positives = 27/45 (60%), Gaps = 2/45 (4%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDF 58
          TR++VGGLG   +   LA+ F   G ++ +D V  KG SF Y+ +
Sbjct: 3  TRLWVGGLGPNTSLAALAREFDRFGSIRTIDYV--KGDSFAYIQY 45

This subgroup corresponds to the RRM3 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 = 76

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

 Score = 39.1 bits (92), Expect = 5e-04
 Identities = 22/81 (27%), Positives = 35/81 (43%), Gaps = 11/81 (13%)

Query: 16 IYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRS---------FGYVDFFPSSHKSL 66
          ++V  L  K T++ L K F   G V++V I + K            +G+V+F   S ++ 
Sbjct: 3  LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEF--KSKEAA 60

Query: 67 SKLFSTYNGCVWKGGRLRLER 87
           K      G V  G  L L+ 
Sbjct: 61 QKALKRLQGTVLDGHALELKL 81

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

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

 Score = 38.7 bits (91), Expect = 5e-04
 Identities = 12/43 (27%), Positives = 25/43 (58%), Gaps = 2/43 (4%)

Query: 16 IYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDF 58
          ++VGGLG   +  +L + F   G ++ +D     GR++ Y+++
Sbjct: 1  LWVGGLGPWTSLAELEREFDRFGAIRRIDYD--PGRNYAYIEY 41

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

 Score = 38.7 bits (91), Expect = 5e-04
 Identities = 20/49 (40%), Positives = 27/49 (55%), Gaps = 8/49 (16%)

Query: 16 IYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV----RTKGRS--FGYVDF 58
          +++GGL    T++ L + FS  GEV  VD V       GRS  FG+V F
Sbjct: 1  LFIGGLSWDTTEESLREYFSKYGEV--VDCVIMKDPITGRSRGFGFVTF 47

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

 Score = 38.1 bits (89), Expect = 0.001
 Identities = 22/77 (28%), Positives = 35/77 (45%), Gaps = 10/77 (12%)

Query: 16 IYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV------RTKGRSFGYVDFFPSSHKSLSKL 69
          ++VG L     +D + + F   GE+ +V +       R KG  FGYV+F  SS ++    
Sbjct: 1  LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKG--FGYVEF--SSQEAAQAA 56

Query: 70 FSTYNGCVWKGGRLRLE 86
               G    G  +RL+
Sbjct: 57 LDALGGTDLLGRPVRLD 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|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 38.1 bits (89), Expect = 0.001
 Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 6/75 (8%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK--GRSFGY--VDFFPSSHKSLSKL 69
          T + V  L + +T ++L  +F ++G +++  IVR +  G+S GY  VD+         K 
Sbjct: 1  TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDY--VDENDAQKA 58

Query: 70 FSTYNGCVWKGGRLR 84
           +T NG   +  RL+
Sbjct: 59 INTLNGFEIRNKRLK 73

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|241064 cd12620, RRM3_TIAR, RNA recognition motif 3 in nucleolysin TIAR and similar proteins

 Score = 37.7 bits (87), Expect = 0.002
 Identities = 20/75 (26%), Positives = 38/75 (50%), Gaps = 4/75 (5%)

Query: 16 IYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNG 75
          +Y GG+   +T+  + + FS  G++  + +   KG SF  + F  S+H+S +    + NG
Sbjct: 3  VYCGGIASGLTEQLMRQTFSPFGQIMEIRVFPEKGYSF--IRF--STHESAAHAIVSVNG 58

Query: 76 CVWKGGRLRLERAKE 90
             +G  ++    KE
Sbjct: 59 TTIEGHVVKCYWGKE 73

This subgroup corresponds to the RRM3 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 = 73

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

 Score = 37.1 bits (87), Expect = 0.002
 Identities = 17/47 (36%), Positives = 26/47 (55%), Gaps = 4/47 (8%)

Query: 16 IYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKG----RSFGYVDF 58
          ++VG L   V  D L ++FS+ G VK VD+   +     R + YV+F
Sbjct: 1  LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEF 47

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

 Score = 37.3 bits (87), Expect = 0.002
 Identities = 27/81 (33%), Positives = 39/81 (48%), Gaps = 10/81 (12%)

Query: 15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT-KGRS--FGYVDF--FPSSHKSLSKL 69
           ++VG L      DDL + F   GEV  V I +   GRS  FG+V+F     + K+L K 
Sbjct: 1  TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALEK- 59

Query: 70 FSTYNGCVWKGGRLRLERAKE 90
              +G    G  +R++ A E
Sbjct: 60 ----SGEELLGREIRVDLATE 76

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

>gnl|CDD|241125 cd12681, RRM_SKAR, RNA recognition motif in S6K1 Aly/REF-like target (SKAR) and similar proteins

 Score = 37.2 bits (87), Expect = 0.002
 Identities = 14/35 (40%), Positives = 23/35 (65%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT 48
          TR+ V  L   VT+DD+ ++FS++G +K   +VR 
Sbjct: 1  TRLVVSNLHPSVTEDDIVELFSAIGALKRARLVRP 35

This subgroup corresponds to the RRM of SKAR, also termed polymerase delta-interacting protein 3 (PDIP3), 46 kDa DNA polymerase delta interaction protein (PDIP46), belonging to the Aly/REF family of RNA binding proteins that have been implicated in coupling transcription with pre-mRNA splicing and nucleo-cytoplasmic mRNA transport. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. SKAR contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Length = 69

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

 Score = 37.5 bits (88), Expect = 0.002
 Identities = 15/46 (32%), Positives = 25/46 (54%), Gaps = 4/46 (8%)

Query: 17 YVGGLGEKVTDDDLAKVFSSLGEVKAV----DIVRTKGRSFGYVDF 58
          YVG L   VT+  L ++FS  G V ++    D++  +   + YV+F
Sbjct: 3  YVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNF 48

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|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 = 36.8 bits (86), Expect = 0.003
 Identities = 13/48 (27%), Positives = 27/48 (56%), Gaps = 4/48 (8%)

Query: 16 IYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RTKGRS--FGYVDFF 59
          ++VG +    T++ L ++FS +G V +  +V  R  G+   +G+ +F 
Sbjct: 1  VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFE 48

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

 Score = 37.0 bits (86), Expect = 0.003
 Identities = 19/71 (26%), Positives = 32/71 (45%), Gaps = 7/71 (9%)

Query: 16 IYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVR----TKGRSFGYVDFFPSSHKSLSKLFS 71
          I+VG L  ++  + L   F+  GE+    +V+     K + +G+V F     +       
Sbjct: 2  IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFV--KKEDAENAIQ 59

Query: 72 TYNGCVWKGGR 82
          + NG  W GGR
Sbjct: 60 SMNG-QWLGGR 69

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|241041 cd12597, RRM1_SRSF1, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 36.7 bits (85), Expect = 0.003
 Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 2/72 (2%)

Query: 15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYN 74
          RIYVG L   +   D+  +F   G ++ +D+   +G  F +V+F     +         +
Sbjct: 1  RIYVGNLPPDIRTKDIEDLFYKYGAIRDIDLKNRRGPPFAFVEF--EDPRDAEDAVYGRD 58

Query: 75 GCVWKGGRLRLE 86
          G  + G RLR+E
Sbjct: 59 GYDYDGYRLRVE 70

This subgroup corresponds to the RRM1 of SRSF1, also termed alternative-splicing factor 1 (ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit. SRSF1 is a splicing regulatory serine/arginine (SR) protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF1 is a shuttling SR protein and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a long glycine-rich spacer, and a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 73

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

 Score = 36.8 bits (85), Expect = 0.003
 Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 5/63 (7%)

Query: 16 IYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV---RTKGRSFGYVDFFPSSHKSLSKLFST 72
          +YVG L  +VT+D L ++F   G V+ V I+     KG ++G+V++  S          T
Sbjct: 1  LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQS--HDAEIALQT 58

Query: 73 YNG 75
           NG
Sbjct: 59 LNG 61

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|241088 cd12644, RRM_CFIm59, RNA recognition motif of pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7) and similar proteins

 Score = 37.2 bits (86), Expect = 0.003
 Identities = 24/83 (28%), Positives = 37/83 (44%), Gaps = 4/83 (4%)

Query: 16 IYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV----RTKGRSFGYVDFFPSSHKSLSKLFS 71
          +YVG      TD  L +V  S+G    V++     R  G+S GY +   +S  S+ KL  
Sbjct: 4  VYVGNFSWWTTDQQLIQVIRSVGVKDVVELKFAENRANGQSKGYAEVVVASENSVHKLLE 63

Query: 72 TYNGCVWKGGRLRLERAKEHYLA 94
             G V  G ++ +  A    L+
Sbjct: 64 LLPGKVLNGEKVDVRPATRQNLS 86

This subgroup corresponds to the RRM of CFIm59. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. The two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. The family includes CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59). CFIm59 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. The N-terminal RRM of CFIm59 mediates the interaction with CFIm25. It also serves to enhance RNA binding and facilitate RNA looping. . Length = 90

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

 Score = 36.8 bits (85), Expect = 0.004
 Identities = 20/58 (34%), Positives = 31/58 (53%), Gaps = 6/58 (10%)

Query: 15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT----KGRSFGYVDFFPSSHKSLSK 68
          +++VGGL   V + DL + FS  G V+  +++      K R FG+V F   +H S  K
Sbjct: 1  KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYF--QNHDSADK 56

This subgroup corresponds to the RRM2 of hnRNP A0, a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

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

 Score = 36.6 bits (85), Expect = 0.004
 Identities = 24/67 (35%), Positives = 35/67 (52%), Gaps = 6/67 (8%)

Query: 15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAV----DIVRTKGRSFGYVDFFP--SSHKSLSK 68
          +I+VGGL   VT+ DL K FS  G V  V    D  + + R FG++ F    S  + +++
Sbjct: 4  KIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVNE 63

Query: 69 LFSTYNG 75
           F   NG
Sbjct: 64 HFHDING 70

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|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 = 36.8 bits (85), Expect = 0.004
 Identities = 15/48 (31%), Positives = 27/48 (56%), Gaps = 4/48 (8%)

Query: 15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVR----TKGRSFGYVDF 58
          ++++GGL     +  L +VFS  G++  V +V+     + R FG+V F
Sbjct: 2  KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTF 49

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

 Score = 36.3 bits (84), Expect = 0.004
 Identities = 19/48 (39%), Positives = 28/48 (58%), Gaps = 4/48 (8%)

Query: 15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKG----RSFGYVDF 58
          +I+VGGL    T+DD+ K FS  G+V+   ++  K     R FG+V F
Sbjct: 1  KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTF 48

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	800
PLN03213	759	repressor of silencing 3; Provisional	100.0
PLN03213	759	repressor of silencing 3; Provisional	100.0
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.8
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.76
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.75
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.73
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.68
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.68
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.68
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.65
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.64
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.63
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.59
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.58
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.58
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.54
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.53
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.52
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.5
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.47
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.43
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.41
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.41
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.4
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.4
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.38
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.31
PLN03120	260	nucleic acid binding protein; Provisional	99.28
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.27
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.23
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.23
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.22
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.22
smart00362	72	RRM_2 RNA recognition motif.	99.21
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.21
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.19
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.17
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.17
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.17
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.16
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.14
KOG0122	270	consensus Translation initiation factor 3, subunit	99.13
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.13
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.12
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.11
smart00360	71	RRM RNA recognition motif.	99.08
PLN03121	243	nucleic acid binding protein; Provisional	99.08
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.06
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	98.99
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	98.95
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.95
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	98.92
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	98.91
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	98.9
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	98.9
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	98.9
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	98.85
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.81
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	98.74
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	98.71
smart00361	70	RRM_1 RNA recognition motif.	98.65
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.63
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	98.59
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	98.59
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.54
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.53
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	98.51
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.51
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.48
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.42
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.41
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.39
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	98.35
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	98.34
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.27
KOG0151	877	consensus Predicted splicing regulator, contains R	98.19
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	98.17
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.15
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.14
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.09
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	98.01
KOG0533	243	consensus RRM motif-containing protein [RNA proces	97.97
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	97.95
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	97.91
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	97.83
KOG0226	290	consensus RNA-binding proteins [General function p	97.75
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	97.66
KOG4660	549	consensus Protein Mei2, essential for commitment t	97.63
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	97.6
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	97.56
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.0
KOG1457	284	consensus RNA binding protein (contains RRM repeat	96.94
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	96.92
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	96.7
KOG4210	285	consensus Nuclear localization sequence binding pr	96.67
KOG4210	285	consensus Nuclear localization sequence binding pr	96.57
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	96.57
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	96.4
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	96.21
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	96.21
KOG0226	290	consensus RNA-binding proteins [General function p	96.2
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	96.07
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	96.01
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	95.97
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	95.77
KOG1548	382	consensus Transcription elongation factor TAT-SF1	95.38
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	95.29
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	95.28
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	95.05
KOG3152	278	consensus TBP-binding protein, activator of basal	94.64
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	94.39
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	94.33
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	94.27
KOG1995	351	consensus Conserved Zn-finger protein [General fun	94.07
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	93.94
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	93.26
smart00361	70	RRM_1 RNA recognition motif.	93.23
smart00360	71	RRM RNA recognition motif.	93.0
KOG0122	270	consensus Translation initiation factor 3, subunit	92.89
KOG2314	698	consensus Translation initiation factor 3, subunit	92.61
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	92.53
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	92.4
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	92.32
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	92.1
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	92.09
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	91.86
KOG1855	484	consensus Predicted RNA-binding protein [General f	91.8
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	91.51
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	91.16
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	90.9
COG0724	306	RNA-binding proteins (RRM domain) [General functio	90.62
PLN03120	260	nucleic acid binding protein; Provisional	90.45
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	90.04
smart00362	72	RRM_2 RNA recognition motif.	89.92
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	89.64
KOG2068	327	consensus MOT2 transcription factor [Transcription	89.39
KOG1996	378	consensus mRNA splicing factor [RNA processing and	88.97
KOG4207	256	consensus Predicted splicing factor, SR protein su	88.89
PLN03121	243	nucleic acid binding protein; Provisional	88.45
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	87.74
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	87.38
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	86.61
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	85.94
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	85.19
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	84.71
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	83.95
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	83.03
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	82.72
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	81.99
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	81.44
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	80.08

>PLN03213 repressor of silencing 3; Provisional

Probab=100.00  E-value=4e-101  Score=830.29  Aligned_cols=346  Identities=47%  Similarity=0.729  Sum_probs=305.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEeccCCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEeccch
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKEH   91 (800)
Q Consensus        12 qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRdTGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~AKpr   91 (800)
                      ...+||||||++.+++++|+.+|..||.|.+|.|+|.+|||||||+|...+..++.+||..|||+.|+||.|+|..|+|+
T Consensus         9 ~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRETGRGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAKP~   88 (759)
T PLN03213          9 GGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKGRSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAKEH   88 (759)
T ss_pred             cceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecccCCceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeeccHH
Confidence            45899999999999999999999999999999999999999999999973347899999999999999999999999999


Q ss_pred             hhHHHhhhHHHHhhhhCCCCCCCCCCCCCCCcccCCCCCCCCCcchhhcccccCccceeeeccCCCCCcccccccccCC-
Q 003717           92 YLARLKREWAEDDAQLVNPPVTDSVAPDNKDATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPFCGTGKHKYSFQRVEAP-  170 (800)
Q Consensus        92 ~~~RlkrEraq~rak~~~sp~sD~Vd~~~~kl~is~~Lkksvdesd~LreyFskyGKVKsVp~pgTGK~KYGF~~ve~P-  170 (800)
                      |+.|++++|+++...      .+    . .     ..+.+...+..+|++||+++|+|+.+||.+||||||.|+++++| 
T Consensus        89 YLeRLkrEReea~s~------~~----~-~-----~kl~k~~~e~~qLnifFPrLrKvKslPfsGTGKHkYSFr~ieVp~  152 (759)
T PLN03213         89 YLARLKREWEAASST------SD----N-T-----IKAPSDSPPATHLNIFFPRLRKVKAMPLSGTGKHKYSFQRVPLSS  152 (759)
T ss_pred             HHHHHHHHHHHhhcc------cc----c-c-----ccccccCCccceeeEeccccccccccccCCCccceeeeeeccCCC
Confidence            999999998876311      11    0 0     11233344448999999999999999999999999999999999 


Q ss_pred             CCCcccccccchhhhhhhhccCccccCCCCccccchhhhcCcccchHHHHHHhHHHHHHhhhhcccCCCCCCCCcccccc
Q 003717          171 PLPKYFCDCEEHSAAFHAAEGKQIHHPAAGQEEIHDMEELGASVINEEELNLMNSVMNKLFERENVSNAGLSGTELTNYE  250 (800)
Q Consensus       171 s~pV~F~sfEea~aA~eAmNG~~i~n~n~~q~~i~~~ee~~gsg~~~~e~n~MnsVmnklfeke~vs~~~~~~~~~d~~~  250 (800)
                      |+|+||||||+||.++.+....|+|          .|++|+| |+|++|+|+|||||||||+|||+++            
T Consensus       153 slP~HFCDCEEH~gp~~~pk~~~~~----------~~e~~~~-g~~~eE~niMNSVMNKLFEken~~n------------  209 (759)
T PLN03213        153 SLPKSFCDCEEHSNNSLTPREIHLH----------DLEALNV-GRNEAEVNVMNSVMNKLFEKNNIDI------------  209 (759)
T ss_pred             CCCccccchhhccCCCCChhhcccc----------chhhhcc-cccHHHHHHHHHHHHHHHhhhcccc------------
Confidence            9999999999999987666555554          5699999 9999999999999999999999877            


Q ss_pred             cCcccccccccCCCCCCcccccccCcEEEEeecCCccccccccccccccccccccccccccccccccccccchhhhhccc
Q 003717          251 RNSYNFIGDLQIGGNEVDSVADEYNLVINAVSGGNNRMVLSRCQEKTTILPTNKKLTLSEARTSKDRSAQSLPREQKKND  330 (800)
Q Consensus       251 ~~s~~~~d~~~~~e~e~~~~~~~~~lvin~~~~~~~~~s~~~~~e~~~i~~~~~~s~~n~~~~s~~~~~~~~~~~~k~~~  330 (800)
                                +++||  +.++|+|||||||+++ +++|+    +++++| +++|++|||+||+++|+|+|    .||+|+
T Consensus       210 ----------~~~en--e~e~D~DnLIiNv~s~-~~~~a----~ele~i-s~~~ks~~N~~~~sed~p~e----~~k~~~  267 (759)
T PLN03213        210 ----------AEEDN--EIEADQDNLIINVASS-GNDMD----SALDKL-SRKRKSILNEKTPSEEGYSE----GRKGNH  267 (759)
T ss_pred             ----------ccccc--cccccccceEEeeccc-cchhH----HHHHHh-hhhhHhhhccccccccCCcc----cccccc
Confidence                      46777  4568999999999999 89998    788888 79999999999999999994    569999


Q ss_pred             cchhhhccccccchh----hhhcCCC-CCCcccccCCCCCCCccCcccccccccccccCCcccccccchhhhccCCCCCc
Q 003717          331 LLRSKKRKSLHNDEI----LMAASPL-DDMNVQTNMNKPSTPLATQHAETDSGVRKSTASHSWSQKMSWKALVGDKDSRA  405 (800)
Q Consensus       331 ~~~~kkrk~~~~~e~----~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~sw~qk~sw~~l~~~~~~~~  405 (800)
                      ++++||||+||++|+    +.+++|+ +|+++||+.+..+.|++  ..    ++.+++++||||||||||+|||++||++
T Consensus       268 ~~s~KKRksls~~ES~~n~~~s~~~~~~K~s~q~p~~~~g~~s~--t~----el~g~~~~vSWSQKSSWreLvg~~~nn~  341 (759)
T PLN03213        268 IHPSKKRQTISLEESGRQESSQAIREKKKPSEVVPDKSLDEPSR--TK----DLEQSIDNISWSQKSSWKSLMANGNSND  341 (759)
T ss_pred             cccchhccccccCccCCcceeeecccCCCccccccccccccccC--Cc----cccccccCcchhhcchHHHHhccCCCCc
Confidence            999999999999999    8899999 99999999999666666  33    3336999999999999999999999999


Q ss_pred             ceecccCCCCCChhhhccC
Q 003717          406 FSVSNILPSDASTEEADNG  424 (800)
Q Consensus       406 ~~~s~~~p~~~s~~~~~~~  424 (800)
                      ||||+||||++|++++.-.
T Consensus       342 fsiS~~lPg~~S~k~~Q~~  360 (759)
T PLN03213        342 FSVSSFLPGVGSSKAVQPA  360 (759)
T ss_pred             cchhhhcCCCCcccccCCC
Confidence            9999999999999986543

>PLN03213 repressor of silencing 3; Provisional

Probab=100.00  E-value=5.8e-35  Score=317.64  Aligned_cols=135  Identities=21%  Similarity=0.290  Sum_probs=123.8

Q ss_pred             cCccceeeeccccCccccccccccccccccccccccccCCCCcccCCCccccccccc----cccccccccccccccCCce
Q 003717          437 ESDDLMINVVSKKKPKMALSSSQKWETTSTTYRKSVSNEDNNTTKDRPIQQEKSTLP----SKKKRKSVIDDESDKNKSV  512 (800)
Q Consensus       437 ~~d~l~~n~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~l~----~~kkrks~~~~e~~~n~~~  512 (800)
                      .-|||||||+|+|| +||    ++||+|++||++||  |++|+++|+|+|.   ++|    ++||||+|+++||++|+++
T Consensus       219 D~DnLIiNv~s~~~-~~a----~ele~is~~~ks~~--N~~~~sed~p~e~---~k~~~~~s~KKRksls~~ES~~n~~~  288 (759)
T PLN03213        219 DQDNLIINVASSGN-DMD----SALDKLSRKRKSIL--NEKTPSEEGYSEG---RKGNHIHPSKKRQTISLEESGRQESS  288 (759)
T ss_pred             cccceEEeeccccc-hhH----HHHHHhhhhhHhhh--ccccccccCCccc---ccccccccchhccccccCccCCccee
Confidence            34999999999999 999    99999999999999  9999999999998   666    8999999999999999999


Q ss_pred             eeccC-CCCcccccc-CCCCCCCCCccCcchhhhcccccCCcCcCCccceeecCCCCCcccccccCCCCchhhhhhc
Q 003717          513 HTVPE-TDGCAQTYT-ESQMPTGPQLVEPESVVEQSISDHSESKKPSQRVVIGSKGNDESSVSNVLPDNSAKEEQRV  587 (800)
Q Consensus       513 ~~~~~-~~~~~q~~~-~~~~~~~~q~~e~~~~~~~~~~~~s~s~k~s~r~~~g~~~n~~~~~s~~~p~~~~~~~~~~  587 (800)
                      +++|+ +|++|||+. +.++|++  +.|++    +++++||||||||||||||++|||+||||+||||+++.++||.
T Consensus       289 s~~~~~~K~s~q~p~~~~g~~s~--t~el~----g~~~~vSWSQKSSWreLvg~~~nn~fsiS~~lPg~~S~k~~Q~  359 (759)
T PLN03213        289 QAIREKKKPSEVVPDKSLDEPSR--TKDLE----QSIDNISWSQKSSWKSLMANGNSNDFSVSSFLPGVGSSKAVQP  359 (759)
T ss_pred             eecccCCCccccccccccccccC--Ccccc----ccccCcchhhcchHHHHhccCCCCccchhhhcCCCCcccccCC
Confidence            99999 999999999 5555555  33433    6999999999999999999999999999999999999999875

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.80  E-value=3e-19  Score=191.87  Aligned_cols=164  Identities=20%  Similarity=0.275  Sum_probs=132.9

Q ss_pred             cCCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc--C--CCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEE
Q 003717           11 EEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--K--GRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLE   86 (800)
Q Consensus        11 ~qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd--T--GRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe   86 (800)
                      ...++|||+|||+++|+++|+++|+.||.|++|+|+++  +  .+|||||+|.+  .++|.+|+..|||..|.+++|+|.
T Consensus       105 ~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~--~e~A~~Ai~~LnG~~l~gr~i~V~  182 (346)
T TIGR01659       105 NSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGS--EADSQRAIKNLNGITVRNKRLKVS  182 (346)
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEcc--HHHHHHHHHHcCCCccCCceeeee
Confidence            35689999999999999999999999999999999854  3  37999999997  999999999999999999999999


Q ss_pred             eccchhhHHHhhhHHHHhhhhCCCCCCCCCCCCCCCcccCCCCCCCCCcchhhcccccCcccee---eeccCCCCCcc-c
Q 003717           87 RAKEHYLARLKREWAEDDAQLVNPPVTDSVAPDNKDATRLDTPKKLLDKDKKLNIFFPRLRKVK---TLPFCGTGKHK-Y  162 (800)
Q Consensus        87 ~AKpr~~~RlkrEraq~rak~~~sp~sD~Vd~~~~kl~is~~Lkksvdesd~LreyFskyGKVK---sVp~pgTGK~K-Y  162 (800)
                      +|++...                       .....++++.+ |+..+++ ++|+.+|.+||.|.   +++++.+|+++ |
T Consensus       183 ~a~p~~~-----------------------~~~~~~lfV~n-Lp~~vte-e~L~~~F~~fG~V~~v~i~~d~~tg~~kG~  237 (346)
T TIGR01659       183 YARPGGE-----------------------SIKDTNLYVTN-LPRTITD-DQLDTIFGKYGQIVQKNILRDKLTGTPRGV  237 (346)
T ss_pred             ccccccc-----------------------ccccceeEEeC-CCCcccH-HHHHHHHHhcCCEEEEEEeecCCCCccceE
Confidence            9875310                       00122355544 6777766 89999999999864   45667799987 7


Q ss_pred             ccccccCCCCCcccccccchhhhhhhhccCccccCCCCccccchhhhcC
Q 003717          163 SFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPAAGQEEIHDMEELG  211 (800)
Q Consensus       163 GF~~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n~~q~~i~~~ee~~  211 (800)
                      +|         |.|.+.+++..|+++||+..+.. .+..+.|+.++++.
T Consensus       238 aF---------V~F~~~e~A~~Ai~~lng~~~~g-~~~~l~V~~a~~~~  276 (346)
T TIGR01659       238 AF---------VRFNKREEAQEAISALNNVIPEG-GSQPLTVRLAEEHG  276 (346)
T ss_pred             EE---------EEECCHHHHHHHHHHhCCCccCC-CceeEEEEECCccc
Confidence            77         99999999999999999887643 23456666666654

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.76  E-value=3.5e-18  Score=178.04  Aligned_cols=147  Identities=20%  Similarity=0.329  Sum_probs=121.6

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc--C--CCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEec
Q 003717           13 QTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--K--GRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERA   88 (800)
Q Consensus        13 srTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd--T--GRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~A   88 (800)
                      ..+|||||||+.+++++|+++|+.||+|.+|+|+++  +  .+|||||+|.+  .++|.+|+..|||..|.|++|+|.++
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   80 (352)
T TIGR01661         3 KTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVR--PEDAEKAVNSLNGLRLQNKTIKVSYA   80 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECc--HHHHHHHHhhcccEEECCeeEEEEee
Confidence            479999999999999999999999999999999954  3  37999999997  99999999999999999999999998


Q ss_pred             cchhhHHHhhhHHHHhhhhCCCCCCCCCCCCCCCcccCCCCCCCCCcchhhcccccCccceee---eccCCCCCcc-ccc
Q 003717           89 KEHYLARLKREWAEDDAQLVNPPVTDSVAPDNKDATRLDTPKKLLDKDKKLNIFFPRLRKVKT---LPFCGTGKHK-YSF  164 (800)
Q Consensus        89 Kpr~~~RlkrEraq~rak~~~sp~sD~Vd~~~~kl~is~~Lkksvdesd~LreyFskyGKVKs---Vp~pgTGK~K-YGF  164 (800)
                      ++....                       .....+++.+ |+..+++ ++|+.+|..||.|..   +.+..+|.++ |||
T Consensus        81 ~~~~~~-----------------------~~~~~l~v~~-l~~~~~~-~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~f  135 (352)
T TIGR01661        81 RPSSDS-----------------------IKGANLYVSG-LPKTMTQ-HELESIFSPFGQIITSRILSDNVTGLSKGVGF  135 (352)
T ss_pred             cccccc-----------------------cccceEEECC-ccccCCH-HHHHHHHhccCCEEEEEEEecCCCCCcCcEEE
Confidence            764210                       0012345543 5677766 899999999999754   4445677776 777


Q ss_pred             ccccCCCCCcccccccchhhhhhhhccCccc
Q 003717          165 QRVEAPPLPKYFCDCEEHSAAFHAAEGKQIH  195 (800)
Q Consensus       165 ~~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~  195 (800)
                               |.|.+.+++..|+..|||..+.
T Consensus       136 ---------v~f~~~~~A~~ai~~l~g~~~~  157 (352)
T TIGR01661       136 ---------IRFDKRDEADRAIKTLNGTTPS  157 (352)
T ss_pred             ---------EEECCHHHHHHHHHHhCCCccC
Confidence                     8999999999999999998664

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

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

Probab=99.75  E-value=1.8e-18  Score=171.88  Aligned_cols=154  Identities=22%  Similarity=0.338  Sum_probs=129.2

Q ss_pred             hccCCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc----CCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEE
Q 003717            9 EVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT----KGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLR   84 (800)
Q Consensus         9 Ev~qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd----TGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~Lr   84 (800)
                      +.++..+||||||+..++++.|+++|-+.|+|+++.++++    .++|||||+|.+  +++|+.|+..||+..|.||+|+
T Consensus         5 ~rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~--eedadYAikiln~VkLYgrpIr   82 (203)
T KOG0131|consen    5 ERNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRT--EEDADYAIKILNMVKLYGRPIR   82 (203)
T ss_pred             ccCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEec--hhhhHHHHHHHHHHHhcCceeE
Confidence            4567799999999999999999999999999999999854    358999999998  9999999999999999999999


Q ss_pred             EEeccchhhHHHhhhHHHHhhhhCCCCCCCCCCCCCCCcccCCCCCCCCCcchhhcccccCccce----eeeccCCCCCc
Q 003717           85 LERAKEHYLARLKREWAEDDAQLVNPPVTDSVAPDNKDATRLDTPKKLLDKDKKLNIFFPRLRKV----KTLPFCGTGKH  160 (800)
Q Consensus        85 Ve~AKpr~~~RlkrEraq~rak~~~sp~sD~Vd~~~~kl~is~~Lkksvdesd~LreyFskyGKV----KsVp~pgTGK~  160 (800)
                      |..|..+..                     ..+. ..++++++ |.+.+++ ..|...|+.||.+    +++|++.||.+
T Consensus        83 v~kas~~~~---------------------nl~v-ganlfvgN-Ld~~vDe-~~L~dtFsafG~l~~~P~i~rd~~tg~~  138 (203)
T KOG0131|consen   83 VNKASAHQK---------------------NLDV-GANLFVGN-LDPEVDE-KLLYDTFSAFGVLISPPKIMRDPDTGNP  138 (203)
T ss_pred             EEecccccc---------------------cccc-cccccccc-cCcchhH-HHHHHHHHhccccccCCcccccccCCCC
Confidence            998762210                     0111 12455544 5667766 7888888888884    67899999999


Q ss_pred             c-cccccccCCCCCcccccccchhhhhhhhccCccccC
Q 003717          161 K-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHP  197 (800)
Q Consensus       161 K-YGF~~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~  197 (800)
                      + |||         +.|.+||.+++|+++|||+++|++
T Consensus       139 ~~~g~---------i~~~sfeasd~ai~s~ngq~l~nr  167 (203)
T KOG0131|consen  139 KGFGF---------INYASFEASDAAIGSMNGQYLCNR  167 (203)
T ss_pred             CCCeE---------EechhHHHHHHHHHHhccchhcCC
Confidence            8 665         899999999999999999999997

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

Probab=99.73  E-value=8.5e-18  Score=191.67  Aligned_cols=170  Identities=15%  Similarity=0.230  Sum_probs=128.3

Q ss_pred             cCCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc--C--CCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEE
Q 003717           11 EEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--K--GRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLE   86 (800)
Q Consensus        11 ~qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd--T--GRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe   86 (800)
                      ....+||||||++.+++++|+++|.+||.|.+|+|+++  +  .+|||||+|.+  .++|..|+..|||..|+||.|+|.
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s--~e~A~~Ai~~lnG~~i~GR~IkV~  182 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEV--PEAAQLALEQMNGQMLGGRNIKVG  182 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCc--HHHHHHHHHhcCCeEEecceeeec
Confidence            34679999999999999999999999999999999854  3  47999999997  999999999999999999999998


Q ss_pred             eccchhhHHHhhhHHHHhhhhCCCCCCCCCCCCCCCcccCCCCCCCCCcchhhcccccCccceeee---ccCCCCCcc-c
Q 003717           87 RAKEHYLARLKREWAEDDAQLVNPPVTDSVAPDNKDATRLDTPKKLLDKDKKLNIFFPRLRKVKTL---PFCGTGKHK-Y  162 (800)
Q Consensus        87 ~AKpr~~~RlkrEraq~rak~~~sp~sD~Vd~~~~kl~is~~Lkksvdesd~LreyFskyGKVKsV---p~pgTGK~K-Y  162 (800)
                      +.......+   .   .... .   ..  .......+++++ |...+++ ++|+.+|..||.|..+   +++.+|+++ |
T Consensus       183 rp~~~p~a~---~---~~~~-~---~~--~~~~~~rLfVgn-Lp~~vte-edLk~lFs~FG~I~svrl~~D~~tgksKGf  248 (612)
T TIGR01645       183 RPSNMPQAQ---P---IIDM-V---QE--EAKKFNRIYVAS-VHPDLSE-TDIKSVFEAFGEIVKCQLARAPTGRGHKGY  248 (612)
T ss_pred             ccccccccc---c---cccc-c---cc--cccccceEEeec-CCCCCCH-HHHHHHHhhcCCeeEEEEEecCCCCCcCCe
Confidence            643221000   0   0000 0   00  011123455544 6777766 8999999999997654   556788887 7


Q ss_pred             ccccccCCCCCcccccccchhhhhhhhccCccccCCCCccccchhh
Q 003717          163 SFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPAAGQEEIHDME  208 (800)
Q Consensus       163 GF~~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n~~q~~i~~~e  208 (800)
                      ||         |.|.+.+++..|+++|||..+   +|...+|.++-
T Consensus       249 GF---------VeFe~~e~A~kAI~amNg~el---gGr~LrV~kAi  282 (612)
T TIGR01645       249 GF---------IEYNNLQSQSEAIASMNLFDL---GGQYLRVGKCV  282 (612)
T ss_pred             EE---------EEECCHHHHHHHHHHhCCCee---CCeEEEEEecC
Confidence            77         899999999999999998865   35556665433

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.

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

Probab=99.68  E-value=1.3e-16  Score=178.05  Aligned_cols=147  Identities=24%  Similarity=0.349  Sum_probs=119.3

Q ss_pred             EEEEeCCCCCCCHHHHHHhhhcCCceeEEEEeccC----CCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEeccc
Q 003717           15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK----GRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKE   90 (800)
Q Consensus        15 TLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRdT----GRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~AKp   90 (800)
                      .|||||||+++|+++|+++|++||.|.+|+|+++.    .+|||||+|.+  .++|.+|+..||+..|.|+.|+|.++..
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~--~~~A~~Al~~ln~~~i~gk~i~i~~s~~   79 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQN--PADAERALETMNFKRLGGKPIRIMWSQR   79 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECC--HHHHHHHHHHhCCCEECCeeEEeecccc
Confidence            79999999999999999999999999999999652    36999999997  9999999999999999999999998753


Q ss_pred             hhhHHHhhhHHHHhhhhCCCCCCCCCCCCCCCcccCCCCCCCCCcchhhcccccCccceeeecc--CCCCCcc-cccccc
Q 003717           91 HYLARLKREWAEDDAQLVNPPVTDSVAPDNKDATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPF--CGTGKHK-YSFQRV  167 (800)
Q Consensus        91 r~~~RlkrEraq~rak~~~sp~sD~Vd~~~~kl~is~~Lkksvdesd~LreyFskyGKVKsVp~--pgTGK~K-YGF~~v  167 (800)
                      ....+                     .....++++.+ |..+++. +.|+.+|+.||.|..+..  ..+|+++ |||   
T Consensus        80 ~~~~~---------------------~~~~~~vfV~n-Lp~~~~~-~~L~~~F~~~G~i~~~~i~~~~~g~skg~af---  133 (562)
T TIGR01628        80 DPSLR---------------------RSGVGNIFVKN-LDKSVDN-KALFDTFSKFGNILSCKVATDENGKSRGYGF---  133 (562)
T ss_pred             ccccc---------------------ccCCCceEEcC-CCccCCH-HHHHHHHHhcCCcceeEeeecCCCCcccEEE---
Confidence            21000                     00122355544 5777766 899999999999765544  2467776 777   


Q ss_pred             cCCCCCcccccccchhhhhhhhccCccc
Q 003717          168 EAPPLPKYFCDCEEHSAAFHAAEGKQIH  195 (800)
Q Consensus       168 e~Ps~pV~F~sfEea~aA~eAmNG~~i~  195 (800)
                            |.|.+.+++..|++.+||..+.
T Consensus       134 ------V~F~~~e~A~~Ai~~lng~~~~  155 (562)
T TIGR01628       134 ------VHFEKEESAKAAIQKVNGMLLN  155 (562)
T ss_pred             ------EEECCHHHHHHHHHHhcccEec
Confidence                  8999999999999999987664

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

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

Probab=99.68  E-value=2.8e-16  Score=170.13  Aligned_cols=168  Identities=19%  Similarity=0.309  Sum_probs=126.8

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc--C--CCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEe
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--K--GRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLER   87 (800)
Q Consensus        12 qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd--T--GRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~   87 (800)
                      ..++|||+|||+.+++++|+++|++||.|..|.++++  +  .+|||||+|.+  .++|.+||. |+|..|.|++|.|..
T Consensus        88 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~--~e~A~~Al~-l~g~~~~g~~i~v~~  164 (457)
T TIGR01622        88 DDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYD--VESVIKALA-LTGQMLLGRPIIVQS  164 (457)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECC--HHHHHHHHH-hCCCEECCeeeEEee
Confidence            4579999999999999999999999999999999954  2  37999999997  999999996 999999999999987


Q ss_pred             ccchhhHHHhhhHHHHhhhhCCCCCCCCCCCCCCCcccCCCCCCCCCcchhhcccccCccceee---eccCCCCCcc-cc
Q 003717           88 AKEHYLARLKREWAEDDAQLVNPPVTDSVAPDNKDATRLDTPKKLLDKDKKLNIFFPRLRKVKT---LPFCGTGKHK-YS  163 (800)
Q Consensus        88 AKpr~~~RlkrEraq~rak~~~sp~sD~Vd~~~~kl~is~~Lkksvdesd~LreyFskyGKVKs---Vp~pgTGK~K-YG  163 (800)
                      +.......      .....  .   .....+....+++++ |...+++ ++|+.+|..||.|..   ++++.+|+++ ||
T Consensus       165 ~~~~~~~~------~~~~~--~---~~~~~p~~~~l~v~n-l~~~~te-~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~a  231 (457)
T TIGR01622       165 SQAEKNRA------AKAAT--H---QPGDIPNFLKLYVGN-LHFNITE-QELRQIFEPFGDIEDVQLHRDPETGRSKGFG  231 (457)
T ss_pred             cchhhhhh------hhccc--c---cCCCCCCCCEEEEcC-CCCCCCH-HHHHHHHHhcCCeEEEEEEEcCCCCccceEE
Confidence            65432110      00000  0   000111133455544 5677766 899999999999754   4556788887 77


Q ss_pred             cccccCCCCCcccccccchhhhhhhhccCccccCCCCccccchh
Q 003717          164 FQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPAAGQEEIHDM  207 (800)
Q Consensus       164 F~~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n~~q~~i~~~  207 (800)
                      |         |.|.+.+++..|+..|||..+   .|..+.|..+
T Consensus       232 f---------V~f~~~e~A~~A~~~l~g~~i---~g~~i~v~~a  263 (457)
T TIGR01622       232 F---------IQFHDAEEAKEALEVMNGFEL---AGRPIKVGYA  263 (457)
T ss_pred             E---------EEECCHHHHHHHHHhcCCcEE---CCEEEEEEEc
Confidence            7         899999999999999999655   3555555543

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=99.68  E-value=2.5e-16  Score=164.26  Aligned_cols=172  Identities=20%  Similarity=0.317  Sum_probs=121.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc----CCCcEEEEEecCCCHHHHHHHHHhcCCcEeCC--eEEEE
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT----KGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKG--GRLRL   85 (800)
Q Consensus        12 qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd----TGRGFGFVEFeS~D~EdAekAIe~LNG~eLdG--R~LrV   85 (800)
                      ...+|||+|||..+++++|+.+|++||.|..+.++.+    ..+|||||+|.+  .++|..|+..|||..+.|  ++|.|
T Consensus        88 ~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~--~~~A~~ai~~l~g~~~~g~~~~i~v  165 (352)
T TIGR01661        88 KGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDK--RDEADRAIKTLNGTTPSGCTEPITV  165 (352)
T ss_pred             ccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECC--HHHHHHHHHHhCCCccCCCceeEEE
Confidence            3568999999999999999999999999999998843    247999999997  999999999999999987  67889


Q ss_pred             EeccchhhHHHhhhHH--H--Hhh----------------------------------------------------hhCC
Q 003717           86 ERAKEHYLARLKREWA--E--DDA----------------------------------------------------QLVN  109 (800)
Q Consensus        86 e~AKpr~~~RlkrEra--q--~ra----------------------------------------------------k~~~  109 (800)
                      .+|.............  .  ...                                                    ....
T Consensus       166 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  245 (352)
T TIGR01661       166 KFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRAS  245 (352)
T ss_pred             EECCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhhhcccccccccccCC
Confidence            8885432100000000  0  000                                                    0000


Q ss_pred             CCCCCC----C--CCCC-------CCcccCCCCCCCCCcchhhcccccCccceee---eccCCCCCcc-cccccccCCCC
Q 003717          110 PPVTDS----V--APDN-------KDATRLDTPKKLLDKDKKLNIFFPRLRKVKT---LPFCGTGKHK-YSFQRVEAPPL  172 (800)
Q Consensus       110 sp~sD~----V--d~~~-------~kl~is~~Lkksvdesd~LreyFskyGKVKs---Vp~pgTGK~K-YGF~~ve~Ps~  172 (800)
                      .+..+.    .  ....       ..+++.+ |+..+++ ++|+.+|+.||.|..   ++++.||++| |||        
T Consensus       246 ~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~N-L~~~~~e-~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aF--------  315 (352)
T TIGR01661       246 PPATDGQTAGLAAGAQIAASDGAGYCIFVYN-LSPDTDE-TVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGF--------  315 (352)
T ss_pred             CccccccccccccCCCCCCCCCCCcEEEEeC-CCCCCCH-HHHHHHHHhCCCeEEEEEeEcCCCCCccceEE--------
Confidence            000000    0  0000       0144443 5666655 899999999999754   5566799997 777        


Q ss_pred             CcccccccchhhhhhhhccCcccc
Q 003717          173 PKYFCDCEEHSAAFHAAEGKQIHH  196 (800)
Q Consensus       173 pV~F~sfEea~aA~eAmNG~~i~n  196 (800)
                       |.|.+.+++..|+.+|||..+..
T Consensus       316 -V~F~~~~~A~~Ai~~lnG~~~~g  338 (352)
T TIGR01661       316 -VSMTNYDEAAMAILSLNGYTLGN  338 (352)
T ss_pred             -EEECCHHHHHHHHHHhCCCEECC
Confidence             99999999999999999988743

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

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

Probab=99.65  E-value=6.5e-16  Score=171.15  Aligned_cols=173  Identities=18%  Similarity=0.265  Sum_probs=123.3

Q ss_pred             CCcEEEEeCCCC-CCCHHHHHHhhhcCCceeEEEEeccCCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEeccc
Q 003717           12 EQTRIYVGGLGE-KVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKE   90 (800)
Q Consensus        12 qsrTLFVGNLP~-nVTEEDLrelFSqFG~VksVrVIRdTGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~AKp   90 (800)
                      ...+|||+||++ .+++++|+++|+.||.|..|+++++ .+|||||+|.+  .++|..|+..|||+.|.|++|+|.+++.
T Consensus       274 ~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~-~~g~afV~f~~--~~~A~~Ai~~lng~~l~g~~l~v~~s~~  350 (481)
T TIGR01649       274 PGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKN-KKETALIEMAD--PYQAQLALTHLNGVKLFGKPLRVCPSKQ  350 (481)
T ss_pred             CCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeC-CCCEEEEEECC--HHHHHHHHHHhCCCEECCceEEEEEccc
Confidence            457999999998 6999999999999999999999875 47999999997  9999999999999999999999999865


Q ss_pred             hhhHHHhhhH-H------HHh--hh--hCCCCCC---CCCCCCCCCcccCCCCCCCCCcchhhcccccCccc--eeeecc
Q 003717           91 HYLARLKREW-A------EDD--AQ--LVNPPVT---DSVAPDNKDATRLDTPKKLLDKDKKLNIFFPRLRK--VKTLPF  154 (800)
Q Consensus        91 r~~~RlkrEr-a------q~r--ak--~~~sp~s---D~Vd~~~~kl~is~~Lkksvdesd~LreyFskyGK--VKsVp~  154 (800)
                      ......+... .      .+.  ..  ....+..   ....+....+++.+ |+..+++ ++|+.+|..||.  |..+..
T Consensus       351 ~~~~~~~~~~~~~~~~~~~d~~~~~~~r~~~~~~~~~~~~~~ps~~L~v~N-Lp~~~te-e~L~~lF~~~G~~~i~~ik~  428 (481)
T TIGR01649       351 QNVQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLHLSN-IPLSVSE-EDLKELFAENGVHKVKKFKF  428 (481)
T ss_pred             ccccCCCCCcCcCCCcccccccCCccccCCCcccccccccCCCCcEEEEec-CCCCCCH-HHHHHHHHhcCCccceEEEE
Confidence            4221100000 0      000  00  0000000   00111223444444 5666765 899999999998  544433


Q ss_pred             -C-CCCCcccccccccCCCCCcccccccchhhhhhhhccCccccCC
Q 003717          155 -C-GTGKHKYSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPA  198 (800)
Q Consensus       155 -p-gTGK~KYGF~~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n  198 (800)
                       + .+++.+|||         |.|.+.+++..|+.+|||..+....
T Consensus       429 ~~~~~~~~~~gf---------VeF~~~e~A~~Al~~ln~~~l~~~~  465 (481)
T TIGR01649       429 FPKDNERSKMGL---------LEWESVEDAVEALIALNHHQLNEPN  465 (481)
T ss_pred             ecCCCCcceeEE---------EEcCCHHHHHHHHHHhcCCccCCCC
Confidence             2 234556888         8999999999999999998886553

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).

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

Probab=99.64  E-value=1.1e-15  Score=170.94  Aligned_cols=176  Identities=19%  Similarity=0.326  Sum_probs=130.8

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc---CCCcEEEEEecCCCHHHHHHHHHhcCCcEeC----CeEEE
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT---KGRSFGYVDFFPSSHKSLSKLFSTYNGCVWK----GGRLR   84 (800)
Q Consensus        12 qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd---TGRGFGFVEFeS~D~EdAekAIe~LNG~eLd----GR~Lr   84 (800)
                      ..++|||+||++.+|+++|+++|+.||.|.++.++++   ..+|||||+|.+  .++|.+|+..|||..|.    |+.|.
T Consensus       177 ~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~~g~~~G~afV~F~~--~e~A~~Av~~l~g~~i~~~~~g~~l~  254 (562)
T TIGR01628       177 KFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEK--HEDAAKAVEEMNGKKIGLAKEGKKLY  254 (562)
T ss_pred             CCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECC--HHHHHHHHHHhCCcEecccccceeeE
Confidence            3468999999999999999999999999999999854   237999999997  99999999999999999    99999


Q ss_pred             EEeccchhhHHHhhhHHHHhhhhCCCCCCCCCCCCCCCcccCCCCCCCCCcchhhcccccCccceeeecc--CCCCCcc-
Q 003717           85 LERAKEHYLARLKREWAEDDAQLVNPPVTDSVAPDNKDATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPF--CGTGKHK-  161 (800)
Q Consensus        85 Ve~AKpr~~~RlkrEraq~rak~~~sp~sD~Vd~~~~kl~is~~Lkksvdesd~LreyFskyGKVKsVp~--pgTGK~K-  161 (800)
                      |.++..+........+.........     .......++++.+ |...+++ +.|+.+|..||.|..+..  ..+|+++ 
T Consensus       255 v~~a~~k~er~~~~~~~~~~~~~~~-----~~~~~~~~l~V~n-l~~~~~~-~~L~~~F~~~G~i~~~~i~~d~~g~~~g  327 (562)
T TIGR01628       255 VGRAQKRAEREAELRRKFEELQQER-----KMKAQGVNLYVKN-LDDTVTD-EKLRELFSECGEITSAKVMLDEKGVSRG  327 (562)
T ss_pred             eecccChhhhHHHHHhhHHhhhhhh-----hcccCCCEEEEeC-CCCccCH-HHHHHHHHhcCCeEEEEEEECCCCCcCC
Confidence            9998776433211111111000000     0112233455544 5666766 899999999999765433  2678877 


Q ss_pred             cccccccCCCCCcccccccchhhhhhhhccCccccCCCCccccchhh
Q 003717          162 YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPAAGQEEIHDME  208 (800)
Q Consensus       162 YGF~~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n~~q~~i~~~e  208 (800)
                      |||         |.|.+.+++..|+..|||..+   +|+...|.-+.
T Consensus       328 ~gf---------V~f~~~~~A~~A~~~~~g~~~---~gk~l~V~~a~  362 (562)
T TIGR01628       328 FGF---------VCFSNPEEANRAVTEMHGRML---GGKPLYVALAQ  362 (562)
T ss_pred             eEE---------EEeCCHHHHHHHHHHhcCCee---CCceeEEEecc
Confidence            777         899999999999999999555   46666666443

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

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

Probab=99.63  E-value=1.3e-15  Score=168.82  Aligned_cols=157  Identities=15%  Similarity=0.107  Sum_probs=117.3

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEeccCCCcEEEEEecCCCHHHHHHHHHh--cCCcEeCCeEEEEEeccc
Q 003717           13 QTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFST--YNGCVWKGGRLRLERAKE   90 (800)
Q Consensus        13 srTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRdTGRGFGFVEFeS~D~EdAekAIe~--LNG~eLdGR~LrVe~AKp   90 (800)
                      .+.|||||||+.+++++|+++|++||.|.+|.+++  .+|||||+|.+  .++|.+|+..  +++..|.|++|+|.++..
T Consensus         2 s~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~--~k~~afVef~~--~e~A~~Ai~~~~~~~~~l~g~~l~v~~s~~   77 (481)
T TIGR01649         2 SPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLP--GKRQALVEFED--EESAKACVNFATSVPIYIRGQPAFFNYSTS   77 (481)
T ss_pred             ccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEEC--CCCEEEEEeCc--hHHHHHHHHHhhcCCceEcCeEEEEEecCC
Confidence            47899999999999999999999999999999986  57899999997  9999999987  478999999999999976


Q ss_pred             hhhHHHhhhHHHHhhhhCCCCCCCCCCCCCCCcccCCCCCCCCCcchhhcccccCccceeeecc-CCCCCcccccccccC
Q 003717           91 HYLARLKREWAEDDAQLVNPPVTDSVAPDNKDATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPF-CGTGKHKYSFQRVEA  169 (800)
Q Consensus        91 r~~~RlkrEraq~rak~~~sp~sD~Vd~~~~kl~is~~Lkksvdesd~LreyFskyGKVKsVp~-pgTGK~KYGF~~ve~  169 (800)
                      +...+..     .  . ..  ..... .....+++.+ |...+++ +.|+.+|+.||.|..+.. +..+. .|||     
T Consensus        78 ~~~~~~~-----~--~-~~--~~~~~-~~~~~v~v~n-l~~~vt~-~~L~~~F~~~G~V~~v~i~~~~~~-~~af-----  138 (481)
T TIGR01649        78 QEIKRDG-----N--S-DF--DSAGP-NKVLRVIVEN-PMYPITL-DVLYQIFNPYGKVLRIVTFTKNNV-FQAL-----  138 (481)
T ss_pred             cccccCC-----C--C-cc--cCCCC-CceEEEEEcC-CCCCCCH-HHHHHHHhccCCEEEEEEEecCCc-eEEE-----
Confidence            5322110     0  0 00  00000 0111233333 4556655 899999999999765432 22221 2577     


Q ss_pred             CCCCcccccccchhhhhhhhccCcccc
Q 003717          170 PPLPKYFCDCEEHSAAFHAAEGKQIHH  196 (800)
Q Consensus       170 Ps~pV~F~sfEea~aA~eAmNG~~i~n  196 (800)
                          |.|.+.++|..|+++|||..+..
T Consensus       139 ----Vef~~~~~A~~A~~~Lng~~i~~  161 (481)
T TIGR01649       139 ----VEFESVNSAQHAKAALNGADIYN  161 (481)
T ss_pred             ----EEECCHHHHHHHHHHhcCCcccC
Confidence                99999999999999999999864

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).

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

Probab=99.59  E-value=2e-15  Score=167.91  Aligned_cols=170  Identities=18%  Similarity=0.248  Sum_probs=127.8

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEeccC----CCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEec
Q 003717           13 QTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK----GRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERA   88 (800)
Q Consensus        13 srTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRdT----GRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~A   88 (800)
                      ..||||++||+.++.++|.++|+.+|+|..|.++.++    +||||||+|+-  .++++.|+...++..|.||.|+|+.|
T Consensus         5 g~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam--~ED~qrA~~e~~~~kf~Gr~l~v~~A   82 (678)
T KOG0127|consen    5 GATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAM--EEDVQRALAETEQSKFEGRILNVDPA   82 (678)
T ss_pred             CceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeeh--HhHHHHHHHHhhcCcccceecccccc
Confidence            3799999999999999999999999999999999654    38999999998  99999999999999999999999999


Q ss_pred             cchhhHHHhhh-HHHHhhhhCCCCCC--CCCCCCCCCcccCCCCCCCCCcchhhcccccCccceeeecc--CCCC-Cccc
Q 003717           89 KEHYLARLKRE-WAEDDAQLVNPPVT--DSVAPDNKDATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPF--CGTG-KHKY  162 (800)
Q Consensus        89 Kpr~~~RlkrE-raq~rak~~~sp~s--D~Vd~~~~kl~is~~Lkksvdesd~LreyFskyGKVKsVp~--pgTG-K~KY  162 (800)
                      +++........ ...+.......+..  +.++...+.+.| +.|++.... .+|..+|+.||+|.-|.+  +..| .+.|
T Consensus        83 ~~R~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLII-RNLPf~~k~-~dLk~vFs~~G~V~Ei~IP~k~dgklcGF  160 (678)
T KOG0127|consen   83 KKRARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLII-RNLPFKCKK-PDLKNVFSNFGKVVEIVIPRKKDGKLCGF  160 (678)
T ss_pred             cccccchhcccccchhhhcccccCCcchhhccCccceEEe-ecCCcccCc-HHHHHHHhhcceEEEEEcccCCCCCccce
Confidence            87743321110 01111111222222  222322444544 557888877 699999999999765433  3444 4557


Q ss_pred             ccccccCCCCCcccccccchhhhhhhhccCccc
Q 003717          163 SFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIH  195 (800)
Q Consensus       163 GF~~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~  195 (800)
                      ||         |.|...-++..|++-+||..|-
T Consensus       161 aF---------V~fk~~~dA~~Al~~~N~~~i~  184 (678)
T KOG0127|consen  161 AF---------VQFKEKKDAEKALEFFNGNKID  184 (678)
T ss_pred             EE---------EEEeeHHHHHHHHHhccCceec
Confidence            77         8999999999999999988773

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

Probab=99.58  E-value=4.2e-15  Score=162.88  Aligned_cols=173  Identities=14%  Similarity=0.214  Sum_probs=112.7

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc--C--CCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEe
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--K--GRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLER   87 (800)
Q Consensus        12 qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd--T--GRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~   87 (800)
                      ...+|||||||+.+++++|+++|..||.|..+.++++  +  .+|||||+|.+  .++|..|+..|||..|+|+.|.|.+
T Consensus       294 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~--~~~a~~A~~~l~g~~~~~~~l~v~~  371 (509)
T TIGR01642       294 SKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKD--PSVTDVAIAALNGKDTGDNKLHVQR  371 (509)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECC--HHHHHHHHHHcCCCEECCeEEEEEE
Confidence            4579999999999999999999999999999998854  3  47999999997  9999999999999999999999999


Q ss_pred             ccchhhHHHhhhHHHHhhhhCCCCCC--CCC----CCCCCCcccCCCC-CCCC-Cc-----c-hhhcccccCccceeeec
Q 003717           88 AKEHYLARLKREWAEDDAQLVNPPVT--DSV----APDNKDATRLDTP-KKLL-DK-----D-KKLNIFFPRLRKVKTLP  153 (800)
Q Consensus        88 AKpr~~~RlkrEraq~rak~~~sp~s--D~V----d~~~~kl~is~~L-kksv-de-----s-d~LreyFskyGKVKsVp  153 (800)
                      |......... ............+..  ...    ......+.+.+.. ...+ ++     . ++|+..|.+||.|..|.
T Consensus       372 a~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~  450 (509)
T TIGR01642       372 ACVGANQATI-DTSNGMAPVTLLAKALSQSILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIV  450 (509)
T ss_pred             CccCCCCCCc-cccccccccccccccchhhhccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEE
Confidence            8643211000 000000000000000  000    0000001111100 0001 11     0 46889999999988665


Q ss_pred             cCC------CCCcccccccccCCCCCcccccccchhhhhhhhccCccc
Q 003717          154 FCG------TGKHKYSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIH  195 (800)
Q Consensus       154 ~pg------TGK~KYGF~~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~  195 (800)
                      ++-      ++.. +||.       +|.|.+.++|..|+.+|||..+.
T Consensus       451 i~~~~~~~~~~~~-~G~~-------fV~F~~~e~A~~A~~~lnGr~~~  490 (509)
T TIGR01642       451 IPRPNGDRNSTPG-VGKV-------FLEYADVRSAEKAMEGMNGRKFN  490 (509)
T ss_pred             eeccCcCCCcCCC-cceE-------EEEECCHHHHHHHHHHcCCCEEC
Confidence            431      2222 2332       49999999999999999998873

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

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

Probab=99.58  E-value=3.9e-15  Score=163.06  Aligned_cols=178  Identities=17%  Similarity=0.310  Sum_probs=119.0

Q ss_pred             cCCcEEEEeCCCCCCCHHHHHHhhhcC------------CceeEEEEeccCCCcEEEEEecCCCHHHHHHHHHhcCCcEe
Q 003717           11 EEQTRIYVGGLGEKVTDDDLAKVFSSL------------GEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVW   78 (800)
Q Consensus        11 ~qsrTLFVGNLP~nVTEEDLrelFSqF------------G~VksVrVIRdTGRGFGFVEFeS~D~EdAekAIe~LNG~eL   78 (800)
                      ...++|||||||+.+|+++|+++|.+|            +.|..+.+  ...+|||||+|.+  .++|..|| .|||..|
T Consensus       173 ~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~--~~~kg~afVeF~~--~e~A~~Al-~l~g~~~  247 (509)
T TIGR01642       173 RQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI--NKEKNFAFLEFRT--VEEATFAM-ALDSIIY  247 (509)
T ss_pred             ccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE--CCCCCEEEEEeCC--HHHHhhhh-cCCCeEe
Confidence            346799999999999999999999975            23443333  2358999999998  99999999 5999999


Q ss_pred             CCeEEEEEeccchhhHH-HhhhHHHH----hhhhCC-CCCCCCCCCCCCCcccCCCCCCCCCcchhhcccccCccceee-
Q 003717           79 KGGRLRLERAKEHYLAR-LKREWAED----DAQLVN-PPVTDSVAPDNKDATRLDTPKKLLDKDKKLNIFFPRLRKVKT-  151 (800)
Q Consensus        79 dGR~LrVe~AKpr~~~R-lkrEraq~----rak~~~-sp~sD~Vd~~~~kl~is~~Lkksvdesd~LreyFskyGKVKs-  151 (800)
                      .|+.|+|.......... ........    ...... ......+......+++++ |+..+++ ++|+.+|..||.|.. 
T Consensus       248 ~g~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~n-lp~~~~~-~~l~~~f~~~G~i~~~  325 (509)
T TIGR01642       248 SNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGN-LPLYLGE-DQIKELLESFGDLKAF  325 (509)
T ss_pred             eCceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeC-CCCCCCH-HHHHHHHHhcCCeeEE
Confidence            99999997543211000 00000000    000000 000001111223455554 5777766 899999999999764 


Q ss_pred             --eccCCCCCcc-cccccccCCCCCcccccccchhhhhhhhccCccccCCCCccccchh
Q 003717          152 --LPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPAAGQEEIHDM  207 (800)
Q Consensus       152 --Vp~pgTGK~K-YGF~~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n~~q~~i~~~  207 (800)
                        +.++.+|+++ |||         |.|.+.+.+..|+.+|||..+.   |..+.|..+
T Consensus       326 ~~~~~~~~g~~~g~af---------v~f~~~~~a~~A~~~l~g~~~~---~~~l~v~~a  372 (509)
T TIGR01642       326 NLIKDIATGLSKGYAF---------CEYKDPSVTDVAIAALNGKDTG---DNKLHVQRA  372 (509)
T ss_pred             EEEecCCCCCcCeEEE---------EEECCHHHHHHHHHHcCCCEEC---CeEEEEEEC
Confidence              4556789886 777         8999999999999999998874   333444443

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

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

Probab=99.54  E-value=1.5e-14  Score=150.96  Aligned_cols=164  Identities=18%  Similarity=0.316  Sum_probs=121.7

Q ss_pred             ccCCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc----CCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEE
Q 003717           10 VEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT----KGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRL   85 (800)
Q Consensus        10 v~qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd----TGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrV   85 (800)
                      .++.-.+|||-|...++.++|++.|.+||+|.+++|+||    +++|||||.|..  .++|+.||..|||..|++|.||-
T Consensus        59 ~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~--k~dAEnAI~~MnGqWlG~R~IRT  136 (321)
T KOG0148|consen   59 SNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPN--KEDAENAIQQMNGQWLGRRTIRT  136 (321)
T ss_pred             cccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccc--hHHHHHHHHHhCCeeeccceeec
Confidence            334567999999999999999999999999999999977    347999999998  99999999999999999999999


Q ss_pred             EeccchhhHHHhhhHHHHhhhhCCCCCCCCCCCCCCCcccCCCCCCCCCcchhhcccccCccceeeeccCCCCCcccccc
Q 003717           86 ERAKEHYLARLKREWAEDDAQLVNPPVTDSVAPDNKDATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPFCGTGKHKYSFQ  165 (800)
Q Consensus        86 e~AKpr~~~RlkrEraq~rak~~~sp~sD~Vd~~~~kl~is~~Lkksvdesd~LreyFskyGKVKsVp~pgTGK~KYGF~  165 (800)
                      .||..+..++......-+  +...+.     .+.+.....++ +...+.+ +.+|..|+.||.|..||.--  -..|+| 
T Consensus       137 NWATRKp~e~n~~~ltfd--eV~NQs-----sp~NtsVY~G~-I~~~lte-~~mr~~Fs~fG~I~EVRvFk--~qGYaF-  204 (321)
T KOG0148|consen  137 NWATRKPSEMNGKPLTFD--EVYNQS-----SPDNTSVYVGN-IASGLTE-DLMRQTFSPFGPIQEVRVFK--DQGYAF-  204 (321)
T ss_pred             cccccCccccCCCCccHH--HHhccC-----CCCCceEEeCC-cCccccH-HHHHHhcccCCcceEEEEec--ccceEE-
Confidence            999765422111110000  111111     22233333333 3333544 89999999999987665421  113888 


Q ss_pred             cccCCCCCcccccccchhhhhhhhccCccc
Q 003717          166 RVEAPPLPKYFCDCEEHSAAFHAAEGKQIH  195 (800)
Q Consensus       166 ~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~  195 (800)
                              |.|..-|.|..|+..|||..++
T Consensus       205 --------VrF~tkEaAahAIv~mNntei~  226 (321)
T KOG0148|consen  205 --------VRFETKEAAAHAIVQMNNTEIG  226 (321)
T ss_pred             --------EEecchhhHHHHHHHhcCceeC
Confidence                    8899999999999999998884

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

Probab=99.53  E-value=8.9e-15  Score=156.02  Aligned_cols=167  Identities=17%  Similarity=0.247  Sum_probs=126.1

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc--C--CCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEe
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--K--GRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLER   87 (800)
Q Consensus        12 qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd--T--GRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~   87 (800)
                      ...+||||+|+|.++++.|+.+|++||.|.+|.++++  +  .|||+||+|++  .+....++ ...-+.|+|+.|.++.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~--~~~v~~vl-~~~~h~~dgr~ve~k~   81 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFAT--PEGVDAVL-NARTHKLDGRSVEPKR   81 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCC--Ccchheee-cccccccCCcccccee
Confidence            4589999999999999999999999999999999965  3  37999999996  55555544 3456899999999999


Q ss_pred             ccchhhHHHhhhHHHHhhhhCCCCCCCCCCCCCCCcccCCCCCCCCCcchhhcccccCcccee---eeccCCCCCccccc
Q 003717           88 AKEHYLARLKREWAEDDAQLVNPPVTDSVAPDNKDATRLDTPKKLLDKDKKLNIFFPRLRKVK---TLPFCGTGKHKYSF  164 (800)
Q Consensus        88 AKpr~~~RlkrEraq~rak~~~sp~sD~Vd~~~~kl~is~~Lkksvdesd~LreyFskyGKVK---sVp~pgTGK~KYGF  164 (800)
                      |.++......                 .......+++++ .++.++.+ .+++.||.+||+|.   ++.+..+.+++ ||
T Consensus        82 av~r~~~~~~-----------------~~~~~tkkiFvG-G~~~~~~e-~~~r~yfe~~g~v~~~~~~~d~~~~~~r-gF  141 (311)
T KOG4205|consen   82 AVSREDQTKV-----------------GRHLRTKKIFVG-GLPPDTTE-EDFKDYFEQFGKVADVVIMYDKTTSRPR-GF  141 (311)
T ss_pred             ccCccccccc-----------------ccccceeEEEec-CcCCCCch-HHHhhhhhccceeEeeEEeecccccccc-cc
Confidence            9887311100                 001123456665 46777766 99999999999854   55666777776 44


Q ss_pred             ccccCCCCCcccccccchhhhhhhhccCccccCCCCccccchhhhcCc
Q 003717          165 QRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPAAGQEEIHDMEELGA  212 (800)
Q Consensus       165 ~~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n~~q~~i~~~ee~~g  212 (800)
                                +|..|++++++-.++. ++.|++++++|||++|.+++.
T Consensus       142 ----------gfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA~pk~~  178 (311)
T KOG4205|consen  142 ----------GFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRAIPKEV  178 (311)
T ss_pred             ----------eeeEeccccccceecc-cceeeecCceeeEeeccchhh
Confidence                      3455555555656565 899999999999999999984

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

Probab=99.52  E-value=5.6e-14  Score=152.35  Aligned_cols=75  Identities=23%  Similarity=0.560  Sum_probs=69.8

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc--C--CCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEec
Q 003717           13 QTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--K--GRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERA   88 (800)
Q Consensus        13 srTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd--T--GRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~A   88 (800)
                      ..+|||+|||+.+++++|+++|++||.|..|.++++  +  .+|||||+|.+  .++|.+|+..|||..|.|++|.|.+|
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  263 (457)
T TIGR01622       186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHD--AEEAKEALEVMNGFELAGRPIKVGYA  263 (457)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECC--HHHHHHHHHhcCCcEECCEEEEEEEc
Confidence            479999999999999999999999999999999844  2  37999999997  99999999999999999999999997


Q ss_pred             c
Q 003717           89 K   89 (800)
Q Consensus        89 K   89 (800)
                      .
T Consensus       264 ~  264 (457)
T TIGR01622       264 Q  264 (457)
T ss_pred             c
Confidence            5

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.

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

Probab=99.50  E-value=1.1e-13  Score=132.30  Aligned_cols=78  Identities=24%  Similarity=0.534  Sum_probs=71.8

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc----CCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEe
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT----KGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLER   87 (800)
Q Consensus        12 qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd----TGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~   87 (800)
                      ..++|||+|||+.+++++|+++|.+||.|.+|.++.+    ..+|||||+|.+  .++|+.|++.|||+.|+|++|+|++
T Consensus        33 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~--~e~A~~Al~~lng~~i~Gr~l~V~~  110 (144)
T PLN03134         33 MSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFND--EGAATAAISEMDGKELNGRHIRVNP  110 (144)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECC--HHHHHHHHHHcCCCEECCEEEEEEe
Confidence            4579999999999999999999999999999999844    247999999997  9999999999999999999999999


Q ss_pred             ccch
Q 003717           88 AKEH   91 (800)
Q Consensus        88 AKpr   91 (800)
                      +.++
T Consensus       111 a~~~  114 (144)
T PLN03134        111 ANDR  114 (144)
T ss_pred             CCcC
Confidence            8754

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

Probab=99.47  E-value=1.8e-13  Score=156.10  Aligned_cols=180  Identities=17%  Similarity=0.279  Sum_probs=123.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc---CCCcEEEEEecCCCHHHHHHHHHhcCCcEeC-CeEEEEEe
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT---KGRSFGYVDFFPSSHKSLSKLFSTYNGCVWK-GGRLRLER   87 (800)
Q Consensus        12 qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd---TGRGFGFVEFeS~D~EdAekAIe~LNG~eLd-GR~LrVe~   87 (800)
                      ..++|||||||+++++++|+++|++||.|.+|+|+++   ..||||||+|.+  .++|.+||+.||+..|. |+.|.|..
T Consensus        57 ~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~sG~sRGfaFV~F~~--~e~A~~Ai~~lng~~i~~Gr~l~V~~  134 (578)
T TIGR01648        57 RGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCG--KEEAKEAVKLLNNYEIRPGRLLGVCI  134 (578)
T ss_pred             CCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECCCCCccceEEEEeCC--HHHHHHHHHHcCCCeecCCccccccc
Confidence            4589999999999999999999999999999999865   348999999997  99999999999999985 77776654


Q ss_pred             ccc----------hhhHH--Hhh----------------------------------hHHHHhh--hhCC----------
Q 003717           88 AKE----------HYLAR--LKR----------------------------------EWAEDDA--QLVN----------  109 (800)
Q Consensus        88 AKp----------r~~~R--lkr----------------------------------Eraq~ra--k~~~----------  109 (800)
                      +..          .....  +..                                  ......+  +...          
T Consensus       135 S~~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I  214 (578)
T TIGR01648       135 SVDNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVI  214 (578)
T ss_pred             cccCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceE
Confidence            421          00000  000                                  0000000  0000          


Q ss_pred             -----CCCCC---CCCCCCCCcccCCCCCCCCCcchhhcccccCc--cceeeeccCCCCCcccccccccCCCCCcccccc
Q 003717          110 -----PPVTD---SVAPDNKDATRLDTPKKLLDKDKKLNIFFPRL--RKVKTLPFCGTGKHKYSFQRVEAPPLPKYFCDC  179 (800)
Q Consensus       110 -----sp~sD---~Vd~~~~kl~is~~Lkksvdesd~LreyFsky--GKVKsVp~pgTGK~KYGF~~ve~Ps~pV~F~sf  179 (800)
                           .+...   ........+++.+ |...+++ +.|+.+|..|  |.|..+...    ..|+|         |.|.+.
T Consensus       215 ~VdwA~p~~~~d~~~~~~~k~LfVgN-L~~~~te-e~L~~~F~~f~~G~I~rV~~~----rgfAF---------VeF~s~  279 (578)
T TIGR01648       215 AVDWAEPEEEVDEDVMAKVKILYVRN-LMTTTTE-EIIEKSFSEFKPGKVERVKKI----RDYAF---------VHFEDR  279 (578)
T ss_pred             EEEeecccccccccccccccEEEEeC-CCCCCCH-HHHHHHHHhcCCCceEEEEee----cCeEE---------EEeCCH
Confidence                 00000   0001122344543 5677766 8999999999  998876432    13777         899999


Q ss_pred             cchhhhhhhhccCccccCCCCccccchhhhcC
Q 003717          180 EEHSAAFHAAEGKQIHHPAAGQEEIHDMEELG  211 (800)
Q Consensus       180 Eea~aA~eAmNG~~i~n~n~~q~~i~~~ee~~  211 (800)
                      +++..|+++|||..+   +|..++|..+.+.+
T Consensus       280 e~A~kAi~~lnG~~i---~Gr~I~V~~Akp~~  308 (578)
T TIGR01648       280 EDAVKAMDELNGKEL---EGSEIEVTLAKPVD  308 (578)
T ss_pred             HHHHHHHHHhCCCEE---CCEEEEEEEccCCC
Confidence            999999999999876   45677777555443

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.

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

Probab=99.43  E-value=1.3e-13  Score=150.49  Aligned_cols=164  Identities=15%  Similarity=0.272  Sum_probs=125.4

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEeccCC----CcEEEEEecCCCHHHHHHHHHhcCCc-EeCC--eEEE
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKG----RSFGYVDFFPSSHKSLSKLFSTYNGC-VWKG--GRLR   84 (800)
Q Consensus        12 qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRdTG----RGFGFVEFeS~D~EdAekAIe~LNG~-eLdG--R~Lr   84 (800)
                      ..-+||||.+|..++|.+|+.+|++||.|.+|.|++|+.    +|||||.|.+  .++|.+|+.+|+.. .|-|  .+|.
T Consensus        33 ~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~t--rk~a~~a~~Alhn~ktlpG~~~pvq  110 (510)
T KOG0144|consen   33 SAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYT--RKEADEAINALHNQKTLPGMHHPVQ  110 (510)
T ss_pred             hhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEecc--HHHHHHHHHHhhcccccCCCCccee
Confidence            356899999999999999999999999999999997742    7999999998  99999999999874 5544  6888


Q ss_pred             EEeccchhhHHHhhhHHHHhhhhCCCCCCCCCCCCCCCcccCCCCCCCCCcchhhcccccCccceeeecc--CCCCCcc-
Q 003717           85 LERAKEHYLARLKREWAEDDAQLVNPPVTDSVAPDNKDATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPF--CGTGKHK-  161 (800)
Q Consensus        85 Ve~AKpr~~~RlkrEraq~rak~~~sp~sD~Vd~~~~kl~is~~Lkksvdesd~LreyFskyGKVKsVp~--pgTGK~K-  161 (800)
                      |++|....      ++.                +...++|++. |.+...+ .+++++|.+||.|+.+..  ...|.++ 
T Consensus       111 vk~Ad~E~------er~----------------~~e~KLFvg~-lsK~~te-~evr~iFs~fG~Ied~~ilrd~~~~sRG  166 (510)
T KOG0144|consen  111 VKYADGER------ERI----------------VEERKLFVGM-LSKQCTE-NEVREIFSRFGHIEDCYILRDPDGLSRG  166 (510)
T ss_pred             ecccchhh------hcc----------------ccchhhhhhh-ccccccH-HHHHHHHHhhCccchhhheecccccccc
Confidence            88875321      100                1233566655 5666656 899999999999875432  2345555 


Q ss_pred             cccccccCCCCCcccccccchhhhhhhhccCccccCCCCccccchhhhc
Q 003717          162 YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPAAGQEEIHDMEEL  210 (800)
Q Consensus       162 YGF~~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n~~q~~i~~~ee~  210 (800)
                      ++|         |.|..-|-+.+|+++|||.+.+-.-..-.-|+-++.+
T Consensus       167 caF---------V~fstke~A~~Aika~ng~~tmeGcs~PLVVkFADtq  206 (510)
T KOG0144|consen  167 CAF---------VKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQ  206 (510)
T ss_pred             eeE---------EEEehHHHHHHHHHhhccceeeccCCCceEEEecccC
Confidence            888         8999999999999999999987654444444544443

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

Probab=99.41  E-value=3.6e-13  Score=140.22  Aligned_cols=145  Identities=23%  Similarity=0.383  Sum_probs=119.4

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEeccC--C--CcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEec
Q 003717           13 QTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK--G--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERA   88 (800)
Q Consensus        13 srTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRdT--G--RGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~A   88 (800)
                      .++|.|.-||.++|+++|+.+|+..|+|.+|+++|++  |  -|||||.|..  +.+|++|+..|||..|..+.|+|.+|
T Consensus        41 kTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~--p~DAe~AintlNGLrLQ~KTIKVSyA  118 (360)
T KOG0145|consen   41 KTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVR--PKDAEKAINTLNGLRLQNKTIKVSYA  118 (360)
T ss_pred             cceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecC--hHHHHHHHhhhcceeeccceEEEEec
Confidence            4689999999999999999999999999999999874  4  3999999996  99999999999999999999999999


Q ss_pred             cchhhHHHhhhHHHHhhhhCCCCCCCCCCCCCCCcccCCCCCCCCCcchhhcccccCcccee---eeccCCCCCcc-ccc
Q 003717           89 KEHYLARLKREWAEDDAQLVNPPVTDSVAPDNKDATRLDTPKKLLDKDKKLNIFFPRLRKVK---TLPFCGTGKHK-YSF  164 (800)
Q Consensus        89 Kpr~~~RlkrEraq~rak~~~sp~sD~Vd~~~~kl~is~~Lkksvdesd~LreyFskyGKVK---sVp~pgTGK~K-YGF  164 (800)
                      +|....                     .  .-.++.+++ |++.+.. ..|..+|..||.|.   ++-+..||-.+ .||
T Consensus       119 RPSs~~---------------------I--k~aNLYvSG-lPktMtq-kelE~iFs~fGrIItSRiL~dqvtg~srGVgF  173 (360)
T KOG0145|consen  119 RPSSDS---------------------I--KDANLYVSG-LPKTMTQ-KELEQIFSPFGRIITSRILVDQVTGLSRGVGF  173 (360)
T ss_pred             cCChhh---------------------h--cccceEEec-CCccchH-HHHHHHHHHhhhhhhhhhhhhcccceecceeE
Confidence            986311                     0  112456665 4566645 88999999999964   45566788876 677


Q ss_pred             ccccCCCCCcccccccchhhhhhhhccCc
Q 003717          165 QRVEAPPLPKYFCDCEEHSAAFHAAEGKQ  193 (800)
Q Consensus       165 ~~ve~Ps~pV~F~sfEea~aA~eAmNG~~  193 (800)
                               +.|--.+|+..|+..+||+.
T Consensus       174 ---------iRFDKr~EAe~AIk~lNG~~  193 (360)
T KOG0145|consen  174 ---------IRFDKRIEAEEAIKGLNGQK  193 (360)
T ss_pred             ---------EEecchhHHHHHHHhccCCC
Confidence                     77888888999999988764

>PF00076 RRM_1: RNA recognition motif

Probab=99.41  E-value=9.1e-13  Score=106.11  Aligned_cols=67  Identities=27%  Similarity=0.644  Sum_probs=62.4

Q ss_pred             EEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc-C--CCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEE
Q 003717           16 IYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT-K--GRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLR   84 (800)
Q Consensus        16 LFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd-T--GRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~Lr   84 (800)
                      |||+|||+++++++|+++|++||.|..+.++++ .  .+|||||+|.+  .++|.+|+..|+|..++|+.|+
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 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFES--EEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESS--HHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcC--HHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999999999863 2  36999999997  9999999999999999999986

(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 ....

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

Probab=99.40  E-value=4.7e-13  Score=146.70  Aligned_cols=160  Identities=17%  Similarity=0.289  Sum_probs=123.3

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhhcCCc-eeEEEEec---c--CCCcEEEEEecCCCHHHHHHHHHhc-CC-cEeCCeEEE
Q 003717           13 QTRIYVGGLGEKVTDDDLAKVFSSLGE-VKAVDIVR---T--KGRSFGYVDFFPSSHKSLSKLFSTY-NG-CVWKGGRLR   84 (800)
Q Consensus        13 srTLFVGNLP~nVTEEDLrelFSqFG~-VksVrVIR---d--TGRGFGFVEFeS~D~EdAekAIe~L-NG-~eLdGR~Lr   84 (800)
                      ..+|||||+|.+.+.++|.+.|.+.++ |++|.|..   +  ++||||||+|.+  ...|..|-+.| +| ..+.|..+.
T Consensus       164 n~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~--H~~Aa~aRrKl~~g~~klwgn~~t  241 (506)
T KOG0117|consen  164 NCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYES--HRAAAMARRKLMPGKIKLWGNAIT  241 (506)
T ss_pred             cceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeec--chhHHHHHhhccCCceeecCCcce
Confidence            579999999999999999999999987 77776662   2  468999999997  77777776664 44 577899999


Q ss_pred             EEeccchhhHHHhhhHHHHhhhhCCCCCCCCCCCCCCCcccCCCCCCCCCcchhhcccccCccceeeeccCCCCCcc-cc
Q 003717           85 LERAKEHYLARLKREWAEDDAQLVNPPVTDSVAPDNKDATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPFCGTGKHK-YS  163 (800)
Q Consensus        85 Ve~AKpr~~~RlkrEraq~rak~~~sp~sD~Vd~~~~kl~is~~Lkksvdesd~LreyFskyGKVKsVp~pgTGK~K-YG  163 (800)
                      |+||.|....                 ..+ +..+.+.+++.+ |..++++ +.|+..|.+||+|.-|..     .+ |+
T Consensus       242 VdWAep~~e~-----------------ded-~ms~VKvLYVRN-L~~~tTe-E~lk~~F~~~G~veRVkk-----~rDYa  296 (506)
T KOG0117|consen  242 VDWAEPEEEP-----------------DED-TMSKVKVLYVRN-LMESTTE-ETLKKLFNEFGKVERVKK-----PRDYA  296 (506)
T ss_pred             eeccCcccCC-----------------Chh-hhhheeeeeeec-cchhhhH-HHHHHHHHhccceEEeec-----cccee
Confidence            9999886311                 011 222334454533 5666655 999999999999876522     23 99


Q ss_pred             cccccCCCCCcccccccchhhhhhhhccCccccCCCCccccchhhhcC
Q 003717          164 FQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPAAGQEEIHDMEELG  211 (800)
Q Consensus       164 F~~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n~~q~~i~~~ee~~  211 (800)
                      |         |||...+++-.|++.|||..|   +|+-.||.-+-+++
T Consensus       297 F---------VHf~eR~davkAm~~~ngkel---dG~~iEvtLAKP~~  332 (506)
T KOG0117|consen  297 F---------VHFAEREDAVKAMKETNGKEL---DGSPIEVTLAKPVD  332 (506)
T ss_pred             E---------EeecchHHHHHHHHHhcCcee---cCceEEEEecCChh
Confidence            9         999999999999999999987   67778888777766

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

Probab=99.40  E-value=4e-13  Score=143.09  Aligned_cols=87  Identities=21%  Similarity=0.418  Sum_probs=78.4

Q ss_pred             cchhhccCCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEe-ccCC-CcEEEEEecCCCHHHHHHHHHhcCCcEeCCeE
Q 003717            5 EAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV-RTKG-RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGR   82 (800)
Q Consensus         5 eAe~Ev~qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVI-RdTG-RGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~   82 (800)
                      +.++.....+||+|.|||+...+.||+.+|++||.|.+|.|| .++| +|||||+|++  .++|++|-.+|||..+.||+
T Consensus        88 t~s~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen--~~dadRARa~LHgt~VEGRk  165 (376)
T KOG0125|consen   88 TNSSSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMEN--PADADRARAELHGTVVEGRK  165 (376)
T ss_pred             CcCCCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecC--hhhHHHHHHHhhcceeeceE
Confidence            344445567899999999999999999999999999999999 5555 8999999998  99999999999999999999


Q ss_pred             EEEEeccchhh
Q 003717           83 LRLERAKEHYL   93 (800)
Q Consensus        83 LrVe~AKpr~~   93 (800)
                      |+|..|.+|..
T Consensus       166 IEVn~ATarV~  176 (376)
T KOG0125|consen  166 IEVNNATARVH  176 (376)
T ss_pred             EEEeccchhhc
Confidence            99999988743

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

Probab=99.38  E-value=3.9e-13  Score=144.59  Aligned_cols=157  Identities=17%  Similarity=0.367  Sum_probs=113.9

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc----CCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEec
Q 003717           13 QTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT----KGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERA   88 (800)
Q Consensus        13 srTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd----TGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~A   88 (800)
                      ..+||||.+++.+.++.||..|..||+|+++.+-.+    +++||+||+|+-  ++.|.-|++.|||..++||.|+|..-
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEv--PEaAqLAlEqMNg~mlGGRNiKVgrP  190 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEV--PEAAQLALEQMNGQMLGGRNIKVGRP  190 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeC--cHHHHHHHHHhccccccCccccccCC
Confidence            579999999999999999999999999999998744    468999999998  99999999999999999999999843


Q ss_pred             cchhhHHHhh--hHHHHhhhhCCCCCCCCCCCCCCCcccCCCCCCCCCcchhhcccccCccceee---eccCCCCCcc-c
Q 003717           89 KEHYLARLKR--EWAEDDAQLVNPPVTDSVAPDNKDATRLDTPKKLLDKDKKLNIFFPRLRKVKT---LPFCGTGKHK-Y  162 (800)
Q Consensus        89 Kpr~~~Rlkr--Eraq~rak~~~sp~sD~Vd~~~~kl~is~~Lkksvdesd~LreyFskyGKVKs---Vp~pgTGK~K-Y  162 (800)
                        ..+.....  ..-+..++...     .+.       + .-.-.++.+ ++++..|..||+|..   .+.+.++.|| |
T Consensus       191 --sNmpQAQpiID~vqeeAk~fn-----RiY-------V-aSvHpDLSe-~DiKSVFEAFG~I~~C~LAr~pt~~~HkGy  254 (544)
T KOG0124|consen  191 --SNMPQAQPIIDMVQEEAKKFN-----RIY-------V-ASVHPDLSE-TDIKSVFEAFGEIVKCQLARAPTGRGHKGY  254 (544)
T ss_pred             --CCCcccchHHHHHHHHHHhhh-----eEE-------e-eecCCCccH-HHHHHHHHhhcceeeEEeeccCCCCCccce
Confidence              22211110  00011111111     111       0 011234555 788888888888654   4556777887 7


Q ss_pred             ccccccCCCCCcccccccchhhhhhhhc-----cCcccc
Q 003717          163 SFQRVEAPPLPKYFCDCEEHSAAFHAAE-----GKQIHH  196 (800)
Q Consensus       163 GF~~ve~Ps~pV~F~sfEea~aA~eAmN-----G~~i~n  196 (800)
                      ||         +.|......+.|+..||     |+|+-+
T Consensus       255 Gf---------iEy~n~qs~~eAiasMNlFDLGGQyLRV  284 (544)
T KOG0124|consen  255 GF---------IEYNNLQSQSEAIASMNLFDLGGQYLRV  284 (544)
T ss_pred             ee---------EEeccccchHHHhhhcchhhcccceEec
Confidence            77         78888888888888887     666655

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

Probab=99.31  E-value=3.9e-12  Score=134.10  Aligned_cols=133  Identities=19%  Similarity=0.349  Sum_probs=104.7

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEeccCCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEeccchhh
Q 003717           14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKEHYL   93 (800)
Q Consensus        14 rTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRdTGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~AKpr~~   93 (800)
                      .+|||||||..+++.+|+.+|++||.|.+|.|+++    ||||..++  ...+..||..|+|.+|+|..|+|+.++.+. 
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN----YgFVHiEd--ktaaedairNLhgYtLhg~nInVeaSksKs-   75 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN----YGFVHIED--KTAAEDAIRNLHGYTLHGVNINVEASKSKS-   75 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc----cceEEeec--ccccHHHHhhcccceecceEEEEEeccccC-
Confidence            57999999999999999999999999999999864    99999996  999999999999999999999999887541 


Q ss_pred             HHHhhhHHHHhhhhCCCCCCCCCCCCCCCcccCCCCCCCCCcchhhcccccCccceeeeccCCCCCcc-cccccccCCCC
Q 003717           94 ARLKREWAEDDAQLVNPPVTDSVAPDNKDATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPFCGTGKHK-YSFQRVEAPPL  172 (800)
Q Consensus        94 ~RlkrEraq~rak~~~sp~sD~Vd~~~~kl~is~~Lkksvdesd~LreyFskyGKVKsVp~pgTGK~K-YGF~~ve~Ps~  172 (800)
                                              ...+++++++ +...... ..+|.-|.+||.|..+     --.| |+|        
T Consensus        76 ------------------------k~stkl~vgN-is~tctn-~ElRa~fe~ygpviec-----divkdy~f--------  116 (346)
T KOG0109|consen   76 ------------------------KASTKLHVGN-ISPTCTN-QELRAKFEKYGPVIEC-----DIVKDYAF--------  116 (346)
T ss_pred             ------------------------CCccccccCC-CCccccC-HHHhhhhcccCCceee-----eeecceeE--------
Confidence                                    1123344443 2222322 7899999999997533     1124 888        


Q ss_pred             CcccccccchhhhhhhhccCc
Q 003717          173 PKYFCDCEEHSAAFHAAEGKQ  193 (800)
Q Consensus       173 pV~F~sfEea~aA~eAmNG~~  193 (800)
                       |+|--.+++-.|...+++..
T Consensus       117 -vh~d~~eda~~air~l~~~~  136 (346)
T KOG0109|consen  117 -VHFDRAEDAVEAIRGLDNTE  136 (346)
T ss_pred             -EEEeeccchHHHHhcccccc
Confidence             78888888888886666443

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.28  E-value=1.2e-11  Score=129.44  Aligned_cols=75  Identities=17%  Similarity=0.308  Sum_probs=69.5

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEeccC-CCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEeccc
Q 003717           13 QTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK-GRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKE   90 (800)
Q Consensus        13 srTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRdT-GRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~AKp   90 (800)
                      .++|||||||+.+++++|+++|+.||.|.+|.|+++. .+|||||+|.+  .++|..|+. |||..|.|+.|+|..+..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~~~GfAFVtF~d--~eaAe~All-LnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKD--PQGAETALL-LSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEeCc--HHHHHHHHH-hcCCeeCCceEEEEeccC
Confidence            4799999999999999999999999999999999764 47999999997  999999995 999999999999999864

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

Probab=99.27  E-value=1.3e-11  Score=134.51  Aligned_cols=153  Identities=16%  Similarity=0.298  Sum_probs=115.7

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEeccC-C-CcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEeccch
Q 003717           14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK-G-RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKEH   91 (800)
Q Consensus        14 rTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRdT-G-RGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~AKpr   91 (800)
                      ..|||.||+..++..+|.++|+.||.|.+|++.++. | +|| ||+|++  .+.|.+|+..|||..+.|++|.|..+..+
T Consensus        77 ~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g~kg~-FV~f~~--e~~a~~ai~~~ng~ll~~kki~vg~~~~~  153 (369)
T KOG0123|consen   77 SLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENGSKGY-FVQFES--EESAKKAIEKLNGMLLNGKKIYVGLFERK  153 (369)
T ss_pred             ceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCCceee-EEEeCC--HHHHHHHHHHhcCcccCCCeeEEeeccch
Confidence            449999999999999999999999999999999553 3 799 999997  99999999999999999999999988765


Q ss_pred             hhHHHhhhHHHHhhhhCCCCCCCCCCCCCCCcccCCCCCCCCCcchhhcccccCccceeeeccC--CCCCcc-ccccccc
Q 003717           92 YLARLKREWAEDDAQLVNPPVTDSVAPDNKDATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPFC--GTGKHK-YSFQRVE  168 (800)
Q Consensus        92 ~~~RlkrEraq~rak~~~sp~sD~Vd~~~~kl~is~~Lkksvdesd~LreyFskyGKVKsVp~p--gTGK~K-YGF~~ve  168 (800)
                      ..+.. .... . .+     ..       .+..+.. +....+. ..|..+|+.||.|.++...  ..|+++ |||    
T Consensus       154 ~er~~-~~~~-~-~~-----~~-------t~v~vk~-~~~~~~~-~~l~~~f~~~g~i~s~~v~~~~~g~~~~~gf----  212 (369)
T KOG0123|consen  154 EEREA-PLGE-Y-KK-----RF-------TNVYVKN-LEEDSTD-EELKDLFSAYGSITSVAVMRDSIGKSKGFGF----  212 (369)
T ss_pred             hhhcc-cccc-h-hh-----hh-------hhhheec-cccccch-HHHHHhhcccCcceEEEEeecCCCCCCCccc----
Confidence            32211 1100 0 00     00       0111111 1122323 7999999999998876554  567765 777    


Q ss_pred             CCCCCcccccccchhhhhhhhccCccc
Q 003717          169 APPLPKYFCDCEEHSAAFHAAEGKQIH  195 (800)
Q Consensus       169 ~Ps~pV~F~sfEea~aA~eAmNG~~i~  195 (800)
                           |.|..-+++..|++.|+|..+-
T Consensus       213 -----v~f~~~e~a~~av~~l~~~~~~  234 (369)
T KOG0123|consen  213 -----VNFENPEDAKKAVETLNGKIFG  234 (369)
T ss_pred             -----eeecChhHHHHHHHhccCCcCC
Confidence                 8999999999999999988774

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

Probab=99.23  E-value=3.1e-11  Score=135.10  Aligned_cols=187  Identities=22%  Similarity=0.252  Sum_probs=124.7

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEeccC-C--CcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEecc
Q 003717           13 QTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK-G--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAK   89 (800)
Q Consensus        13 srTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRdT-G--RGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~AK   89 (800)
                      ..+|.|.||||.+...+|+.+|+.||.|..|.|++.. +  +|||||.|..  ..+|..|+..|||++|+||+|-|+||-
T Consensus       117 k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~fk~--~~dA~~Al~~~N~~~i~gR~VAVDWAV  194 (678)
T KOG0127|consen  117 KWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQFKE--KKDAEKALEFFNGNKIDGRPVAVDWAV  194 (678)
T ss_pred             cceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEEee--HHHHHHHHHhccCceecCceeEEeeec
Confidence            5799999999999999999999999999999998432 2  6999999997  999999999999999999999999996


Q ss_pred             ch--hhHHH-------hh--hHHHHhh------h----------hCCCC-----------------CCCCCCC-------
Q 003717           90 EH--YLARL-------KR--EWAEDDA------Q----------LVNPP-----------------VTDSVAP-------  118 (800)
Q Consensus        90 pr--~~~Rl-------kr--Eraq~ra------k----------~~~sp-----------------~sD~Vd~-------  118 (800)
                      ++  |....       +.  ....+..      .          .....                 ..+.++.       
T Consensus       195 ~Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~edeEe~D~~se~~ee~~~~Eee~~~vDd~e~S~~~  274 (678)
T KOG0127|consen  195 DKDTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDEEETDGNSEAFEEGEESEEEEDDVDDEESSGKK  274 (678)
T ss_pred             ccccccccchhhhhhhhhccchhhhcccccccccccchhcccccccccccccccchhhhccccccccccccccccccccC
Confidence            54  22200       00  0000000      0          00000                 0000000       


Q ss_pred             ------CCC---------CcccCCCCCCCCCcchhhcccccCcccee---eeccCCCCCcc-cccccccCCCCCcccccc
Q 003717          119 ------DNK---------DATRLDTPKKLLDKDKKLNIFFPRLRKVK---TLPFCGTGKHK-YSFQRVEAPPLPKYFCDC  179 (800)
Q Consensus       119 ------~~~---------kl~is~~Lkksvdesd~LreyFskyGKVK---sVp~pgTGK~K-YGF~~ve~Ps~pV~F~sf  179 (800)
                            ++.         ...+.+.|+.++.+ +.|...|.+||.|+   +|..+.||.++ -+|         |+|.+-
T Consensus       275 ~~~k~~q~k~~~en~~~~~tVFvRNL~fD~tE-Eel~~~fskFG~v~ya~iV~~k~T~~skGtAF---------v~Fkt~  344 (678)
T KOG0127|consen  275 ESDKKAQNKTTRENITEGKTVFVRNLPFDTTE-EELKEHFSKFGEVKYAIIVKDKDTGHSKGTAF---------VKFKTQ  344 (678)
T ss_pred             cccchhccccccccccccceEEEecCCccccH-HHHHHHHHhhccceeEEEEeccCCCCcccceE---------EEeccH
Confidence                  000         11222334555545 88999999999976   56778999987 566         788888


Q ss_pred             cchhhhhhhh---ccCccccCCCCccccchhhhcC
Q 003717          180 EEHSAAFHAA---EGKQIHHPAAGQEEIHDMEELG  211 (800)
Q Consensus       180 Eea~aA~eAm---NG~~i~n~n~~q~~i~~~ee~~  211 (800)
                      .++..+++++   +|---..+.|.|..|..+-.+.
T Consensus       345 ~~~~~ci~~Aspa~e~g~~ll~GR~Lkv~~Av~Rk  379 (678)
T KOG0127|consen  345 IAAQNCIEAASPASEDGSVLLDGRLLKVTLAVTRK  379 (678)
T ss_pred             HHHHHHHHhcCccCCCceEEEeccEEeeeeccchH
Confidence            8888887776   2222234555666665554444

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

Probab=99.23  E-value=2.1e-11  Score=127.36  Aligned_cols=175  Identities=19%  Similarity=0.265  Sum_probs=120.2

Q ss_pred             ccCCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc--CC--CcEEEEEecCCCHHHHHHHHHhcCCcEeCC--eEE
Q 003717           10 VEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--KG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKG--GRL   83 (800)
Q Consensus        10 v~qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd--TG--RGFGFVEFeS~D~EdAekAIe~LNG~eLdG--R~L   83 (800)
                      .-...+|||.+||..+|..+|.++|++||.|..-+|+.+  ++  ||.|||.|..  ..+|+.||..|||..-.|  .+|
T Consensus       124 ~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDK--r~EAe~AIk~lNG~~P~g~tepI  201 (360)
T KOG0145|consen  124 SIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDK--RIEAEEAIKGLNGQKPSGCTEPI  201 (360)
T ss_pred             hhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecc--hhHHHHHHHhccCCCCCCCCCCe
Confidence            334679999999999999999999999999988888743  33  8999999998  999999999999998876  589


Q ss_pred             EEEeccchhhHH-Hh------h----------hHHHHhh-----------hhCCCCCC-CCCCCCC-CCcc--cCCC---
Q 003717           84 RLERAKEHYLAR-LK------R----------EWAEDDA-----------QLVNPPVT-DSVAPDN-KDAT--RLDT---  128 (800)
Q Consensus        84 rVe~AKpr~~~R-lk------r----------Eraq~ra-----------k~~~sp~s-D~Vd~~~-~kl~--is~~---  128 (800)
                      .|++|....... ..      .          ..+..+-           ....+|.. |....-. .++.  .+..   
T Consensus       202 tVKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~~~~~~~~~~~rfsP~~~d~m~~l~~~~lp~~~~~g~ci  281 (360)
T KOG0145|consen  202 TVKFANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLDNLLNPHAAQARFSPMTIDGMSGLAGVNLPGGPGGGWCI  281 (360)
T ss_pred             EEEecCCcccccchhhhHHhhcCccccCCCcccchhhhhccccccchhhhhccCCCccccccceeeeeccCCCCCCeeEE
Confidence            999984321100 00      0          0000000           00011111 1110000 0000  0000   


Q ss_pred             ----CCCCCCcchhhcccccCccc---eeeeccCCCCCcc-cccccccCCCCCcccccccchhhhhhhhccCcccc
Q 003717          129 ----PKKLLDKDKKLNIFFPRLRK---VKTLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHH  196 (800)
Q Consensus       129 ----Lkksvdesd~LreyFskyGK---VKsVp~pgTGK~K-YGF~~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n  196 (800)
                          |..+.++ .-|+.+|+.||-   ||++++..|.++| |||         |.+...+|+.-|+..+||-.+-+
T Consensus       282 FvYNLspd~de-~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgF---------VtMtNYdEAamAi~sLNGy~lg~  347 (360)
T KOG0145|consen  282 FVYNLSPDADE-SILWQLFGPFGAVTNVKVIRDFTTNKCKGFGF---------VTMTNYDEAAMAIASLNGYRLGD  347 (360)
T ss_pred             EEEecCCCchH-hHHHHHhCcccceeeEEEEecCCcccccceeE---------EEecchHHHHHHHHHhcCccccc
Confidence                2344444 778889999988   6789999999998 877         89999999999999999876643

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

Probab=99.22  E-value=1.2e-11  Score=141.22  Aligned_cols=156  Identities=21%  Similarity=0.319  Sum_probs=108.1

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEec-cCC------CcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEE
Q 003717           14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVR-TKG------RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLE   86 (800)
Q Consensus        14 rTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIR-dTG------RGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe   86 (800)
                      .+|||.||+|.+|.++|...|..+|.|.++.|.. ..+      .|||||+|.+  .++|..|+..|+|+.|+|+.|.|.
T Consensus       516 t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~--~e~A~~a~k~lqgtvldGH~l~lk  593 (725)
T KOG0110|consen  516 TKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAK--PESAQAALKALQGTVLDGHKLELK  593 (725)
T ss_pred             hhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecC--HHHHHHHHHHhcCceecCceEEEE
Confidence            3499999999999999999999999999998872 212      3999999997  999999999999999999999999


Q ss_pred             eccchhhHHHhhhHHHHhhhhCCCCCCCCCCCCCCCcccCCCCCCCCCcchhhcccccCccceeeeccCCC-CCcc-ccc
Q 003717           87 RAKEHYLARLKREWAEDDAQLVNPPVTDSVAPDNKDATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPFCGT-GKHK-YSF  164 (800)
Q Consensus        87 ~AKpr~~~RlkrEraq~rak~~~sp~sD~Vd~~~~kl~is~~Lkksvdesd~LreyFskyGKVKsVp~pgT-GK~K-YGF  164 (800)
                      ++..+.....        ++ .     .......+++.+.+ +++...- ..++.+|+.||.+++|++|-- |+.. +||
T Consensus       594 ~S~~k~~~~~--------gK-~-----~~~kk~~tKIlVRN-ipFeAt~-rEVr~LF~aFGqlksvRlPKK~~k~a~rGF  657 (725)
T KOG0110|consen  594 ISENKPASTV--------GK-K-----KSKKKKGTKILVRN-IPFEATK-REVRKLFTAFGQLKSVRLPKKIGKGAHRGF  657 (725)
T ss_pred             eccCcccccc--------cc-c-----cccccccceeeeec-cchHHHH-HHHHHHHhcccceeeeccchhhcchhhccc
Confidence            9862211100        00 0     00111123343322 3333322 889999999999999988732 3322 344


Q ss_pred             ccccCCCCCcccccccchhhhhhhhccCcc
Q 003717          165 QRVEAPPLPKYFCDCEEHSAAFHAAEGKQI  194 (800)
Q Consensus       165 ~~ve~Ps~pV~F~sfEea~aA~eAmNG~~i  194 (800)
                      +       .|.|.+-.++..|++++..-|+
T Consensus       658 ~-------Fv~f~t~~ea~nA~~al~STHl  680 (725)
T KOG0110|consen  658 G-------FVDFLTPREAKNAFDALGSTHL  680 (725)
T ss_pred             e-------eeeccCcHHHHHHHHhhcccce
Confidence            2       2555555566667766664443

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.22  E-value=5.8e-11  Score=97.54  Aligned_cols=67  Identities=30%  Similarity=0.617  Sum_probs=60.1

Q ss_pred             EEEeCCCCCCCHHHHHHhhhcCCceeEEEEeccC---CCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEE
Q 003717           16 IYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK---GRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLR   84 (800)
Q Consensus        16 LFVGNLP~nVTEEDLrelFSqFG~VksVrVIRdT---GRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~Lr   84 (800)
                      |||+|||+.+++++|+++|+.||.|..+.++..+   .+|+|||+|.+  .++|.+|+..++|..|+|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~--~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSS--EEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESS--HHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCC--HHHHHHHHHHCCCcEECCEEcC
Confidence            7999999999999999999999999999998542   36999999997  9999999999999999999985

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 ....

>smart00362 RRM_2 RNA recognition motif

Probab=99.21  E-value=8.1e-11  Score=92.28  Aligned_cols=70  Identities=31%  Similarity=0.622  Sum_probs=64.3

Q ss_pred             EEEEeCCCCCCCHHHHHHhhhcCCceeEEEEeccC--CCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEE
Q 003717           15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK--GRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLE   86 (800)
Q Consensus        15 TLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRdT--GRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe   86 (800)
                      +|||+|||..++.++|+++|.+||.|..+.+++..  .+|+|||+|.+  .++|..|+..++|..+.|++|.|.
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~--~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFES--EEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCC--HHHHHHHHHHhCCcEECCEEEeeC
Confidence            58999999999999999999999999999888543  47999999997  999999999999999999999873

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

Probab=99.21  E-value=3.1e-11  Score=131.57  Aligned_cols=138  Identities=22%  Similarity=0.297  Sum_probs=112.8

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc-CCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEeccchh
Q 003717           14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT-KGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKEHY   92 (800)
Q Consensus        14 rTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd-TGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~AKpr~   92 (800)
                      ..||||   +.+|+..|.++|+.+|+|.+++|+++ ++-|||||.|.+  ..+|++|+.+||...+.|++|+|-|+....
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~tslgy~yvnf~~--~~da~~A~~~~n~~~~~~~~~rim~s~rd~   76 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDATSLGYAYVNFQQ--PADAERALDTMNFDVLKGKPIRIMWSQRDP   76 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecCCccceEEEecCC--HHHHHHHHHHcCCcccCCcEEEeehhccCC
Confidence            469999   99999999999999999999999965 445999999997  999999999999999999999999875321


Q ss_pred             hHHHhhhHHHHhhhhCCCCCCCCCCCCCCCcccCCCCCCCCCcchhhcccccCccceeeeccC--CCCCcccccccccCC
Q 003717           93 LARLKREWAEDDAQLVNPPVTDSVAPDNKDATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPFC--GTGKHKYSFQRVEAP  170 (800)
Q Consensus        93 ~~RlkrEraq~rak~~~sp~sD~Vd~~~~kl~is~~Lkksvdesd~LreyFskyGKVKsVp~p--gTGK~KYGF~~ve~P  170 (800)
                      .                   .         +++.+ |..+++. ..|..+|+.||+|.++...  ..| .|++|      
T Consensus        77 ~-------------------~---------~~i~n-l~~~~~~-~~~~d~f~~~g~ilS~kv~~~~~g-~kg~F------  119 (369)
T KOG0123|consen   77 S-------------------L---------VFIKN-LDESIDN-KSLYDTFSEFGNILSCKVATDENG-SKGYF------  119 (369)
T ss_pred             c-------------------e---------eeecC-CCcccCc-HHHHHHHHhhcCeeEEEEEEcCCC-ceeeE------
Confidence            0                   0         23322 4555655 8999999999997765443  334 56228      


Q ss_pred             CCCcccccccchhhhhhhhccCcccc
Q 003717          171 PLPKYFCDCEEHSAAFHAAEGKQIHH  196 (800)
Q Consensus       171 s~pV~F~sfEea~aA~eAmNG~~i~n  196 (800)
                         |+|.+-+++..|++.+||..++.
T Consensus       120 ---V~f~~e~~a~~ai~~~ng~ll~~  142 (369)
T KOG0123|consen  120 ---VQFESEESAKKAIEKLNGMLLNG  142 (369)
T ss_pred             ---EEeCCHHHHHHHHHHhcCcccCC
Confidence               89999999999999999998865

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

Probab=99.19  E-value=9e-11  Score=111.12  Aligned_cols=76  Identities=34%  Similarity=0.615  Sum_probs=70.2

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc--C--CCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEec
Q 003717           13 QTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--K--GRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERA   88 (800)
Q Consensus        13 srTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd--T--GRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~A   88 (800)
                      ..+|||||||+.+++++|+++|.+||.|..+.+..+  +  .+|||||+|.+  .++|..|+..|+|..|.|++|.|..+
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~--~~~~~~a~~~~~~~~~~~~~~~v~~~  192 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFES--EESAEKAIEELNGKELEGRPLRVQKA  192 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecC--HHHHHHHHHHcCCCeECCceeEeecc
Confidence            489999999999999999999999999999998854  2  37999999997  99999999999999999999999996


Q ss_pred             cc
Q 003717           89 KE   90 (800)
Q Consensus        89 Kp   90 (800)
                      .+
T Consensus       193 ~~  194 (306)
T COG0724         193 QP  194 (306)
T ss_pred             cc
Confidence            53

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

Probab=99.17  E-value=3.4e-11  Score=124.11  Aligned_cols=74  Identities=23%  Similarity=0.469  Sum_probs=65.7

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc--CC--CcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEec
Q 003717           13 QTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--KG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERA   88 (800)
Q Consensus        13 srTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd--TG--RGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~A   88 (800)
                      -++||||||+|.+..+.|+++|++||+|+++.||.|  ++  +|||||+|.+  .+.|.+|+...| -.|+||+-.|..|
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d--~~aa~rAc~dp~-piIdGR~aNcnlA   88 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRD--AEAATRACKDPN-PIIDGRKANCNLA   88 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeec--HHHHHHHhcCCC-Ccccccccccchh
Confidence            478999999999999999999999999999999954  33  6999999995  999999998654 5789999999887


Q ss_pred             c
Q 003717           89 K   89 (800)
Q Consensus        89 K   89 (800)
                      -
T Consensus        89 ~   89 (247)
T KOG0149|consen   89 S   89 (247)
T ss_pred             h
Confidence            3

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

Probab=99.17  E-value=7.8e-11  Score=135.39  Aligned_cols=78  Identities=22%  Similarity=0.451  Sum_probs=71.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc--C--CCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEe
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--K--GRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLER   87 (800)
Q Consensus        12 qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd--T--GRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~   87 (800)
                      ...+||||||++.+++++|+++|+.||.|.+|+|+++  +  .||||||+|.+  .++|.+|+..|||..|+|+.|+|.+
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~--~e~A~kAI~amNg~elgGr~LrV~k  280 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNN--LQSQSEAIASMNLFDLGGQYLRVGK  280 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECC--HHHHHHHHHHhCCCeeCCeEEEEEe
Confidence            3479999999999999999999999999999999954  2  47999999997  9999999999999999999999999


Q ss_pred             ccch
Q 003717           88 AKEH   91 (800)
Q Consensus        88 AKpr   91 (800)
                      |.+.
T Consensus       281 Ai~p  284 (612)
T TIGR01645       281 CVTP  284 (612)
T ss_pred             cCCC
Confidence            8754

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.

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

Probab=99.17  E-value=1.2e-10  Score=133.30  Aligned_cols=75  Identities=25%  Similarity=0.407  Sum_probs=69.7

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhhcC--CceeEEEEeccCCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEecc
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSL--GEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAK   89 (800)
Q Consensus        12 qsrTLFVGNLP~nVTEEDLrelFSqF--G~VksVrVIRdTGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~AK   89 (800)
                      ..++|||+||++.+++++|+++|++|  |.|.+|.++    ++||||+|.+  .++|.+|+..|||..|+|+.|+|.+|+
T Consensus       232 ~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~----rgfAFVeF~s--~e~A~kAi~~lnG~~i~Gr~I~V~~Ak  305 (578)
T TIGR01648       232 KVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI----RDYAFVHFED--REDAVKAMDELNGKELEGSEIEVTLAK  305 (578)
T ss_pred             cccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee----cCeEEEEeCC--HHHHHHHHHHhCCCEECCEEEEEEEcc
Confidence            35789999999999999999999999  999999875    4699999997  999999999999999999999999998


Q ss_pred             chh
Q 003717           90 EHY   92 (800)
Q Consensus        90 pr~   92 (800)
                      |..
T Consensus       306 p~~  308 (578)
T TIGR01648       306 PVD  308 (578)
T ss_pred             CCC
Confidence            863

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.

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

Probab=99.16  E-value=4.5e-11  Score=114.53  Aligned_cols=81  Identities=15%  Similarity=0.360  Sum_probs=72.1

Q ss_pred             hhhccCCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEec----cCCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeE
Q 003717            7 EAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVR----TKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGR   82 (800)
Q Consensus         7 e~Ev~qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIR----dTGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~   82 (800)
                      ....+...+||||||++-+++++|.++|+.+|.|..|.|-.    .+..|||||+|.+  .++|..|+.-++|..|+.++
T Consensus        30 ~~a~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~--~~dA~~AlryisgtrLddr~  107 (153)
T KOG0121|consen   30 LEALRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYS--RDDAEDALRYISGTRLDDRP  107 (153)
T ss_pred             HHHHhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEec--chhHHHHHHHhccCcccccc
Confidence            34556788999999999999999999999999999986652    2457999999998  99999999999999999999


Q ss_pred             EEEEecc
Q 003717           83 LRLERAK   89 (800)
Q Consensus        83 LrVe~AK   89 (800)
                      |+|++.-
T Consensus       108 ir~D~D~  114 (153)
T KOG0121|consen  108 IRIDWDA  114 (153)
T ss_pred             eeeeccc
Confidence            9999853

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.14  E-value=1.3e-10  Score=125.72  Aligned_cols=78  Identities=29%  Similarity=0.538  Sum_probs=70.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc--CC--CcEEEEEecCCCHHHHHHHHHhcCCcEeCC--eEEEE
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--KG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKG--GRLRL   85 (800)
Q Consensus        12 qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd--TG--RGFGFVEFeS~D~EdAekAIe~LNG~eLdG--R~LrV   85 (800)
                      ..++|||+|||+.+|+++|+++|++||.|..|.|+++  ++  +|||||+|.+  .++|++||..||++.+.|  ++|+|
T Consensus       192 ~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~--~e~A~~Ai~~lng~~~~g~~~~l~V  269 (346)
T TIGR01659       192 KDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNK--REEAQEAISALNNVIPEGGSQPLTV  269 (346)
T ss_pred             ccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECC--HHHHHHHHHHhCCCccCCCceeEEE
Confidence            3578999999999999999999999999999999855  33  6999999997  999999999999999976  79999


Q ss_pred             Eeccch
Q 003717           86 ERAKEH   91 (800)
Q Consensus        86 e~AKpr   91 (800)
                      .+|..+
T Consensus       270 ~~a~~~  275 (346)
T TIGR01659       270 RLAEEH  275 (346)
T ss_pred             EECCcc
Confidence            998765

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).

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

Probab=99.13  E-value=1.4e-10  Score=120.34  Aligned_cols=81  Identities=26%  Similarity=0.509  Sum_probs=74.3

Q ss_pred             hccCCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc--CC--CcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEE
Q 003717            9 EVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--KG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLR   84 (800)
Q Consensus         9 Ev~qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd--TG--RGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~Lr   84 (800)
                      +.+...+|-|.||+.++++++|+++|..||.|..|.+.++  +|  ||||||.|.+  .++|.+||..|||+-++.-.|+
T Consensus       185 ~R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~s--RddA~rAI~~LnG~gyd~LILr  262 (270)
T KOG0122|consen  185 ERDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFES--RDDAARAIADLNGYGYDNLILR  262 (270)
T ss_pred             cCCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEec--HHHHHHHHHHccCcccceEEEE
Confidence            3345678999999999999999999999999999999854  45  7999999997  9999999999999999999999


Q ss_pred             EEeccch
Q 003717           85 LERAKEH   91 (800)
Q Consensus        85 Ve~AKpr   91 (800)
                      |+|++|+
T Consensus       263 vEwskP~  269 (270)
T KOG0122|consen  263 VEWSKPS  269 (270)
T ss_pred             EEecCCC
Confidence            9999986

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

Probab=99.13  E-value=1.1e-10  Score=116.47  Aligned_cols=79  Identities=27%  Similarity=0.495  Sum_probs=70.9

Q ss_pred             cCCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEeccCCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEeccc
Q 003717           11 EEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKE   90 (800)
Q Consensus        11 ~qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRdTGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~AKp   90 (800)
                      .-.++||||||+..++..+|..+|..||.|..|-|.+ ...|||||+|+.  ..+|+.|+..|+|..|+|..|+|++..-
T Consensus         8 ~~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvAr-nPPGfAFVEFed--~RDA~DAvr~LDG~~~cG~r~rVE~S~G   84 (195)
T KOG0107|consen    8 NGNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVAR-NPPGFAFVEFED--PRDAEDAVRYLDGKDICGSRIRVELSTG   84 (195)
T ss_pred             CCCceEEeccCCCCcchHHHHHHHHhcCcceeEEEee-cCCCceEEeccC--cccHHHHHhhcCCccccCceEEEEeecC
Confidence            3468999999999999999999999999999886655 467999999996  9999999999999999999999999865


Q ss_pred             hh
Q 003717           91 HY   92 (800)
Q Consensus        91 r~   92 (800)
                      ++
T Consensus        85 ~~   86 (195)
T KOG0107|consen   85 RP   86 (195)
T ss_pred             Cc
Confidence            53

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

Probab=99.12  E-value=7.5e-11  Score=120.13  Aligned_cols=85  Identities=29%  Similarity=0.499  Sum_probs=77.3

Q ss_pred             ccchhhccCCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEeccC----CCcEEEEEecCCCHHHHHHHHHhcCCcEeC
Q 003717            4 KEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK----GRSFGYVDFFPSSHKSLSKLFSTYNGCVWK   79 (800)
Q Consensus         4 keAe~Ev~qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRdT----GRGFGFVEFeS~D~EdAekAIe~LNG~eLd   79 (800)
                      .--+++++.+..|-|-||.+.++.++|+.+|++||.|-+|.|.++.    .+|||||-|..  ..+|+.|+++|+|.+|+
T Consensus         4 g~~PPdv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~--k~daedA~damDG~~ld   81 (256)
T KOG4207|consen    4 GRPPPDVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHD--KRDAEDALDAMDGAVLD   81 (256)
T ss_pred             CCCCCCcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeee--cchHHHHHHhhcceeec
Confidence            3346788888999999999999999999999999999999999663    37999999996  99999999999999999


Q ss_pred             CeEEEEEeccc
Q 003717           80 GGRLRLERAKE   90 (800)
Q Consensus        80 GR~LrVe~AKp   90 (800)
                      |+.|+|.+|+-
T Consensus        82 gRelrVq~ary   92 (256)
T KOG4207|consen   82 GRELRVQMARY   92 (256)
T ss_pred             cceeeehhhhc
Confidence            99999999863

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

Probab=99.11  E-value=4.7e-11  Score=122.51  Aligned_cols=78  Identities=29%  Similarity=0.538  Sum_probs=72.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEec----cCCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEe
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVR----TKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLER   87 (800)
Q Consensus        12 qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIR----dTGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~   87 (800)
                      +.++||||+|...+++.-|...|-.||.|.++.++.    .++||||||+|..  .++|.+||..||+.+|.||.|+|.+
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~--aEDAaaAiDNMnesEL~GrtirVN~   86 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEE--AEDAAAAIDNMNESELFGRTIRVNL   86 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeec--cchhHHHhhcCchhhhcceeEEEee
Confidence            357999999999999999999999999999999983    3679999999997  9999999999999999999999999


Q ss_pred             ccch
Q 003717           88 AKEH   91 (800)
Q Consensus        88 AKpr   91 (800)
                      |+|.
T Consensus        87 AkP~   90 (298)
T KOG0111|consen   87 AKPE   90 (298)
T ss_pred             cCCc
Confidence            9885

>smart00360 RRM RNA recognition motif

Probab=99.08  E-value=4.4e-10  Score=87.60  Aligned_cols=67  Identities=31%  Similarity=0.629  Sum_probs=61.0

Q ss_pred             EeCCCCCCCHHHHHHhhhcCCceeEEEEeccC----CCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEE
Q 003717           18 VGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK----GRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLE   86 (800)
Q Consensus        18 VGNLP~nVTEEDLrelFSqFG~VksVrVIRdT----GRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe   86 (800)
                      |+|||..+++++|+++|.+||.|..+.+....    .+|||||+|.+  .++|..|+..|++..+.|+.|+|.
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~--~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFES--EEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCC--HHHHHHHHHHcCCCeeCCcEEEeC
Confidence            68999999999999999999999999888542    37999999997  999999999999999999999873

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.08  E-value=4.2e-10  Score=116.84  Aligned_cols=75  Identities=24%  Similarity=0.317  Sum_probs=68.0

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEeccCC-CcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEecc
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKG-RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAK   89 (800)
Q Consensus        12 qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRdTG-RGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~AK   89 (800)
                      ...+|||+||++.+|+++|+++|+.||.|.+|+|+++.. +|||||+|.+  .+++..|+ .|+|..|.+++|.|..+.
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~et~gfAfVtF~d--~~aaetAl-lLnGa~l~d~~I~It~~~   79 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKD--AYALETAV-LLSGATIVDQRVCITRWG   79 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCCcceEEEEEECC--HHHHHHHH-hcCCCeeCCceEEEEeCc
Confidence            357999999999999999999999999999999997643 5899999996  89998888 699999999999998764

>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=99.06  E-value=1e-09  Score=86.41  Aligned_cols=71  Identities=37%  Similarity=0.639  Sum_probs=65.2

Q ss_pred             EEEEeCCCCCCCHHHHHHhhhcCCceeEEEEeccC---CCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEe
Q 003717           15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK---GRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLER   87 (800)
Q Consensus        15 TLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRdT---GRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~   87 (800)
                      +|||+|||+.+++++|+++|..||.|..+.+....   ++|+|||+|.+  .++|..|+..+++..+.|+.|.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s--~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFED--EEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECC--HHHHHHHHHHhCCCeECCeEEEEeC
Confidence            48999999999999999999999999999988543   47999999998  9999999999999999999998863

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).

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

Probab=98.99  E-value=3.2e-10  Score=124.57  Aligned_cols=87  Identities=24%  Similarity=0.445  Sum_probs=75.5

Q ss_pred             ccchhhccC---CcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc---CCCcEEEEEecCCCHHHHHHHHHhcCCc-
Q 003717            4 KEAEAEVEE---QTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT---KGRSFGYVDFFPSSHKSLSKLFSTYNGC-   76 (800)
Q Consensus         4 keAe~Ev~q---srTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd---TGRGFGFVEFeS~D~EdAekAIe~LNG~-   76 (800)
                      +-|+.|.+.   .++||||.|+..+++.+++++|++||.|.+|.|+|+   ..||||||.|.+  .+.|..||+.|||. 
T Consensus       112 k~Ad~E~er~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fst--ke~A~~Aika~ng~~  189 (510)
T KOG0144|consen  112 KYADGERERIVEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFST--KEMAVAAIKALNGTQ  189 (510)
T ss_pred             cccchhhhccccchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEeh--HHHHHHHHHhhccce
Confidence            445555554   689999999999999999999999999999999976   459999999998  99999999999995 


Q ss_pred             EeCC--eEEEEEeccchh
Q 003717           77 VWKG--GRLRLERAKEHY   92 (800)
Q Consensus        77 eLdG--R~LrVe~AKpr~   92 (800)
                      ++.|  .+|.|+||.+..
T Consensus       190 tmeGcs~PLVVkFADtqk  207 (510)
T KOG0144|consen  190 TMEGCSQPLVVKFADTQK  207 (510)
T ss_pred             eeccCCCceEEEecccCC
Confidence            5555  699999997653

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

Probab=98.95  E-value=4.9e-09  Score=97.82  Aligned_cols=77  Identities=18%  Similarity=0.256  Sum_probs=70.6

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEeccC-CCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEeccch
Q 003717           13 QTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK-GRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKEH   91 (800)
Q Consensus        13 srTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRdT-GRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~AKpr   91 (800)
                      .+-|||.|||+.+|.+++.++|++||.|..++|-... -||-|||.|+.  ..+|.+|+..|+|..++++.|.|-+-++.
T Consensus        18 nriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~TrGTAFVVYed--i~dAk~A~dhlsg~n~~~ryl~vlyyq~~   95 (124)
T KOG0114|consen   18 NRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKETRGTAFVVYED--IFDAKKACDHLSGYNVDNRYLVVLYYQPE   95 (124)
T ss_pred             heeEEEecCCccccHHHHHHHhhcccceEEEEecCccCcCceEEEEehH--hhhHHHHHHHhcccccCCceEEEEecCHH
Confidence            4789999999999999999999999999999986443 38999999996  99999999999999999999999987764

>PF13893 RRM_5: RNA recognition motif

Probab=98.95  E-value=3.4e-09  Score=84.85  Aligned_cols=56  Identities=36%  Similarity=0.620  Sum_probs=51.0

Q ss_pred             HHHhhhcCCceeEEEEeccCCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEec
Q 003717           30 LAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERA   88 (800)
Q Consensus        30 LrelFSqFG~VksVrVIRdTGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~A   88 (800)
                      |+++|++||.|..+.+.+.. +|+|||+|.+  .++|..|+..|||..++|++|+|.+|
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-RGFAFVEFAS--VEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-TTEEEEEESS--HHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC-CCEEEEEECC--HHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            68899999999999988654 7999999997  99999999999999999999999986

(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 ....

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

Probab=98.92  E-value=3.2e-10  Score=113.84  Aligned_cols=77  Identities=26%  Similarity=0.549  Sum_probs=70.2

Q ss_pred             cCCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc--CC--CcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEE
Q 003717           11 EEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--KG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLE   86 (800)
Q Consensus        11 ~qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd--TG--RGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe   86 (800)
                      ....-|||||||+..|+.||.-.|++||.|++|.++|+  ||  +||||+.|+.  .....-|+..|||..|.||.|+|+
T Consensus        33 kdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYED--QRSTILAVDN~NGiki~gRtirVD  110 (219)
T KOG0126|consen   33 KDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYED--QRSTILAVDNLNGIKILGRTIRVD  110 (219)
T ss_pred             ccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecC--ccceEEEEeccCCceecceeEEee
Confidence            34678999999999999999999999999999999976  44  6999999995  999999999999999999999999


Q ss_pred             ecc
Q 003717           87 RAK   89 (800)
Q Consensus        87 ~AK   89 (800)
                      ...
T Consensus       111 Hv~  113 (219)
T KOG0126|consen  111 HVS  113 (219)
T ss_pred             ecc
Confidence            753

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

Probab=98.91  E-value=2.2e-09  Score=118.44  Aligned_cols=78  Identities=26%  Similarity=0.402  Sum_probs=72.1

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEeccCCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEeccch
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKEH   91 (800)
Q Consensus        12 qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRdTGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~AKpr   91 (800)
                      +.+-|||.||+.+||++.|+++|.+||.|..|..++|    ||||.|..  .++|.+||+.+||++|+|..|.|.+|+|.
T Consensus       258 ~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD----YaFVHf~e--R~davkAm~~~ngkeldG~~iEvtLAKP~  331 (506)
T KOG0117|consen  258 KVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD----YAFVHFAE--REDAVKAMKETNGKELDGSPIEVTLAKPV  331 (506)
T ss_pred             heeeeeeeccchhhhHHHHHHHHHhccceEEeecccc----eeEEeecc--hHHHHHHHHHhcCceecCceEEEEecCCh
Confidence            4568999999999999999999999999999988766    99999997  99999999999999999999999999997


Q ss_pred             hhHH
Q 003717           92 YLAR   95 (800)
Q Consensus        92 ~~~R   95 (800)
                      ...+
T Consensus       332 ~k~k  335 (506)
T KOG0117|consen  332 DKKK  335 (506)
T ss_pred             hhhc
Confidence            5443

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

Probab=98.90  E-value=3.8e-09  Score=112.22  Aligned_cols=79  Identities=14%  Similarity=0.441  Sum_probs=71.7

Q ss_pred             cCCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc--C--CCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEE
Q 003717           11 EEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--K--GRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLE   86 (800)
Q Consensus        11 ~qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd--T--GRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe   86 (800)
                      ++-+||||+-|++.+++..|+..|+.||.|..++|+++  +  .+|||||+|..  ..+...|....+|..|+|+.|.|+
T Consensus        99 DPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~--erdm~~AYK~adG~~Idgrri~VD  176 (335)
T KOG0113|consen   99 DPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEH--ERDMKAAYKDADGIKIDGRRILVD  176 (335)
T ss_pred             CccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEecc--HHHHHHHHHhccCceecCcEEEEE
Confidence            34589999999999999999999999999999999955  3  47999999996  999999999999999999999999


Q ss_pred             eccch
Q 003717           87 RAKEH   91 (800)
Q Consensus        87 ~AKpr   91 (800)
                      .-..+
T Consensus       177 vERgR  181 (335)
T KOG0113|consen  177 VERGR  181 (335)
T ss_pred             ecccc
Confidence            86544

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

Probab=98.90  E-value=2.1e-09  Score=108.44  Aligned_cols=77  Identities=22%  Similarity=0.504  Sum_probs=69.8

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEeccC-CCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEeccc
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK-GRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKE   90 (800)
Q Consensus        12 qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRdT-GRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~AKp   90 (800)
                      ...+|||||||.++.+.+|.++|.+||.|..|.+.... ..+||||+|+.  ..+|+.||..-+|..++|..|+|+++..
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~g~ppfafVeFEd--~RDAeDAiygRdGYdydg~rLRVEfprg   82 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRPGPPPFAFVEFED--PRDAEDAIYGRDGYDYDGCRLRVEFPRG   82 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCCCCCCeeEEEecC--ccchhhhhhcccccccCcceEEEEeccC
Confidence            45799999999999999999999999999999886333 36899999995  9999999999999999999999999864

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

Probab=98.90  E-value=4.2e-09  Score=110.80  Aligned_cols=76  Identities=22%  Similarity=0.461  Sum_probs=71.1

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEeccCCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEeccch
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKEH   91 (800)
Q Consensus        12 qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRdTGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~AKpr   91 (800)
                      ..++|||||++..+++++||+.|+.||.|.+|+|.+  -+||+||.|.+  .|.|..||..||+.++.|..+++.|.+..
T Consensus       163 ~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk--~qGYaFVrF~t--kEaAahAIv~mNntei~G~~VkCsWGKe~  238 (321)
T KOG0148|consen  163 DNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFK--DQGYAFVRFET--KEAAAHAIVQMNNTEIGGQLVRCSWGKEG  238 (321)
T ss_pred             CCceEEeCCcCccccHHHHHHhcccCCcceEEEEec--ccceEEEEecc--hhhHHHHHHHhcCceeCceEEEEeccccC
Confidence            357999999999999999999999999999999976  57999999998  99999999999999999999999998754

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

Probab=98.85  E-value=5.3e-09  Score=116.53  Aligned_cols=77  Identities=25%  Similarity=0.581  Sum_probs=71.5

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEe--ccCC--CcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEecc
Q 003717           14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RTKG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAK   89 (800)
Q Consensus        14 rTLFVGNLP~nVTEEDLrelFSqFG~VksVrVI--RdTG--RGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~AK   89 (800)
                      ..+||||+|+++++++|..+|+..|.|.+++++  +++|  +||||++|..  .++|..|++.|||.++.||+|+|.++.
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~--~~~~~~a~~~lNg~~~~gr~l~v~~~~   96 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTD--EETAERAIRNLNGAEFNGRKLRVNYAS   96 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCc--hhhHHHHHHhcCCcccCCceEEeeccc
Confidence            789999999999999999999999999999999  4455  7999999996  999999999999999999999999997


Q ss_pred             chh
Q 003717           90 EHY   92 (800)
Q Consensus        90 pr~   92 (800)
                      .+.
T Consensus        97 ~~~   99 (435)
T KOG0108|consen   97 NRK   99 (435)
T ss_pred             ccc
Confidence            653

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

Probab=98.81  E-value=1.6e-08  Score=104.01  Aligned_cols=81  Identities=25%  Similarity=0.468  Sum_probs=72.4

Q ss_pred             hccCCcEEEEeCCCCCCCHHHHHH----hhhcCCceeEEEEe-ccCCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEE
Q 003717            9 EVEEQTRIYVGGLGEKVTDDDLAK----VFSSLGEVKAVDIV-RTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRL   83 (800)
Q Consensus         9 Ev~qsrTLFVGNLP~nVTEEDLre----lFSqFG~VksVrVI-RdTGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~L   83 (800)
                      +..+..||||.||+..+..++|++    +|++||.|..|.+. +.+.||-|||.|..  .+.|..|+..|+|..+.|+++
T Consensus         5 ~~~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~--~~~As~A~r~l~gfpFygK~m   82 (221)
T KOG4206|consen    5 SVNPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKE--TEAASAALRALQGFPFYGKPM   82 (221)
T ss_pred             ccCCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecC--hhHHHHHHHHhcCCcccCchh
Confidence            445556999999999999999888    99999999998877 34569999999997  999999999999999999999


Q ss_pred             EEEeccch
Q 003717           84 RLERAKEH   91 (800)
Q Consensus        84 rVe~AKpr   91 (800)
                      +|.+|+..
T Consensus        83 riqyA~s~   90 (221)
T KOG4206|consen   83 RIQYAKSD   90 (221)
T ss_pred             heecccCc
Confidence            99999754

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

Probab=98.74  E-value=1.3e-08  Score=98.65  Aligned_cols=76  Identities=24%  Similarity=0.459  Sum_probs=70.6

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEe--ccCC--CcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEe
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RTKG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLER   87 (800)
Q Consensus        12 qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVI--RdTG--RGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~   87 (800)
                      ...-|||.++...++++++.+.|..||.|+.+.+-  +.+|  +||+.|+|++  .+.|++|+..|||..|.|+.|.|+|
T Consensus        71 EGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet--~keAq~A~~~~Ng~~ll~q~v~VDw  148 (170)
T KOG0130|consen   71 EGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYET--LKEAQAAIDALNGAELLGQNVSVDW  148 (170)
T ss_pred             eeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHh--HHHHHHHHHhccchhhhCCceeEEE
Confidence            46789999999999999999999999999999887  4456  7999999998  9999999999999999999999999


Q ss_pred             cc
Q 003717           88 AK   89 (800)
Q Consensus        88 AK   89 (800)
                      +-
T Consensus       149 ~F  150 (170)
T KOG0130|consen  149 CF  150 (170)
T ss_pred             EE
Confidence            84

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

Probab=98.71  E-value=1.1e-08  Score=115.20  Aligned_cols=157  Identities=18%  Similarity=0.315  Sum_probs=114.1

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEeccC----CCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEec
Q 003717           13 QTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK----GRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERA   88 (800)
Q Consensus        13 srTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRdT----GRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~A   88 (800)
                      .+++|+-.|+..++.-+|.++|+.+|.|..|++|.++    .+|.|||+|..  ......|| .|.|..+.|.+|.|...
T Consensus       179 ~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D--~~sVp~ai-aLsGqrllg~pv~vq~s  255 (549)
T KOG0147|consen  179 QRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCD--EQSVPLAI-ALSGQRLLGVPVIVQLS  255 (549)
T ss_pred             HHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEec--ccchhhHh-hhcCCcccCceeEeccc
Confidence            5789999999999999999999999999999999542    36999999995  77777777 79999999999999865


Q ss_pred             cchhhHHHhhhHHHHhhhhCCCCCCCCCCCCCCCc-ccCCCCCCCCCcchhhcccccCccceeeecc---CCCCCcc-cc
Q 003717           89 KEHYLARLKREWAEDDAQLVNPPVTDSVAPDNKDA-TRLDTPKKLLDKDKKLNIFFPRLRKVKTLPF---CGTGKHK-YS  163 (800)
Q Consensus        89 Kpr~~~RlkrEraq~rak~~~sp~sD~Vd~~~~kl-~is~~Lkksvdesd~LreyFskyGKVKsVp~---pgTGK~K-YG  163 (800)
                      ....      .+++.     ..+...+.....+-. ...+.|-..+++ ++++.+|..||+|..|.+   ..||..| ||
T Consensus       256 Eaek------nr~a~-----~s~a~~~k~~~~p~~rl~vgnLHfNite-~~lr~ifepfg~Ie~v~l~~d~~tG~skgfG  323 (549)
T KOG0147|consen  256 EAEK------NRAAN-----ASPALQGKGFTGPMRRLYVGNLHFNITE-DMLRGIFEPFGKIENVQLTKDSETGRSKGFG  323 (549)
T ss_pred             HHHH------HHHHh-----ccccccccccccchhhhhhcccccCchH-HHHhhhccCcccceeeeeccccccccccCcc
Confidence            3211      11111     111111100000001 122334556656 899999999999876543   4599998 66


Q ss_pred             cccccCCCCCcccccccchhhhhhhhccCc
Q 003717          164 FQRVEAPPLPKYFCDCEEHSAAFHAAEGKQ  193 (800)
Q Consensus       164 F~~ve~Ps~pV~F~sfEea~aA~eAmNG~~  193 (800)
                      |         +.|..-+.+..|++.|||..
T Consensus       324 f---------i~f~~~~~ar~a~e~lngfe  344 (549)
T KOG0147|consen  324 F---------ITFVNKEDARKALEQLNGFE  344 (549)
T ss_pred             e---------EEEecHHHHHHHHHHhccce
Confidence            6         78999999999999999933

>smart00361 RRM_1 RNA recognition motif

Probab=98.65  E-value=9.2e-08  Score=80.61  Aligned_cols=57  Identities=25%  Similarity=0.452  Sum_probs=49.6

Q ss_pred             HHHHHHhhh----cCCceeEEE-Ee--ccC----CCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEE
Q 003717           27 DDDLAKVFS----SLGEVKAVD-IV--RTK----GRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRL   85 (800)
Q Consensus        27 EEDLrelFS----qFG~VksVr-VI--RdT----GRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrV   85 (800)
                      +++|+++|+    .||.|.++. |+  +.+    .+|||||.|.+  .++|.+|+..|||..+.||.|++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~--~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFER--SEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECC--HHHHHHHHHHhCCCEECCEEEEe
Confidence            578899998    999999995 43  322    38999999997  99999999999999999999986

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

Probab=98.63  E-value=3.3e-08  Score=101.64  Aligned_cols=150  Identities=20%  Similarity=0.380  Sum_probs=105.6

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEeccCCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEeccchhh
Q 003717           14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKEHYL   93 (800)
Q Consensus        14 rTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRdTGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~AKpr~~   93 (800)
                      .++|||+||+.+.+.+|..+|..||.|.+|.+    -.|||||+|..  ..+|..|+..+||..|.|-.+.|++|+...-
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~m----k~gf~fv~fed--~rda~Dav~~l~~~~l~~e~~vve~~r~~~~   75 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADM----KNGFGFVEFED--PRDADDAVHDLDGKELCGERLVVEHARGKRR   75 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhcccccccee----ecccceeccCc--hhhhhcccchhcCceecceeeeeeccccccc
Confidence            57999999999999999999999999999877    34899999995  9999999999999999999999999875421


Q ss_pred             HHHhhhHHHHhhhhCCCCCCC-C---C----CCCCCC-cccCCCCCCCCCcchhhcccccCccceeeeccCCCCCccccc
Q 003717           94 ARLKREWAEDDAQLVNPPVTD-S---V----APDNKD-ATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPFCGTGKHKYSF  164 (800)
Q Consensus        94 ~RlkrEraq~rak~~~sp~sD-~---V----d~~~~k-l~is~~Lkksvdesd~LreyFskyGKVKsVp~pgTGK~KYGF  164 (800)
                      .+             ..+... .   .    -+.... ..+...+...+.. .+|..+|..+|.+.....    ...++|
T Consensus        76 ~~-------------g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~-qdl~d~~~~~g~~~~~~~----~~~~~~  137 (216)
T KOG0106|consen   76 GR-------------GRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSW-QDLKDHFRPAGEVTYVDA----RRNFAF  137 (216)
T ss_pred             cc-------------CCCCCCCccchhhccCCcccccceeeeccchhhhhH-HHHhhhhcccCCCchhhh----hccccc
Confidence            11             000000 0   0    000000 0111112222222 789999999999843211    222344


Q ss_pred             ccccCCCCCcccccccchhhhhhhhccCcccc
Q 003717          165 QRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHH  196 (800)
Q Consensus       165 ~~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n  196 (800)
                               |.|..-++++.|++.++|..+-.
T Consensus       138 ---------v~Fs~~~da~ra~~~l~~~~~~~  160 (216)
T KOG0106|consen  138 ---------VEFSEQEDAKRALEKLDGKKLNG  160 (216)
T ss_pred             ---------eeehhhhhhhhcchhccchhhcC
Confidence                     89999999999999988776644

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

Probab=98.59  E-value=5.4e-08  Score=109.70  Aligned_cols=75  Identities=27%  Similarity=0.595  Sum_probs=68.4

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc--CC--CcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEecc
Q 003717           14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--KG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAK   89 (800)
Q Consensus        14 rTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd--TG--RGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~AK   89 (800)
                      .+||||||.+++++++|+.+|+.||.|..|.++++  +|  +|||||+|..  .++|.+|+..|||.+|-||.|+|..-.
T Consensus       279 ~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~--~~~ar~a~e~lngfelAGr~ikV~~v~  356 (549)
T KOG0147|consen  279 RRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVN--KEDARKALEQLNGFELAGRLIKVSVVT  356 (549)
T ss_pred             hhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEec--HHHHHHHHHHhccceecCceEEEEEee
Confidence            34999999999999999999999999999999865  56  6999999997  999999999999999999999997654


Q ss_pred             c
Q 003717           90 E   90 (800)
Q Consensus        90 p   90 (800)
                      .
T Consensus       357 ~  357 (549)
T KOG0147|consen  357 E  357 (549)
T ss_pred             e
Confidence            3

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

Probab=98.59  E-value=4.3e-08  Score=104.19  Aligned_cols=74  Identities=20%  Similarity=0.431  Sum_probs=69.6

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEeccCCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEeccch
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKEH   91 (800)
Q Consensus        12 qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRdTGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~AKpr   91 (800)
                      ..++||||||.+.++..+|+..|++||+|.+|.|++    +|+||.|..  .++|..|+..||+.+++|++|+|..+..|
T Consensus        77 ~stkl~vgNis~tctn~ElRa~fe~ygpviecdivk----dy~fvh~d~--~eda~~air~l~~~~~~gk~m~vq~stsr  150 (346)
T KOG0109|consen   77 ASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVK----DYAFVHFDR--AEDAVEAIRGLDNTEFQGKRMHVQLSTSR  150 (346)
T ss_pred             CccccccCCCCccccCHHHhhhhcccCCceeeeeec----ceeEEEEee--ccchHHHHhcccccccccceeeeeeeccc
Confidence            467999999999999999999999999999999876    599999998  99999999999999999999999998765

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

Probab=98.54  E-value=9.5e-08  Score=107.98  Aligned_cols=77  Identities=25%  Similarity=0.477  Sum_probs=70.9

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEeccC---C-CcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEec
Q 003717           13 QTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK---G-RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERA   88 (800)
Q Consensus        13 srTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRdT---G-RGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~A   88 (800)
                      .++|||.+|+..+...+|+.+|++||.|+.+.|+++.   | |+||||++.+  .++|.+||..|+.++|.|+.|-|+.|
T Consensus       405 gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSt--s~eAtkCI~hLHrTELHGrmISVEka  482 (940)
T KOG4661|consen  405 GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMST--SAEATKCIEHLHRTELHGRMISVEKA  482 (940)
T ss_pred             ccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecc--hHHHHHHHHHhhhhhhcceeeeeeec
Confidence            5799999999999999999999999999999999542   3 7999999998  99999999999999999999999998


Q ss_pred             cch
Q 003717           89 KEH   91 (800)
Q Consensus        89 Kpr   91 (800)
                      +..
T Consensus       483 KNE  485 (940)
T KOG4661|consen  483 KNE  485 (940)
T ss_pred             ccC
Confidence            754

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

Probab=98.53  E-value=1.9e-07  Score=101.03  Aligned_cols=80  Identities=24%  Similarity=0.495  Sum_probs=70.6

Q ss_pred             hhhccCCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEeccCCCcEEEEEecCCCHHHHHHHHHh-cCCcEeCCeEEEE
Q 003717            7 EAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFST-YNGCVWKGGRLRL   85 (800)
Q Consensus         7 e~Ev~qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRdTGRGFGFVEFeS~D~EdAekAIe~-LNG~eLdGR~LrV   85 (800)
                      .++....++||||+|...+++.+|++.|.+||.|..++++.  ++|+|||+|.+  ..+|+.|... +|...|+|++|.|
T Consensus       222 pPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~--~~~CAFv~ftT--R~aAE~Aae~~~n~lvI~G~Rl~i  297 (377)
T KOG0153|consen  222 PPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILP--RKGCAFVTFTT--REAAEKAAEKSFNKLVINGFRLKI  297 (377)
T ss_pred             CCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeec--ccccceeeehh--hHHHHHHHHhhcceeeecceEEEE
Confidence            45566678999999999999999999999999999998875  56799999998  8888888765 6667889999999


Q ss_pred             Eeccc
Q 003717           86 ERAKE   90 (800)
Q Consensus        86 e~AKp   90 (800)
                      .|+.+
T Consensus       298 ~Wg~~  302 (377)
T KOG0153|consen  298 KWGRP  302 (377)
T ss_pred             EeCCC
Confidence            99988

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

Probab=98.51  E-value=1.1e-07  Score=109.75  Aligned_cols=79  Identities=29%  Similarity=0.503  Sum_probs=72.9

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc----CCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEec
Q 003717           13 QTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT----KGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERA   88 (800)
Q Consensus        13 srTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd----TGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~A   88 (800)
                      ..+|.|.|||+..+-.+++.+|..||.|.+|+++..    .+||||||+|-+  ..+|.+|+..|.++.|.||+|.++||
T Consensus       613 ~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t--~~ea~nA~~al~STHlyGRrLVLEwA  690 (725)
T KOG0110|consen  613 GTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLT--PREAKNAFDALGSTHLYGRRLVLEWA  690 (725)
T ss_pred             cceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccC--cHHHHHHHHhhcccceechhhheehh
Confidence            579999999999999999999999999999999833    358999999998  99999999999999999999999999


Q ss_pred             cchhh
Q 003717           89 KEHYL   93 (800)
Q Consensus        89 Kpr~~   93 (800)
                      +....
T Consensus       691 ~~d~~  695 (725)
T KOG0110|consen  691 KSDNT  695 (725)
T ss_pred             ccchH
Confidence            87654

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

Probab=98.51  E-value=1.9e-07  Score=98.53  Aligned_cols=89  Identities=20%  Similarity=0.464  Sum_probs=75.5

Q ss_pred             CCcccchhhccC--CcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc---CCCcEEEEEecCCCHHHHHHHHHhcCC
Q 003717            1 MEKKEAEAEVEE--QTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT---KGRSFGYVDFFPSSHKSLSKLFSTYNG   75 (800)
Q Consensus         1 mEKkeAe~Ev~q--srTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd---TGRGFGFVEFeS~D~EdAekAIe~LNG   75 (800)
                      |+-|.|+.|.+.  .++||||-|...-.|+|++++|..||.|.+|.+.+.   ..+||+||.|.+  ..+|..||..|+|
T Consensus         5 iqvkpadsesrg~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s--~~eAqaAI~aLHg   82 (371)
T KOG0146|consen    5 IQVKPADSESRGGDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSS--HAEAQAAINALHG   82 (371)
T ss_pred             ccccccccccCCccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEecc--chHHHHHHHHhcc
Confidence            456677766663  679999999999999999999999999999999954   358999999998  9999999999999


Q ss_pred             cEe-CC--eEEEEEeccch
Q 003717           76 CVW-KG--GRLRLERAKEH   91 (800)
Q Consensus        76 ~eL-dG--R~LrVe~AKpr   91 (800)
                      ..- -|  ..|.|++|...
T Consensus        83 SqTmpGASSSLVVK~ADTd  101 (371)
T KOG0146|consen   83 SQTMPGASSSLVVKFADTD  101 (371)
T ss_pred             cccCCCCccceEEEeccch
Confidence            644 34  68999998544

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

Probab=98.48  E-value=2e-07  Score=108.31  Aligned_cols=75  Identities=19%  Similarity=0.448  Sum_probs=70.1

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEeccCCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEeccch
Q 003717           13 QTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKEH   91 (800)
Q Consensus        13 srTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRdTGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~AKpr   91 (800)
                      .+|||||+|+.++++.+|..+|+.||.|.+|.++.  .||||||.+..  ..+|.+|+.+|+.+.+.++.|+|.||...
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~--~R~cAfI~M~~--RqdA~kalqkl~n~kv~~k~Iki~Wa~g~  495 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIP--PRGCAFIKMVR--RQDAEKALQKLSNVKVADKTIKIAWAVGK  495 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeecc--CCceeEEEEee--hhHHHHHHHHHhcccccceeeEEeeeccC
Confidence            57999999999999999999999999999998865  68999999997  99999999999999999999999999543

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

Probab=98.42  E-value=1.7e-07  Score=98.87  Aligned_cols=80  Identities=20%  Similarity=0.381  Sum_probs=72.2

Q ss_pred             cCCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEe--ccC--CCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEE
Q 003717           11 EEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RTK--GRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLE   86 (800)
Q Consensus        11 ~qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVI--RdT--GRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe   86 (800)
                      ....+|||-.||.+..+.+|..+|-.||.|++.+|.  |.+  .++||||.|.+  ...|+.||..|||..|+-++|+|.
T Consensus       283 PeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDN--p~SaQaAIqAMNGFQIGMKRLKVQ  360 (371)
T KOG0146|consen  283 PEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDN--PASAQAAIQAMNGFQIGMKRLKVQ  360 (371)
T ss_pred             CCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCC--chhHHHHHHHhcchhhhhhhhhhh
Confidence            357899999999999999999999999999999887  333  47999999998  999999999999999999999998


Q ss_pred             eccchh
Q 003717           87 RAKEHY   92 (800)
Q Consensus        87 ~AKpr~   92 (800)
                      .-+|+.
T Consensus       361 LKRPkd  366 (371)
T KOG0146|consen  361 LKRPKD  366 (371)
T ss_pred             hcCccc
Confidence            877764

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

Probab=98.41  E-value=1.6e-06  Score=89.88  Aligned_cols=80  Identities=20%  Similarity=0.386  Sum_probs=67.2

Q ss_pred             ccCCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEe-ccCC----CcEEEEEecCCCHHHHHHHHHhcCCcEeC---Ce
Q 003717           10 VEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV-RTKG----RSFGYVDFFPSSHKSLSKLFSTYNGCVWK---GG   81 (800)
Q Consensus        10 v~qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVI-RdTG----RGFGFVEFeS~D~EdAekAIe~LNG~eLd---GR   81 (800)
                      ....+||||.+||.++...+|..+|..|-.-..+.+. ..++    +-+|||+|.+  ...|..|+.+|||..|+   +.
T Consensus        31 ~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s--~q~A~aamnaLNGvrFDpE~~s  108 (284)
T KOG1457|consen   31 PGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTS--HQFALAAMNALNGVRFDPETGS  108 (284)
T ss_pred             ccccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecc--hHHHHHHHHHhcCeeeccccCc
Confidence            3346899999999999999999999998666666554 2222    3699999997  99999999999999997   88


Q ss_pred             EEEEEeccch
Q 003717           82 RLRLERAKEH   91 (800)
Q Consensus        82 ~LrVe~AKpr   91 (800)
                      .|+|++|+..
T Consensus       109 tLhiElAKSN  118 (284)
T KOG1457|consen  109 TLHIELAKSN  118 (284)
T ss_pred             eeEeeehhcC
Confidence            9999998653

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

Probab=98.39  E-value=4.4e-07  Score=98.59  Aligned_cols=78  Identities=18%  Similarity=0.452  Sum_probs=71.1

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc--CC--CcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEe
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--KG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLER   87 (800)
Q Consensus        12 qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd--TG--RGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~   87 (800)
                      +..-|||.-|.+-+++++|.-+|+.||.|.+|.||++  +|  -.||||+|.+  .+++++|.-.|+...|+.++|.|++
T Consensus       238 PeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen--~escE~AyFKMdNvLIDDrRIHVDF  315 (479)
T KOG0415|consen  238 PENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFEN--KESCEQAYFKMDNVLIDDRRIHVDF  315 (479)
T ss_pred             CcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecc--hhhHHHHHhhhcceeeccceEEeeh
Confidence            3567999999999999999999999999999999976  34  2699999998  9999999999999999999999999


Q ss_pred             ccch
Q 003717           88 AKEH   91 (800)
Q Consensus        88 AKpr   91 (800)
                      ++.-
T Consensus       316 SQSV  319 (479)
T KOG0415|consen  316 SQSV  319 (479)
T ss_pred             hhhh
Confidence            8653

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

Probab=98.35  E-value=4.7e-07  Score=91.36  Aligned_cols=81  Identities=19%  Similarity=0.392  Sum_probs=70.1

Q ss_pred             hccCCcEEEEeCCCCCCCHHHHHHhhhcCCceeEE-EEecc----CCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEE
Q 003717            9 EVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAV-DIVRT----KGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRL   83 (800)
Q Consensus         9 Ev~qsrTLFVGNLP~nVTEEDLrelFSqFG~VksV-rVIRd----TGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~L   83 (800)
                      ......+||||||.+.+++..|.+.|+.||.+... .++++    .++|||||.|.+  .+.+.+|+..|||..+..++|
T Consensus        92 nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~s--feasd~ai~s~ngq~l~nr~i  169 (203)
T KOG0131|consen   92 NLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYAS--FEASDAAIGSMNGQYLCNRPI  169 (203)
T ss_pred             cccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechh--HHHHHHHHHHhccchhcCCce
Confidence            34456899999999999999999999999997663 55543    347999999997  999999999999999999999


Q ss_pred             EEEeccch
Q 003717           84 RLERAKEH   91 (800)
Q Consensus        84 rVe~AKpr   91 (800)
                      .|.+|..+
T Consensus       170 tv~ya~k~  177 (203)
T KOG0131|consen  170 TVSYAFKK  177 (203)
T ss_pred             EEEEEEec
Confidence            99999654

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

Probab=98.34  E-value=6.2e-07  Score=97.73  Aligned_cols=79  Identities=23%  Similarity=0.471  Sum_probs=71.3

Q ss_pred             hccCCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc----CCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEE
Q 003717            9 EVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT----KGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLR   84 (800)
Q Consensus         9 Ev~qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd----TGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~Lr   84 (800)
                      |...-.+|||..+..+.+++||+..|+.||.|..|.+.+.    ++|||||++|.+  ......||..||-..|+|+.|+
T Consensus       206 eAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n--~qs~~eAiasMNlFDLGGQyLR  283 (544)
T KOG0124|consen  206 EAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNN--LQSQSEAIASMNLFDLGGQYLR  283 (544)
T ss_pred             HHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEecc--ccchHHHhhhcchhhcccceEe
Confidence            3445679999999999999999999999999999999854    358999999998  9999999999999999999999


Q ss_pred             EEecc
Q 003717           85 LERAK   89 (800)
Q Consensus        85 Ve~AK   89 (800)
                      |..+.
T Consensus       284 VGk~v  288 (544)
T KOG0124|consen  284 VGKCV  288 (544)
T ss_pred             ccccc
Confidence            98763

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

Probab=98.27  E-value=9.6e-07  Score=95.22  Aligned_cols=77  Identities=26%  Similarity=0.465  Sum_probs=66.2

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc----CCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEec
Q 003717           13 QTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT----KGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERA   88 (800)
Q Consensus        13 srTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd----TGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~A   88 (800)
                      .++||||+||..+++++|+++|.+||.|..+.++.+    ..||||||.|..   +++...+.....+.|.|+.+.|..|
T Consensus        97 tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~---e~sVdkv~~~~f~~~~gk~vevkrA  173 (311)
T KOG4205|consen   97 TKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDS---EDSVDKVTLQKFHDFNGKKVEVKRA  173 (311)
T ss_pred             eeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEecc---ccccceecccceeeecCceeeEeec
Confidence            458999999999999999999999999999888843    347999999996   5555555567889999999999999


Q ss_pred             cchh
Q 003717           89 KEHY   92 (800)
Q Consensus        89 Kpr~   92 (800)
                      .|+.
T Consensus       174 ~pk~  177 (311)
T KOG4205|consen  174 IPKE  177 (311)
T ss_pred             cchh
Confidence            9874

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

Probab=98.19  E-value=2e-06  Score=99.51  Aligned_cols=78  Identities=24%  Similarity=0.489  Sum_probs=71.2

Q ss_pred             cCCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEe--c-----cCCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEE
Q 003717           11 EEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--R-----TKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRL   83 (800)
Q Consensus        11 ~qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVI--R-----dTGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~L   83 (800)
                      ...++||||||++.+++..|...|+.||+|.+++++  +     ++.+-||||.|-+  ..+|++|+..|+|..+.+..+
T Consensus       172 P~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmn--R~D~era~k~lqg~iv~~~e~  249 (877)
T KOG0151|consen  172 PQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMN--RADAERALKELQGIIVMEYEM  249 (877)
T ss_pred             CcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehh--hhhHHHHHHHhcceeeeeeee
Confidence            457899999999999999999999999999999998  2     2346899999998  999999999999999999999


Q ss_pred             EEEeccc
Q 003717           84 RLERAKE   90 (800)
Q Consensus        84 rVe~AKp   90 (800)
                      ++.|+++
T Consensus       250 K~gWgk~  256 (877)
T KOG0151|consen  250 KLGWGKA  256 (877)
T ss_pred             eeccccc
Confidence            9999954

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

Probab=98.17  E-value=4.2e-06  Score=93.00  Aligned_cols=74  Identities=19%  Similarity=0.317  Sum_probs=66.8

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhh-cCCceeEEEEecc---CCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEecc
Q 003717           14 TRIYVGGLGEKVTDDDLAKVFS-SLGEVKAVDIVRT---KGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAK   89 (800)
Q Consensus        14 rTLFVGNLP~nVTEEDLrelFS-qFG~VksVrVIRd---TGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~AK   89 (800)
                      +.+||.|+||++.+.+|+++|. +.|.|..|.++-+   +.||||.|+|..  ++.+++|++.||.+.+.||+|.|+...
T Consensus        45 R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~GK~rGcavVEFk~--~E~~qKa~E~lnk~~~~GR~l~vKEd~  122 (608)
T KOG4212|consen   45 RSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDESGKARGCAVVEFKD--PENVQKALEKLNKYEVNGRELVVKEDH  122 (608)
T ss_pred             ceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccCCCcCCceEEEeeC--HHHHHHHHHHhhhccccCceEEEeccC
Confidence            4599999999999999999996 5799999999843   458999999996  999999999999999999999998653

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

Probab=98.15  E-value=4.1e-06  Score=85.85  Aligned_cols=78  Identities=15%  Similarity=0.278  Sum_probs=67.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhhcC-CceeEEEEecc--CC--CcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEE
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSL-GEVKAVDIVRT--KG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLE   86 (800)
Q Consensus        12 qsrTLFVGNLP~nVTEEDLrelFSqF-G~VksVrVIRd--TG--RGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe   86 (800)
                      ...-+||+.+|..+.+.++..+|.+| |.|..+++-|.  ||  +|||||+|++  .+.|.-|.+.||++.|.|+.|.|.
T Consensus        48 ~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs--~eVA~IaAETMNNYLl~e~lL~c~  125 (214)
T KOG4208|consen   48 IEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFES--EEVAKIAAETMNNYLLMEHLLECH  125 (214)
T ss_pred             CccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEecc--HHHHHHHHHHhhhhhhhhheeeeE
Confidence            34568999999999999999999999 66777777543  44  8999999998  999999999999999999999998


Q ss_pred             eccch
Q 003717           87 RAKEH   91 (800)
Q Consensus        87 ~AKpr   91 (800)
                      +-.|.
T Consensus       126 vmppe  130 (214)
T KOG4208|consen  126 VMPPE  130 (214)
T ss_pred             EeCch
Confidence            87665

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

Probab=98.14  E-value=1.1e-05  Score=87.74  Aligned_cols=78  Identities=28%  Similarity=0.438  Sum_probs=66.8

Q ss_pred             ccCCcEEEEeCCCCCCCHHHHHHhhhcCCceeE--------EEEecc-CC--CcEEEEEecCCCHHHHHHHHHhcCCcEe
Q 003717           10 VEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKA--------VDIVRT-KG--RSFGYVDFFPSSHKSLSKLFSTYNGCVW   78 (800)
Q Consensus        10 v~qsrTLFVGNLP~nVTEEDLrelFSqFG~Vks--------VrVIRd-TG--RGFGFVEFeS~D~EdAekAIe~LNG~eL   78 (800)
                      ....+.|||.|||.++|.+++.++|+.||.|..        |.+-++ .|  +|=|.++|-.  .+...-|+..|++..|
T Consensus       131 ~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K--~ESVeLA~~ilDe~~~  208 (382)
T KOG1548|consen  131 PKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIK--RESVELAIKILDEDEL  208 (382)
T ss_pred             cccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeec--ccHHHHHHHHhCcccc
Confidence            445678999999999999999999999998754        333333 23  6999999997  8999999999999999


Q ss_pred             CCeEEEEEecc
Q 003717           79 KGGRLRLERAK   89 (800)
Q Consensus        79 dGR~LrVe~AK   89 (800)
                      .|+.|+|+.|+
T Consensus       209 rg~~~rVerAk  219 (382)
T KOG1548|consen  209 RGKKLRVERAK  219 (382)
T ss_pred             cCcEEEEehhh
Confidence            99999999985

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

Probab=98.09  E-value=1.3e-05  Score=90.09  Aligned_cols=154  Identities=19%  Similarity=0.230  Sum_probs=106.8

Q ss_pred             hccCCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEeccCC--CcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEE
Q 003717            9 EVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLE   86 (800)
Q Consensus         9 Ev~qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRdTG--RGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe   86 (800)
                      +.....-|=+.+|||++|+++|.++|+.++ |.++.+.+.++  .|=|||+|.+  .+++.+|++ .+...+..|-|.|-
T Consensus         6 e~~~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r~~Gr~sGeA~Ve~~s--eedv~~Alk-kdR~~mg~RYIEVf   81 (510)
T KOG4211|consen    6 EGSTAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPRRNGRPSGEAYVEFTS--EEDVEKALK-KDRESMGHRYIEVF   81 (510)
T ss_pred             CCCcceEEEecCCCccccHHHHHHHHhcCc-eeEEEEeccCCCcCcceEEEeec--hHHHHHHHH-hhHHHhCCceEEEE
Confidence            444445677889999999999999999995 67766667656  4999999998  999999996 47788889999998


Q ss_pred             eccchhhHHHhhhHHHHhhhhCCCCCCCCCCCCCCCcccCCCCCCCCCcchhhcccccCccceee-eccC--CCCCcccc
Q 003717           87 RAKEHYLARLKREWAEDDAQLVNPPVTDSVAPDNKDATRLDTPKKLLDKDKKLNIFFPRLRKVKT-LPFC--GTGKHKYS  163 (800)
Q Consensus        87 ~AKpr~~~RlkrEraq~rak~~~sp~sD~Vd~~~~kl~is~~Lkksvdesd~LreyFskyGKVKs-Vp~p--gTGK~KYG  163 (800)
                      .+.+.....         ......+.+..    ....+-++.|++.+++ ++|..||..+--|.. +.++  ..|+    
T Consensus        82 ~~~~~e~d~---------~~~~~g~~s~~----~d~vVRLRGLPfscte-~dI~~FFaGL~Iv~~gi~l~~d~rgR----  143 (510)
T KOG4211|consen   82 TAGGAEADW---------VMRPGGPNSSA----NDGVVRLRGLPFSCTE-EDIVEFFAGLEIVPDGILLPMDQRGR----  143 (510)
T ss_pred             ccCCccccc---------cccCCCCCCCC----CCceEEecCCCccCcH-HHHHHHhcCCcccccceeeeccCCCC----
Confidence            886543211         11111222211    1123455668999977 999999998765543 2222  2222    


Q ss_pred             cccccCCCCCcccccccchhhhhhhhcc
Q 003717          164 FQRVEAPPLPKYFCDCEEHSAAFHAAEG  191 (800)
Q Consensus       164 F~~ve~Ps~pV~F~sfEea~aA~eAmNG  191 (800)
                             +-.-+||.|+..+.|..||.+
T Consensus       144 -------~tGEAfVqF~sqe~ae~Al~r  164 (510)
T KOG4211|consen  144 -------PTGEAFVQFESQESAEIALGR  164 (510)
T ss_pred             -------cccceEEEecCHHHHHHHHHH
Confidence                   223578888888888888773

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

Probab=98.01  E-value=8.7e-06  Score=90.61  Aligned_cols=77  Identities=23%  Similarity=0.351  Sum_probs=67.2

Q ss_pred             hccCCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEeccCCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEec
Q 003717            9 EVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERA   88 (800)
Q Consensus         9 Ev~qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRdTGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~A   88 (800)
                      -.++.++|||.|||++.|+..|++-|..||.|..+.|+. .++.-|.|.|.+  +++|+.|+..|||..|+||.|.|.++
T Consensus       532 aarKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadime-~GkskGVVrF~s--~edAEra~a~Mngs~l~Gr~I~V~y~  608 (608)
T KOG4212|consen  532 AARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIME-NGKSKGVVRFFS--PEDAERACALMNGSRLDGRNIKVTYF  608 (608)
T ss_pred             ccccccEEEEecCCccccHHHHHHHHHhccceehhhhhc-cCCccceEEecC--HHHHHHHHHHhccCcccCceeeeeeC
Confidence            345667899999999999999999999999999999862 243344899998  99999999999999999999999763

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

Probab=97.97  E-value=1.7e-05  Score=83.27  Aligned_cols=77  Identities=26%  Similarity=0.415  Sum_probs=67.7

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc-CC--CcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEecc
Q 003717           13 QTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT-KG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAK   89 (800)
Q Consensus        13 srTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd-TG--RGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~AK   89 (800)
                      ..+|+|.||++.|+++||+++|..||.+..+.|..+ .|  .|.|-|.|..  .++|.+|+..|||..++|++|.+....
T Consensus        83 ~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r--~~DA~~avk~~~gv~ldG~~mk~~~i~  160 (243)
T KOG0533|consen   83 STKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNR--RDDAERAVKKYNGVALDGRPMKIEIIS  160 (243)
T ss_pred             cceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecc--hHhHHHHHHHhcCcccCCceeeeEEec
Confidence            368999999999999999999999998888877743 34  4999999997  889999999999999999999998765


Q ss_pred             ch
Q 003717           90 EH   91 (800)
Q Consensus        90 pr   91 (800)
                      +.
T Consensus       161 ~~  162 (243)
T KOG0533|consen  161 SP  162 (243)
T ss_pred             Cc
Confidence            43

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

Probab=97.95  E-value=5.2e-06  Score=94.25  Aligned_cols=178  Identities=16%  Similarity=0.233  Sum_probs=115.4

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc----CCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEe
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT----KGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLER   87 (800)
Q Consensus        12 qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd----TGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~   87 (800)
                      ...++|||+||...++..+.++...||.+....++.+    .++||||.+|..  ......|+..|||..++++.|.|..
T Consensus       288 ~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~d--psvtd~A~agLnGm~lgd~~lvvq~  365 (500)
T KOG0120|consen  288 SPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCD--PSVTDQAIAGLNGMQLGDKKLVVQR  365 (500)
T ss_pred             ccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeC--CcchhhhhcccchhhhcCceeEeeh
Confidence            4568999999999999999999999999999888843    348999999996  8999999999999999999999998


Q ss_pred             ccchhhHHHhhhHHHHhhhhCCCCCC----CCCCC---CCCCcccCCCCCCCC-Ccc--hhhcccccCccceeeeccC--
Q 003717           88 AKEHYLARLKREWAEDDAQLVNPPVT----DSVAP---DNKDATRLDTPKKLL-DKD--KKLNIFFPRLRKVKTLPFC--  155 (800)
Q Consensus        88 AKpr~~~RlkrEraq~rak~~~sp~s----D~Vd~---~~~kl~is~~Lkksv-des--d~LreyFskyGKVKsVp~p--  155 (800)
                      |-+.......... -.+.+....+..    .+...   -..++.-...|+.+- .++  ++++.-+++||.|.+|..+  
T Consensus       366 A~~g~~~~~~~~~-~~~~~~~~i~~~~~q~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~  444 (500)
T KOG0120|consen  366 AIVGASNANVNFN-ISQSQVPGIPLLMTQMAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRP  444 (500)
T ss_pred             hhccchhccccCC-ccccccccchhhhcccCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCC
Confidence            8553211110000 000000000000    00000   001111111122111 011  6788889999998876443  


Q ss_pred             -CCCCcccccccccCCCCCcccccccchhhhhhhhccCccccC
Q 003717          156 -GTGKHKYSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHP  197 (800)
Q Consensus       156 -gTGK~KYGF~~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~  197 (800)
                       ..+...+|     +.--+|.|.+.++.+.|.++|+|--+.+.
T Consensus       445 ~~~~~~~~G-----~GkVFVefas~ed~qrA~~~L~GrKF~nR  482 (500)
T KOG0120|consen  445 YPDENPVPG-----TGKVFVEFADTEDSQRAMEELTGRKFANR  482 (500)
T ss_pred             CCCCCcCCC-----cccEEEEecChHHHHHHHHHccCceeCCc
Confidence             22222222     23446899999999999999999887664

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

Probab=97.91  E-value=1.9e-05  Score=88.41  Aligned_cols=77  Identities=23%  Similarity=0.390  Sum_probs=65.2

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc----CCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEec
Q 003717           13 QTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT----KGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERA   88 (800)
Q Consensus        13 srTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd----TGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~A   88 (800)
                      ..+|||+|||.+++..+|+++|..||.|+...|...    +..+||||+|.+  .+++..||.+- -..|+|++|.|+.-
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~--~~~~~~~i~As-p~~ig~~kl~Veek  364 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFEN--AAAVQNAIEAS-PLEIGGRKLNVEEK  364 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEee--cchhhhhhhcC-ccccCCeeEEEEec
Confidence            456999999999999999999999999999888732    223899999997  88888888764 88899999999976


Q ss_pred             cchh
Q 003717           89 KEHY   92 (800)
Q Consensus        89 Kpr~   92 (800)
                      ++.+
T Consensus       365 ~~~~  368 (419)
T KOG0116|consen  365 RPGF  368 (419)
T ss_pred             cccc
Confidence            6543

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

Probab=97.83  E-value=7.9e-05  Score=82.70  Aligned_cols=160  Identities=21%  Similarity=0.225  Sum_probs=103.2

Q ss_pred             CcEEEEeCCC-CCCCHHHHHHhhhcCCceeEEEEeccCCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEeccch
Q 003717           13 QTRIYVGGLG-EKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKEH   91 (800)
Q Consensus        13 srTLFVGNLP-~nVTEEDLrelFSqFG~VksVrVIRdTGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~AKpr   91 (800)
                      ...|.|.||. +.+|.+-|..+|+-||.|.+|.|+..++ --|.|.|.+  ...|+-|+..|+|+.|.|++|+|.+++..
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkk-d~ALIQmsd--~~qAqLA~~hL~g~~l~gk~lrvt~SKH~  373 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKK-DNALIQMSD--GQQAQLAMEHLEGHKLYGKKLRVTLSKHT  373 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCC-cceeeeecc--hhHHHHHHHHhhcceecCceEEEeeccCc
Confidence            4678899986 5699999999999999999999986544 579999995  99999999999999999999999998754


Q ss_pred             hhHHHhhhHHHHhhhhCCCCCCCCCCCC--------CCCccc------CCCCCCCCCcchhhcccccCccc-eeeeccCC
Q 003717           92 YLARLKREWAEDDAQLVNPPVTDSVAPD--------NKDATR------LDTPKKLLDKDKKLNIFFPRLRK-VKTLPFCG  156 (800)
Q Consensus        92 ~~~RlkrEraq~rak~~~sp~sD~Vd~~--------~~kl~i------s~~Lkksvdesd~LreyFskyGK-VKsVp~pg  156 (800)
                      ... ++++.+.++.-  ..+.....-+.        ..+.++      .-.++.++.+ ++++..|.+-|- |+..  +.
T Consensus       374 ~vq-lp~egq~d~gl--T~dy~~spLhrfkkpgsKN~~ni~PpsatlHlsnip~svse-e~lk~~f~~~g~~vkaf--kf  447 (492)
T KOG1190|consen  374 NVQ-LPREGQEDQGL--TKDYGNSPLHRFKKPGSKNYQNIFPPSATLHLSNIPPSVSE-EDLKNLFQEPGGQVKAF--KF  447 (492)
T ss_pred             ccc-CCCCCCccccc--cccCCCCchhhccCcccccccccCCchhheeeccCCcccch-hHHHHhhhcCCceEEee--ee
Confidence            322 22221111110  00000000000        001111      1123555655 788888887766 3432  22


Q ss_pred             CCC-cccccccccCCCCCcccccccchhhhhhhhc
Q 003717          157 TGK-HKYSFQRVEAPPLPKYFCDCEEHSAAFHAAE  190 (800)
Q Consensus       157 TGK-~KYGF~~ve~Ps~pV~F~sfEea~aA~eAmN  190 (800)
                      -++ +||+.         .++.++|++..|+..|.
T Consensus       448 f~kd~kmal---------~q~~sveeA~~ali~~h  473 (492)
T KOG1190|consen  448 FQKDRKMAL---------PQLESVEEAIQALIDLH  473 (492)
T ss_pred             cCCCcceee---------cccCChhHhhhhccccc
Confidence            222 23433         78889999888887754

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

Probab=97.75  E-value=3.2e-05  Score=81.63  Aligned_cols=78  Identities=26%  Similarity=0.532  Sum_probs=69.0

Q ss_pred             cCCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc--CC--CcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEE
Q 003717           11 EEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--KG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLE   86 (800)
Q Consensus        11 ~qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd--TG--RGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe   86 (800)
                      ....+||.|.|..+++++.|-+.|.+|-.....+++++  ++  +|||||.|.+  ..++..|+.+|||..++.|+|++.
T Consensus       188 ~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~--pad~~rAmrem~gkyVgsrpiklR  265 (290)
T KOG0226|consen  188 EDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRD--PADYVRAMREMNGKYVGSRPIKLR  265 (290)
T ss_pred             cccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecC--HHHHHHHHHhhcccccccchhHhh
Confidence            34579999999999999999999999988888888865  33  6999999996  999999999999999999999887


Q ss_pred             eccc
Q 003717           87 RAKE   90 (800)
Q Consensus        87 ~AKp   90 (800)
                      ....
T Consensus       266 kS~w  269 (290)
T KOG0226|consen  266 KSEW  269 (290)
T ss_pred             hhhH
Confidence            6543

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

Probab=97.66  E-value=1.8e-05  Score=82.24  Aligned_cols=73  Identities=21%  Similarity=0.204  Sum_probs=64.6

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEec--cCCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEec
Q 003717           14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVR--TKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERA   88 (800)
Q Consensus        14 rTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIR--dTGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~A   88 (800)
                      ++|||+|+...++++-|.++|-+.|+|..|.|..  +...-||||.|..  +-...-|+..|||..+.++.|.|.+-
T Consensus        10 rtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~kFa~v~f~~--E~sv~~a~~L~ng~~l~~~e~q~~~r   84 (267)
T KOG4454|consen   10 RTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQKFAYVFFPN--ENSVQLAGQLENGDDLEEDEEQRTLR   84 (267)
T ss_pred             hHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCceeeeeccc--ccchhhhhhhcccchhccchhhcccc
Confidence            7999999999999999999999999999988773  3223499999996  88999999999999999999888753

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

Probab=97.63  E-value=3e-05  Score=88.30  Aligned_cols=70  Identities=21%  Similarity=0.436  Sum_probs=63.0

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEeccCCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEE
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLR   84 (800)
Q Consensus        12 qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRdTGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~Lr   84 (800)
                      ..++|+|-|||..|++++|+.+|+.||+|+.++.-+ ..+|..||+|.+  ..+|+.|+++||+.++.|+.|.
T Consensus        74 ~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~-~~~~~~~v~FyD--vR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   74 NQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETP-NKRGIVFVEFYD--VRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             ccceEEEEecCCcCCHHHHHHHHHhhcchhhhhccc-ccCceEEEEEee--hHhHHHHHHHHHHHHhhhhhhc
Confidence            467999999999999999999999999999965422 247999999995  9999999999999999999988

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

Probab=97.60  E-value=0.0001  Score=76.80  Aligned_cols=76  Identities=18%  Similarity=0.394  Sum_probs=67.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc--C--CCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEe
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--K--GRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLER   87 (800)
Q Consensus        12 qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd--T--GRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~   87 (800)
                      ..+.+||||+.+.+|.+++...|+.||.|..+.|..+  .  .+||+||+|..  .+.+..|+. |||..|.|+.+.|.+
T Consensus       100 d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~--~~~~~~ay~-l~gs~i~~~~i~vt~  176 (231)
T KOG4209|consen  100 DAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSS--YELVEEAYK-LDGSEIPGPAIEVTL  176 (231)
T ss_pred             CCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEeccc--HhhhHHHhh-cCCcccccccceeee
Confidence            3578999999999999999999999999998888733  3  48999999997  999999998 999999999999987


Q ss_pred             ccc
Q 003717           88 AKE   90 (800)
Q Consensus        88 AKp   90 (800)
                      .+-
T Consensus       177 ~r~  179 (231)
T KOG4209|consen  177 KRT  179 (231)
T ss_pred             eee
Confidence            643

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

Probab=97.56  E-value=9.7e-05  Score=82.02  Aligned_cols=176  Identities=18%  Similarity=0.240  Sum_probs=110.6

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEeccCCCcEEEEEecCCCHHHHHHHHHhcCC--cEeCCeEEEEEecc
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNG--CVWKGGRLRLERAK   89 (800)
Q Consensus        12 qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRdTGRGFGFVEFeS~D~EdAekAIe~LNG--~eLdGR~LrVe~AK   89 (800)
                      ..+-|.++|||+++++++|-.++.+||.|..+.+++  |+..||++|.+  .+.|..-+..+..  -.+.|++|.|.++.
T Consensus        27 pSkV~HlRnlp~e~tE~elI~Lg~pFG~vtn~~~lk--GknQAflem~d--~~sAvtmv~~y~~~~p~lr~~~~yiq~sn  102 (492)
T KOG1190|consen   27 PSKVVHLRNLPWEVTEEELISLGLPFGKVTNLLMLK--GKNQAFLEMAD--EESAVTMVNYYTSVTPVLRGQPIYIQYSN  102 (492)
T ss_pred             CcceeEeccCCccccHHHHHHhcccccceeeeeeec--cchhhhhhhcc--hhhhhheeecccccCccccCcceeehhhh
Confidence            457899999999999999999999999999988876  55589999996  7777664433333  25689999999875


Q ss_pred             chhhHHH---hhhHHHH--hhh----hCCCCCC---CCCCCCCCCcccCCC----CCCCCCcchhhcccccCccce-eee
Q 003717           90 EHYLARL---KREWAED--DAQ----LVNPPVT---DSVAPDNKDATRLDT----PKKLLDKDKKLNIFFPRLRKV-KTL  152 (800)
Q Consensus        90 pr~~~Rl---krEraq~--rak----~~~sp~s---D~Vd~~~~kl~is~~----Lkksvdesd~LreyFskyGKV-KsV  152 (800)
                      -++....   .+.|.+.  .+.    ....+.+   +.+-....+..+...    +-..++- +-|..+|++||.| |++
T Consensus       103 ~~~lkt~s~p~q~r~~~vy~~~s~~q~~~~~~s~~~~~~G~~~~~n~vLr~iie~m~ypVsl-DVLHqvFS~fG~VlKIi  181 (492)
T KOG1190|consen  103 HSELKTDSQPNQIRGQAVYQAVSSVQEIVLPLSASAVVVGNEDGPNPVLRTIIENMFYPVSL-DVLHQVFSKFGFVLKII  181 (492)
T ss_pred             HHHHhccCchhhhhhhhHHhhhhcccccccccccccccccccCCCceeEEEEeccceeeeEH-HHHHHHHhhcceeEEEE
Confidence            5433211   0111111  000    0000101   110000001111111    1111211 7788999999996 677


Q ss_pred             ccCCCCCcccccccccCCCCCcccccccchhhhhhhhccCccccCCCCccccc
Q 003717          153 PFCGTGKHKYSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPAAGQEEIH  205 (800)
Q Consensus       153 p~pgTGK~KYGF~~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n~~q~~i~  205 (800)
                      +|.-.    =||.      .-++|.+.+.+..|--++.|+.|-+   +.|-.+
T Consensus       182 TF~Kn----n~FQ------ALvQy~d~~sAq~AK~aLdGqnIyn---gcCtLr  221 (492)
T KOG1190|consen  182 TFTKN----NGFQ------ALVQYTDAVSAQAAKLALDGQNIYN---GCCTLR  221 (492)
T ss_pred             EEecc----cchh------hhhhccchhhHHHHHHhccCCcccC---ceeEEE
Confidence            66421    2553      5689999999999999999999877   455444

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.00  E-value=0.0013  Score=71.98  Aligned_cols=80  Identities=20%  Similarity=0.453  Sum_probs=66.2

Q ss_pred             CcEEEEeCCCCCCCHHH----H--HHhhhcCCceeEEEEeccCC-----CcEE--EEEecCCCHHHHHHHHHhcCCcEeC
Q 003717           13 QTRIYVGGLGEKVTDDD----L--AKVFSSLGEVKAVDIVRTKG-----RSFG--YVDFFPSSHKSLSKLFSTYNGCVWK   79 (800)
Q Consensus        13 srTLFVGNLP~nVTEED----L--relFSqFG~VksVrVIRdTG-----RGFG--FVEFeS~D~EdAekAIe~LNG~eLd   79 (800)
                      ..-+||-+|+..+..++    |  .++|++||.|..+.|-+.+.     .+.+  ||+|.+  .++|.+||.+.+|..++
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~--kedAarcIa~vDgs~~D  191 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYST--KEDAARCIAEVDGSLLD  191 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecc--hHHHHHHHHHhcccccc
Confidence            44689999999988876    3  48999999999988765431     2433  999998  99999999999999999


Q ss_pred             CeEEEEEeccchhhH
Q 003717           80 GGRLRLERAKEHYLA   94 (800)
Q Consensus        80 GR~LrVe~AKpr~~~   94 (800)
                      ||.|+..+..-+|-.
T Consensus       192 Gr~lkatYGTTKYCt  206 (480)
T COG5175         192 GRVLKATYGTTKYCT  206 (480)
T ss_pred             CceEeeecCchHHHH
Confidence            999999998777543

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

Probab=96.94  E-value=0.00081  Score=70.46  Aligned_cols=67  Identities=16%  Similarity=0.358  Sum_probs=56.7

Q ss_pred             cCCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEeccCCCcEEEEEecCCCHHHHHHHHHhcCCcEeC
Q 003717           11 EEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWK   79 (800)
Q Consensus        11 ~qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRdTGRGFGFVEFeS~D~EdAekAIe~LNG~eLd   79 (800)
                      +.-.+|||.||..++++++|+.+|+.|-.....+|....|-..+||+|..  .+.|..||..|.|..|-
T Consensus       208 ~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~~g~~vaf~~~~~--~~~at~am~~lqg~~~s  274 (284)
T KOG1457|consen  208 RACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRARGGMPVAFADFEE--IEQATDAMNHLQGNLLS  274 (284)
T ss_pred             hhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecCCCcceEeecHHH--HHHHHHHHHHhhcceec
Confidence            34468999999999999999999999987766666544456799999996  99999999999988763

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

Probab=96.92  E-value=0.001  Score=75.84  Aligned_cols=168  Identities=17%  Similarity=0.259  Sum_probs=96.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc---C----CCc---EEEEEecCCCHHHHHHHHHhcCCcEeCCe
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT---K----GRS---FGYVDFFPSSHKSLSKLFSTYNGCVWKGG   81 (800)
Q Consensus        12 qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd---T----GRG---FGFVEFeS~D~EdAekAIe~LNG~eLdGR   81 (800)
                      -.++||||+||+.++++.|...|..||.+. |.+.+.   .    .+|   |.|+.|+.  +......+   +.+.....
T Consensus       258 ~S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~--E~sV~~Ll---~aC~~~~~  331 (520)
T KOG0129|consen  258 YSRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFED--ERSVQSLL---SACSEGEG  331 (520)
T ss_pred             cccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecc--hHHHHHHH---HHHhhccc
Confidence            357999999999999999999999999963 455521   1    246   99999995  44433333   44555666


Q ss_pred             EEEEEeccchhhHHHh--hhHHHHhhhhCCCCCCCCCCCCCCCcccCCCCCCCCCcchhhccccc-CccceeeeccCCCC
Q 003717           82 RLRLERAKEHYLARLK--REWAEDDAQLVNPPVTDSVAPDNKDATRLDTPKKLLDKDKKLNIFFP-RLRKVKTLPFCGTG  158 (800)
Q Consensus        82 ~LrVe~AKpr~~~Rlk--rEraq~rak~~~sp~sD~Vd~~~~kl~is~~Lkksvdesd~LreyFs-kyGKVKsVp~pgTG  158 (800)
                      .+.+....++...+.-  +.|.-.... .-.-..-.+++. ...|+++ +...+.. ..|..+|. -||-|--+-+....
T Consensus       332 ~~yf~vss~~~k~k~VQIrPW~laDs~-fv~d~sq~lDpr-rTVFVGg-vprpl~A-~eLA~imd~lyGgV~yaGIDtD~  407 (520)
T KOG0129|consen  332 NYYFKVSSPTIKDKEVQIRPWVLADSD-FVLDHNQPIDPR-RTVFVGG-LPRPLTA-EELAMIMEDLFGGVLYVGIDTDP  407 (520)
T ss_pred             ceEEEEecCcccccceeEEeeEeccch-hhhccCcccCcc-ceEEecC-CCCcchH-HHHHHHHHHhcCceEEEEeccCc
Confidence            7777666555433210  011000000 000011123332 2344444 5555656 77888888 68888766555444


Q ss_pred             CcccccccccCCCCCcccccccchhhhhhhhccCccccC
Q 003717          159 KHKYSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHP  197 (800)
Q Consensus       159 K~KYGF~~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~  197 (800)
                      +.||==     ..+=|+|.....--+|+.+   .++...
T Consensus       408 k~KYPk-----GaGRVtFsnqqsYi~AIsa---rFvql~  438 (520)
T KOG0129|consen  408 KLKYPK-----GAGRVTFSNQQAYIKAISA---RFVQLD  438 (520)
T ss_pred             ccCCCC-----CcceeeecccHHHHHHHhh---heEEEe
Confidence            666411     1344566665555555555   666554

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

Probab=96.70  E-value=0.0079  Score=55.67  Aligned_cols=75  Identities=15%  Similarity=0.329  Sum_probs=60.4

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhhcC--CceeEEEEecc----CCCcEEEEEecCCCHHHHHHHHHhcCCcEeC----CeEE
Q 003717           14 TRIYVGGLGEKVTDDDLAKVFSSL--GEVKAVDIVRT----KGRSFGYVDFFPSSHKSLSKLFSTYNGCVWK----GGRL   83 (800)
Q Consensus        14 rTLFVGNLP~nVTEEDLrelFSqF--G~VksVrVIRd----TGRGFGFVEFeS~D~EdAekAIe~LNG~eLd----GR~L   83 (800)
                      +||-|.|+|...|.++|.+++...  |...-+.++-|    .+.|||||.|.+  .+.|.+-...++|..|.    .+.+
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~--~~~~~~F~~~f~g~~w~~~~s~Kvc   79 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTS--PQAAIRFYKAFNGKKWPNFNSKKVC   79 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCC--HHHHHHHHHHHcCCccccCCCCcEE
Confidence            689999999999999999888653  44444455422    347999999997  99999999999999996    5677


Q ss_pred             EEEeccc
Q 003717           84 RLERAKE   90 (800)
Q Consensus        84 rVe~AKp   90 (800)
                      .|.+|+-
T Consensus        80 ~i~yAri   86 (97)
T PF04059_consen   80 EISYARI   86 (97)
T ss_pred             EEehhHh
Confidence            8888854

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

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=96.67  E-value=0.001  Score=71.39  Aligned_cols=77  Identities=32%  Similarity=0.484  Sum_probs=66.1

Q ss_pred             CCcEEE-EeCCCCCCCHHHHHHhhhcCCceeEEEEecc--CC--CcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEE
Q 003717           12 EQTRIY-VGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--KG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLE   86 (800)
Q Consensus        12 qsrTLF-VGNLP~nVTEEDLrelFSqFG~VksVrVIRd--TG--RGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe   86 (800)
                      ...++| |++|++.++.++|+.+|..+|.|..+++...  ++  +|||||.|..  ...+..++.. +...+.|+++.+.
T Consensus       183 ~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~--~~~~~~~~~~-~~~~~~~~~~~~~  259 (285)
T KOG4210|consen  183 PSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSA--GNSKKLALND-QTRSIGGRPLRLE  259 (285)
T ss_pred             ccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhh--chhHHHHhhc-ccCcccCcccccc
Confidence            345666 9999999999999999999999999998833  33  6999999997  7888888777 8899999999999


Q ss_pred             eccch
Q 003717           87 RAKEH   91 (800)
Q Consensus        87 ~AKpr   91 (800)
                      +..++
T Consensus       260 ~~~~~  264 (285)
T KOG4210|consen  260 EDEPR  264 (285)
T ss_pred             cCCCC
Confidence            88776

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=96.57  E-value=0.0024  Score=68.54  Aligned_cols=152  Identities=14%  Similarity=0.136  Sum_probs=100.0

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc----CCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEe
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT----KGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLER   87 (800)
Q Consensus        12 qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd----TGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~   87 (800)
                      ...++|+|++.+.+.+.+...+|..+|.+..+.+...    ..+||+++.|..  .+.+..|+.....+.+.++.+....
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~--ks~~~~~l~~s~~~~~~~~~~~~dl  164 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAG--KSQFFAALEESGSKVLDGNKGEKDL  164 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeecccc--HHHHHHHHHhhhccccccccccCcc
Confidence            4678999999999999999999999999888877632    347999999998  8999988877666788888887776


Q ss_pred             ccchhhHHHhhhHHHHhhhhCCCCCCCCCCCCCCCcccCCCCCCCCCcchhhcccccCccceeeeccC---CCCCccccc
Q 003717           88 AKEHYLARLKREWAEDDAQLVNPPVTDSVAPDNKDATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPFC---GTGKHKYSF  164 (800)
Q Consensus        88 AKpr~~~RlkrEraq~rak~~~sp~sD~Vd~~~~kl~is~~Lkksvdesd~LreyFskyGKVKsVp~p---gTGK~KYGF  164 (800)
                      ...+... .+.  ... .. ..       .. ...++....+...++. +.|+.+|..++.|..++.+   .+|..+ ||
T Consensus       165 ~~~~~~~-~~n--~~~-~~-~~-------~~-s~~~~~~~~~~f~~~~-d~~~~~~~~~~~i~~~r~~~~~~s~~~k-g~  229 (285)
T KOG4210|consen  165 NTRRGLR-PKN--KLS-RL-SS-------GP-SDTIFFVGELDFSLTR-DDLKEHFVSSGEITSVRLPTDEESGDSK-GF  229 (285)
T ss_pred             ccccccc-ccc--hhc-cc-cc-------Cc-cccceeecccccccch-HHHhhhccCcCcceeeccCCCCCccchh-hh
Confidence            6544210 000  000 00 00       00 0111222223455544 8888999999998877665   688887 55


Q ss_pred             ccccCCCCCcccccccchhhhhh
Q 003717          165 QRVEAPPLPKYFCDCEEHSAAFH  187 (800)
Q Consensus       165 ~~ve~Ps~pV~F~sfEea~aA~e  187 (800)
                      .       |+.|..-.....++.
T Consensus       230 a-------~~~~~~~~~~~~~~~  245 (285)
T KOG4210|consen  230 A-------YVDFSAGNSKKLALN  245 (285)
T ss_pred             h-------hhhhhhchhHHHHhh
Confidence            2       344544444444444

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

Probab=96.57  E-value=0.0013  Score=63.59  Aligned_cols=75  Identities=17%  Similarity=0.181  Sum_probs=57.6

Q ss_pred             CcccCCCCCCCCCcchhhcccccCccceee---eccCCCCCcc-cccccccCCCCCcccccccchhhhhhhhccCccccC
Q 003717          122 DATRLDTPKKLLDKDKKLNIFFPRLRKVKT---LPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHP  197 (800)
Q Consensus       122 kl~is~~Lkksvdesd~LreyFskyGKVKs---Vp~pgTGK~K-YGF~~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~  197 (800)
                      .+++. .|...+++ ++|+.+|.+||.|..   +.++.+|+++ |+|         |.|.+.+++..|++.|||..+   
T Consensus        36 ~lfVg-nL~~~~te-~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaF---------V~F~~~e~A~~Al~~lng~~i---  101 (144)
T PLN03134         36 KLFIG-GLSWGTDD-ASLRDAFAHFGDVVDAKVIVDRETGRSRGFGF---------VNFNDEGAATAAISEMDGKEL---  101 (144)
T ss_pred             EEEEe-CCCCCCCH-HHHHHHHhcCCCeEEEEEEecCCCCCcceEEE---------EEECCHHHHHHHHHHcCCCEE---
Confidence            45554 46777766 999999999999764   5556899988 777         899999999999999998765   


Q ss_pred             CCCccccchhhhc
Q 003717          198 AAGQEEIHDMEEL  210 (800)
Q Consensus       198 n~~q~~i~~~ee~  210 (800)
                      ++..+.|..+.++
T Consensus       102 ~Gr~l~V~~a~~~  114 (144)
T PLN03134        102 NGRHIRVNPANDR  114 (144)
T ss_pred             CCEEEEEEeCCcC
Confidence            3456666654443

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

Probab=96.40  E-value=0.0094  Score=62.30  Aligned_cols=77  Identities=12%  Similarity=0.296  Sum_probs=66.5

Q ss_pred             ccCCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEeccCCCcEEEEEecCCCHHHHHHHHHhcCCcEeC-CeEEEEEec
Q 003717           10 VEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWK-GGRLRLERA   88 (800)
Q Consensus        10 v~qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRdTGRGFGFVEFeS~D~EdAekAIe~LNG~eLd-GR~LrVe~A   88 (800)
                      ..+...||+-|||..++.+.|..+|.+|.....++++.. -.|.|||+|.+  ...|..|...+.|..|- ...+.|.+|
T Consensus       143 ~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~-~~~iAfve~~~--d~~a~~a~~~lq~~~it~~~~m~i~~a  219 (221)
T KOG4206|consen  143 APPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPP-RSGIAFVEFLS--DRQASAAQQALQGFKITKKNTMQITFA  219 (221)
T ss_pred             CCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccC-CCceeEEecch--hhhhHHHhhhhccceeccCceEEeccc
Confidence            345678999999999999999999999999999988752 35899999997  67789999999999886 788888876


Q ss_pred             c
Q 003717           89 K   89 (800)
Q Consensus        89 K   89 (800)
                      +
T Consensus       220 ~  220 (221)
T KOG4206|consen  220 K  220 (221)
T ss_pred             C
Confidence            4

>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=96.21  E-value=0.0084  Score=55.67  Aligned_cols=70  Identities=33%  Similarity=0.510  Sum_probs=43.2

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEeccCCCcEEEEEecCCCHHHHHHHHHhcCC-----cEeCCeEEEEEe
Q 003717           14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNG-----CVWKGGRLRLER   87 (800)
Q Consensus        14 rTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRdTGRGFGFVEFeS~D~EdAekAIe~LNG-----~eLdGR~LrVe~   87 (800)
                      .-|+|.+++..++.++|+..|.+||.|..|.+.+  |..-|||-|.+  .+.|..|+..+.-     ..+.+..+.+..
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~--G~~~g~VRf~~--~~~A~~a~~~~~~~~~~~~~i~~~~~~~~v   76 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSR--GDTEGYVRFKT--PEAAQKALEKLKEANDGKLKIKGKEVTLEV   76 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--T--T-SEEEEEESS-----HHHHHHHHHHTTTS-B-TTSSSEEEE-
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecC--CCCEEEEEECC--cchHHHHHHHHHhccCCceEEcCceEEEEE
Confidence            3578889999999999999999999999988754  55689999997  7788888876543     355666665554

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

>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=96.21  E-value=0.012  Score=54.02  Aligned_cols=68  Identities=15%  Similarity=0.183  Sum_probs=48.2

Q ss_pred             cEEEEeCCCCCCCHHH----HHHhhhcCCc-eeEEEEeccCCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEec
Q 003717           14 TRIYVGGLGEKVTDDD----LAKVFSSLGE-VKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERA   88 (800)
Q Consensus        14 rTLFVGNLP~nVTEED----LrelFSqFG~-VksVrVIRdTGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~A   88 (800)
                      .-|||.|||.+.+...    |++++..+|. |..|      ..|-|+|.|.+  .+.|.+|...|+|..+-|++|.|.+.
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v------~~~tAilrF~~--~~~A~RA~KRmegEdVfG~kI~v~~~   74 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV------SGGTAILRFPN--QEFAERAQKRMEGEDVFGNKISVSFS   74 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE--------TT-EEEEESS--HHHHHHHHHHHTT--SSSS--EEESS
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE------eCCEEEEEeCC--HHHHHHHHHhhcccccccceEEEEEc
Confidence            4699999999998765    5677777865 6554      34789999998  99999999999999999999999987


Q ss_pred             c
Q 003717           89 K   89 (800)
Q Consensus        89 K   89 (800)
                      .
T Consensus        75 ~   75 (90)
T PF11608_consen   75 P   75 (90)
T ss_dssp             -
T ss_pred             C
Confidence            3

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

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

Probab=96.20  E-value=0.0015  Score=69.39  Aligned_cols=155  Identities=22%  Similarity=0.223  Sum_probs=99.7

Q ss_pred             CcEEEEeCCCCCCCHHH-H--HHhhhcCCceeEEEEeccC---CCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEE
Q 003717           13 QTRIYVGGLGEKVTDDD-L--AKVFSSLGEVKAVDIVRTK---GRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLE   86 (800)
Q Consensus        13 srTLFVGNLP~nVTEED-L--relFSqFG~VksVrVIRdT---GRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe   86 (800)
                      ...+|++++-..+..+- |  ...|+.|-.+....++++.   -++++|+.|..  .....++-..-+++.++-+++++.
T Consensus        96 vf~p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~p~~~~~~~~~~~k~--s~a~~k~~~~~~~Kki~~~~VR~a  173 (290)
T KOG0226|consen   96 VFRPFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDRPQPIRPEAFESFKA--SDALLKAETEKEKKKIGKPPVRLA  173 (290)
T ss_pred             cccccccccccccCCCCCCcchhhhccchhhhhhhhhhcCCCccCcccccCcch--hhhhhhhccccccccccCcceeec
Confidence            34678888877776665 3  6778877766666666442   36999999984  555555555556666666666555


Q ss_pred             eccchhhHHHhhhHHHHhhhhCCCCCCCCCCCCCCCcccCCCCCCCCCcchhhcccccCccc---eeeeccCCCCCcc-c
Q 003717           87 RAKEHYLARLKREWAEDDAQLVNPPVTDSVAPDNKDATRLDTPKKLLDKDKKLNIFFPRLRK---VKTLPFCGTGKHK-Y  162 (800)
Q Consensus        87 ~AKpr~~~RlkrEraq~rak~~~sp~sD~Vd~~~~kl~is~~Lkksvdesd~LreyFskyGK---VKsVp~pgTGK~K-Y  162 (800)
                      .+..-...-+ .+|             +..|.   .++-++ |--++.. +.|.-.|.+|..   .++++++-|||.| |
T Consensus       174 ~gtswedPsl-~ew-------------~~~Df---RIfcgd-lgNevnd-~vl~raf~Kfpsf~~akviRdkRTgKSkgy  234 (290)
T KOG0226|consen  174 AGTSWEDPSL-AEW-------------DEDDF---RIFCGD-LGNEVND-DVLARAFKKFPSFQKAKVIRDKRTGKSKGY  234 (290)
T ss_pred             cccccCCccc-ccC-------------ccccc---eeeccc-ccccccH-HHHHHHHHhccchhhccccccccccccccc
Confidence            4432211100 011             11111   122221 2333434 666666666654   6789999999998 9


Q ss_pred             ccccccCCCCCcccccccchhhhhhhhccCccccC
Q 003717          163 SFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHP  197 (800)
Q Consensus       163 GF~~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~  197 (800)
                      ||         |.|.+..+...|+..|+|.|.-+.
T Consensus       235 gf---------VSf~~pad~~rAmrem~gkyVgsr  260 (290)
T KOG0226|consen  235 GF---------VSFRDPADYVRAMREMNGKYVGSR  260 (290)
T ss_pred             ee---------eeecCHHHHHHHHHhhcccccccc
Confidence            88         899999999999999999998764

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

Probab=96.07  E-value=0.004  Score=64.89  Aligned_cols=70  Identities=29%  Similarity=0.490  Sum_probs=62.2

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEeccCCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEec
Q 003717           13 QTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERA   88 (800)
Q Consensus        13 srTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRdTGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~A   88 (800)
                      ..+|+|-+++..+.+.+|.+.|+++|.+....+    .++|+||.|..  .++|..|+..++|..+.|+.|.+..+
T Consensus        99 ~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~----~~~~~~v~Fs~--~~da~ra~~~l~~~~~~~~~l~~~~~  168 (216)
T KOG0106|consen   99 HFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA----RRNFAFVEFSE--QEDAKRALEKLDGKKLNGRRISVEKN  168 (216)
T ss_pred             cceeeeccchhhhhHHHHhhhhcccCCCchhhh----hccccceeehh--hhhhhhcchhccchhhcCceeeeccc
Confidence            568999999999999999999999999855433    56899999998  99999999999999999999999443

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

Probab=96.01  E-value=0.0021  Score=67.59  Aligned_cols=63  Identities=19%  Similarity=0.216  Sum_probs=50.6

Q ss_pred             CCCCCCcccCCCCCCCCCcchhhcccccCccce---eeeccCCCCCcc-cccccccCCCCCcccccccchhhhhhhhc
Q 003717          117 APDNKDATRLDTPKKLLDKDKKLNIFFPRLRKV---KTLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAE  190 (800)
Q Consensus       117 d~~~~kl~is~~Lkksvdesd~LreyFskyGKV---KsVp~pgTGK~K-YGF~~ve~Ps~pV~F~sfEea~aA~eAmN  190 (800)
                      |...+++++++ |.+.... +.|+.||.+||.|   .+|.++.|||+| |||         |.|+|.|.+..|..-.|
T Consensus         9 DT~~TKifVgg-L~w~T~~-~~l~~yFeqfGeI~eavvitd~~t~rskGyGf---------VTf~d~~aa~rAc~dp~   75 (247)
T KOG0149|consen    9 DTTFTKIFVGG-LAWETHK-ETLRRYFEQFGEIVEAVVITDKNTGRSKGYGF---------VTFRDAEAATRACKDPN   75 (247)
T ss_pred             CceEEEEEEcC-cccccch-HHHHHHHHHhCceEEEEEEeccCCccccceee---------EEeecHHHHHHHhcCCC
Confidence            34456677765 6777756 8999999999996   468999999998 999         89999888888876554

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

Probab=95.97  E-value=0.037  Score=61.76  Aligned_cols=172  Identities=15%  Similarity=0.202  Sum_probs=107.7

Q ss_pred             CCcEEEEeCCCCC-CCHHHHHHhhhcCCceeEEEEeccCCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEeccc
Q 003717           12 EQTRIYVGGLGEK-VTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKE   90 (800)
Q Consensus        12 qsrTLFVGNLP~n-VTEEDLrelFSqFG~VksVrVIRdTGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~AKp   90 (800)
                      +..-+.|-+|... +.-+.|..+|..||.|..|.+|+ +..|-|.|++.+  ..+.++|+..||+..+-|.+|.|..++.
T Consensus       286 ~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmk-Tk~gtamVemgd--~~aver~v~hLnn~~lfG~kl~v~~SkQ  362 (494)
T KOG1456|consen  286 PGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMK-TKPGTAMVEMGD--AYAVERAVTHLNNIPLFGGKLNVCVSKQ  362 (494)
T ss_pred             CCcEEEEEeccccccchhhhhhhhhhcCceeeEEEee-cccceeEEEcCc--HHHHHHHHHHhccCccccceEEEeeccc
Confidence            3566888999876 45577999999999999999986 245889999996  9999999999999999999999998875


Q ss_pred             hhhHHHh-----------hhHHHHhhhhCCCCCCCCCCCCCCCcccCCCC-----CCCCCcchhhcccccCccc----ee
Q 003717           91 HYLARLK-----------REWAEDDAQLVNPPVTDSVAPDNKDATRLDTP-----KKLLDKDKKLNIFFPRLRK----VK  150 (800)
Q Consensus        91 r~~~Rlk-----------rEraq~rak~~~sp~sD~Vd~~~~kl~is~~L-----kksvdesd~LreyFskyGK----VK  150 (800)
                      .......           .+....+.....+|...   ..+--.+++..|     +..+++ +.|-.+|.....    |+
T Consensus       363 ~~v~~~~pflLpDgSpSfKdys~SkNnRFssp~qA---sKNrIq~Ps~vLHffNaP~~vtE-e~l~~i~nek~v~~~svk  438 (494)
T KOG1456|consen  363 NFVSPVQPFLLPDGSPSFKDYSGSKNNRFSSPEQA---SKNRIQPPSNVLHFFNAPLGVTE-EQLIGICNEKDVPPTSVK  438 (494)
T ss_pred             cccccCCceecCCCCcchhhcccccccccCChhHh---hcccccCCcceeEEecCCCccCH-HHHHHHhhhcCCCcceEE
Confidence            4332110           00000000001110000   000001111111     334544 666666655433    44


Q ss_pred             eeccCCCCCcccccccccCCCCCcccccccchhhhhhhhccCccccCCCC
Q 003717          151 TLPFCGTGKHKYSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPAAG  200 (800)
Q Consensus       151 sVp~pgTGK~KYGF~~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n~~  200 (800)
                      +.+.+ +.+.-         ++-..|...+++-.|+..+|--.+.+++|+
T Consensus       439 vFp~k-serSs---------sGllEfe~~s~Aveal~~~NH~pi~~p~gs  478 (494)
T KOG1456|consen  439 VFPLK-SERSS---------SGLLEFENKSDAVEALMKLNHYPIEGPNGS  478 (494)
T ss_pred             eeccc-ccccc---------cceeeeehHHHHHHHHHHhccccccCCCCC
Confidence            44443 22332         445788888899999988887777777655

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

Probab=95.77  E-value=0.0045  Score=74.31  Aligned_cols=148  Identities=17%  Similarity=0.255  Sum_probs=104.2

Q ss_pred             ccCCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc---CCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEE
Q 003717           10 VEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT---KGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLE   86 (800)
Q Consensus        10 v~qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd---TGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe   86 (800)
                      ...+++||+|||+..+++.+|+..|..||.|..|.|-+.   ++--||||.|.+  ...+-.|...+.|..|....+++.
T Consensus       369 ~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n--~dmtp~ak~e~s~~~I~~g~~r~g  446 (975)
T KOG0112|consen  369 FRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLN--TDMTPSAKFEESGPLIGNGTHRIG  446 (975)
T ss_pred             hhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhc--cccCcccchhhcCCccccCccccc
Confidence            345789999999999999999999999999999988632   234699999998  788888888888887766566655


Q ss_pred             eccchhhHHHhhhHHHHhhhhCCCCCCCCCCCCCCCcccCCCCCCCCCcchhhcccccCccceeeeccCCCCCccccccc
Q 003717           87 RAKEHYLARLKREWAEDDAQLVNPPVTDSVAPDNKDATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPFCGTGKHKYSFQR  166 (800)
Q Consensus        87 ~AKpr~~~RlkrEraq~rak~~~sp~sD~Vd~~~~kl~is~~Lkksvdesd~LreyFskyGKVKsVp~pgTGK~KYGF~~  166 (800)
                      +..+...                         ..+.+.+++ |..-. +-..|.-.|..||.|..|-..    |.     
T Consensus       447 lG~~kst-------------------------~ttr~~sgg-lg~w~-p~~~l~r~fd~fGpir~Idy~----hg-----  490 (975)
T KOG0112|consen  447 LGQPKST-------------------------PTTRLQSGG-LGPWS-PVSRLNREFDRFGPIRIIDYR----HG-----  490 (975)
T ss_pred             ccccccc-------------------------cceeeccCC-CCCCC-hHHHHHHHhhccCcceeeecc----cC-----
Confidence            5433100                         001111211 11112 226788889999999887332    21     


Q ss_pred             ccCCCCCcccccccchhhhhhhhccCccccC
Q 003717          167 VEAPPLPKYFCDCEEHSAAFHAAEGKQIHHP  197 (800)
Q Consensus       167 ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~  197 (800)
                        -|=.|+.+-+...+.+|.+.|.|..+--+
T Consensus       491 --q~yayi~yes~~~aq~a~~~~rgap~G~P  519 (975)
T KOG0112|consen  491 --QPYAYIQYESPPAAQAATHDMRGAPLGGP  519 (975)
T ss_pred             --CcceeeecccCccchhhHHHHhcCcCCCC
Confidence              01136888889999999999998888665

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

Probab=95.38  E-value=0.042  Score=60.74  Aligned_cols=77  Identities=14%  Similarity=0.200  Sum_probs=62.0

Q ss_pred             ccCCcEEEEeCCC----CCCC-------HHHHHHhhhcCCceeEEEEeccCCCcEEEEEecCCCHHHHHHHHHhcCCcEe
Q 003717           10 VEEQTRIYVGGLG----EKVT-------DDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVW   78 (800)
Q Consensus        10 v~qsrTLFVGNLP----~nVT-------EEDLrelFSqFG~VksVrVIRdTGRGFGFVEFeS~D~EdAekAIe~LNG~eL   78 (800)
                      .+..++|.+.|+=    +..+       .++|++...+||.|..|.|.-....|.+-|.|.+  .++|..||..|+|..|
T Consensus       262 ~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d~hPdGvvtV~f~n--~eeA~~ciq~m~GR~f  339 (382)
T KOG1548|consen  262 ARADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYDRHPDGVVTVSFRN--NEEADQCIQTMDGRWF  339 (382)
T ss_pred             ccCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEeccCCCceeEEEeCC--hHHHHHHHHHhcCeee
Confidence            3456788888872    2333       3567777899999999987654567999999997  9999999999999999


Q ss_pred             CCeEEEEEec
Q 003717           79 KGGRLRLERA   88 (800)
Q Consensus        79 dGR~LrVe~A   88 (800)
                      +||.|....-
T Consensus       340 dgRql~A~i~  349 (382)
T KOG1548|consen  340 DGRQLTASIW  349 (382)
T ss_pred             cceEEEEEEe
Confidence            9999987654

>PF00076 RRM_1: RNA recognition motif

Probab=95.29  E-value=0.0071  Score=48.65  Aligned_cols=58  Identities=26%  Similarity=0.451  Sum_probs=45.9

Q ss_pred             CCCCCCcchhhcccccCccceeeeccC--CCCCcc-cccccccCCCCCcccccccchhhhhhhhccCcccc
Q 003717          129 PKKLLDKDKKLNIFFPRLRKVKTLPFC--GTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHH  196 (800)
Q Consensus       129 Lkksvdesd~LreyFskyGKVKsVp~p--gTGK~K-YGF~~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n  196 (800)
                      |+..+++ ++|+.+|+.||.|..+...  .+|+.+ |||         |.|.+.+++..|++.++|..+..
T Consensus         6 lp~~~t~-~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~---------V~F~~~~~a~~a~~~l~g~~~~~   66 (70)
T PF00076_consen    6 LPPDVTE-EELRDFFSQFGKIESIKVMRNSSGKSKGYAF---------VEFESEEDAEKALEELNGKKING   66 (70)
T ss_dssp             ETTTSSH-HHHHHHHHTTSTEEEEEEEEETTSSEEEEEE---------EEESSHHHHHHHHHHHTTEEETT
T ss_pred             CCCcCCH-HHHHHHHHHhhhcccccccccccccccceEE---------EEEcCHHHHHHHHHHcCCCEECc
Confidence            4566656 8999999999998655443  456654 888         89999999999999999976644

(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 ....

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

Probab=95.28  E-value=0.017  Score=69.70  Aligned_cols=80  Identities=23%  Similarity=0.414  Sum_probs=70.1

Q ss_pred             hccCCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEeccCCCcEEEEEecCCCHHHHHHHHHhcCCcEeCC--eEEEEE
Q 003717            9 EVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKG--GRLRLE   86 (800)
Q Consensus         9 Ev~qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRdTGRGFGFVEFeS~D~EdAekAIe~LNG~eLdG--R~LrVe   86 (800)
                      .....+++|||+|..++.-..|...|..||.|..+.+  +.+..|+||.|++  ...+..|+..|-|..|+|  ++|+|.
T Consensus       451 kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy--~hgq~yayi~yes--~~~aq~a~~~~rgap~G~P~~r~rvd  526 (975)
T KOG0112|consen  451 KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDY--RHGQPYAYIQYES--PPAAQAATHDMRGAPLGGPPRRLRVD  526 (975)
T ss_pred             ccccceeeccCCCCCCChHHHHHHHhhccCcceeeec--ccCCcceeeeccc--CccchhhHHHHhcCcCCCCCcccccc
Confidence            3445689999999999999999999999999987655  5577899999998  999999999999999986  789999


Q ss_pred             eccchh
Q 003717           87 RAKEHY   92 (800)
Q Consensus        87 ~AKpr~   92 (800)
                      +|.+-.
T Consensus       527 la~~~~  532 (975)
T KOG0112|consen  527 LASPPG  532 (975)
T ss_pred             cccCCC
Confidence            997653

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

Probab=95.05  E-value=0.053  Score=62.60  Aligned_cols=61  Identities=18%  Similarity=0.319  Sum_probs=52.2

Q ss_pred             HHHHHhhhcCCceeEEEEecc-------CCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEeccc
Q 003717           28 DDLAKVFSSLGEVKAVDIVRT-------KGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKE   90 (800)
Q Consensus        28 EDLrelFSqFG~VksVrVIRd-------TGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~AKp   90 (800)
                      ++++..+++||.|..|.+.+.       .|-|--||+|.+  .+++++|+.+|+|.+|.||.+...+.-+
T Consensus       424 Edvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas--~ed~qrA~~~L~GrKF~nRtVvtsYyde  491 (500)
T KOG0120|consen  424 EDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFAD--TEDSQRAMEELTGRKFANRTVVASYYDE  491 (500)
T ss_pred             HHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecC--hHHHHHHHHHccCceeCCcEEEEEecCH
Confidence            456677889999999998854       246889999997  9999999999999999999999887643

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

Probab=94.64  E-value=0.021  Score=60.94  Aligned_cols=69  Identities=20%  Similarity=0.350  Sum_probs=58.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEeccC----------C--C----cEEEEEecCCCHHHHHHHHHhcCC
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK----------G--R----SFGYVDFFPSSHKSLSKLFSTYNG   75 (800)
Q Consensus        12 qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRdT----------G--R----GFGFVEFeS~D~EdAekAIe~LNG   75 (800)
                      ...-||+++||+.+.-..|+++|+.||.|-.|.+-+..          +  +    --|+|+|.+  ...|..+...||+
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~--KrvAK~iAe~Lnn  150 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFIS--KRVAKRIAELLNN  150 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHH--HHHHHHHHHHhCC
Confidence            45679999999999999999999999999999886321          1  1    247899997  9999999999999


Q ss_pred             cEeCCeE
Q 003717           76 CVWKGGR   82 (800)
Q Consensus        76 ~eLdGR~   82 (800)
                      ..|+|++
T Consensus       151 ~~Iggkk  157 (278)
T KOG3152|consen  151 TPIGGKK  157 (278)
T ss_pred             CccCCCC
Confidence            9999975

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

Probab=94.39  E-value=0.0059  Score=73.02  Aligned_cols=125  Identities=22%  Similarity=0.329  Sum_probs=86.6

Q ss_pred             cCCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEe--cc--CCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEE
Q 003717           11 EEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RT--KGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLE   86 (800)
Q Consensus        11 ~qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVI--Rd--TGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe   86 (800)
                      +...++||.||+..+.+++|...|..+|.+..+++.  ..  .-||+|||+|..  .+.+.+|+....++.++-..    
T Consensus       665 R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~--~~~~~aaV~f~d~~~~gK~~----  738 (881)
T KOG0128|consen  665 RDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLK--PEHAGAAVAFRDSCFFGKIS----  738 (881)
T ss_pred             HHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeec--CCchhhhhhhhhhhhhhhhh----
Confidence            345689999999999999999999999998777655  22  337999999997  88899888765555444000    


Q ss_pred             eccchhhHHHhhhHHHHhhhhCCCCCCCCCCCCCCCcccCCCCCCCCCcchhhcccccCccceeeeccC--CCCCccccc
Q 003717           87 RAKEHYLARLKREWAEDDAQLVNPPVTDSVAPDNKDATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPFC--GTGKHKYSF  164 (800)
Q Consensus        87 ~AKpr~~~RlkrEraq~rak~~~sp~sD~Vd~~~~kl~is~~Lkksvdesd~LreyFskyGKVKsVp~p--gTGK~KYGF  164 (800)
                                                          +++.+. ++.-+. +.++.+|+..|.++.++..  -.|++|   
T Consensus       739 ------------------------------------v~i~g~-pf~gt~-e~~k~l~~~~gn~~~~~~vt~r~gkpk---  777 (881)
T KOG0128|consen  739 ------------------------------------VAISGP-PFQGTK-EELKSLASKTGNVTSLRLVTVRAGKPK---  777 (881)
T ss_pred             ------------------------------------hheeCC-CCCCch-HHHHhhccccCCccccchhhhhccccc---
Confidence                                                111111 111212 6788999999999877654  356666   


Q ss_pred             ccccCCCCCcccccccchhhhhhhhc
Q 003717          165 QRVEAPPLPKYFCDCEEHSAAFHAAE  190 (800)
Q Consensus       165 ~~ve~Ps~pV~F~sfEea~aA~eAmN  190 (800)
                              .+.|+++++...+....+
T Consensus       778 --------g~a~v~y~~ea~~s~~~~  795 (881)
T KOG0128|consen  778 --------GKARVDYNTEADASRKVA  795 (881)
T ss_pred             --------cceeccCCCcchhhhhcc
Confidence                    356777777766665533

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

Probab=94.33  E-value=0.05  Score=60.34  Aligned_cols=82  Identities=20%  Similarity=0.228  Sum_probs=62.7

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhhcCCc--eeEEEEe--ccC--CCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEe
Q 003717           14 TRIYVGGLGEKVTDDDLAKVFSSLGE--VKAVDIV--RTK--GRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLER   87 (800)
Q Consensus        14 rTLFVGNLP~nVTEEDLrelFSqFG~--VksVrVI--RdT--GRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~   87 (800)
                      --+|||||-|.+|++||.+.....|-  +.++++.  |..  .+|||.|...+  .....+.++.|-..+|.|+.-.|.-
T Consensus        81 ~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~S--dAa~Kq~MeiLP~k~iHGQ~P~V~~  158 (498)
T KOG4849|consen   81 YCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNS--DAAVKQTMEILPTKTIHGQSPTVLS  158 (498)
T ss_pred             EEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecc--hHHHHHHHHhcccceecCCCCeeec
Confidence            35899999999999999998888775  4444444  222  37999999997  7888888999999999998777766


Q ss_pred             ccchhhHHHh
Q 003717           88 AKEHYLARLK   97 (800)
Q Consensus        88 AKpr~~~Rlk   97 (800)
                      ....+..++.
T Consensus       159 ~NK~~~ak~E  168 (498)
T KOG4849|consen  159 YNKTNQAKLE  168 (498)
T ss_pred             cchhhHHHHH
Confidence            5555544443

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

Probab=94.27  E-value=0.05  Score=61.51  Aligned_cols=149  Identities=19%  Similarity=0.236  Sum_probs=96.6

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEeccCCCcEEEEEecCCCHHHHHHHHHhcCC-cEeCCeEEEEEeccchh
Q 003717           14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNG-CVWKGGRLRLERAKEHY   92 (800)
Q Consensus        14 rTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRdTGRGFGFVEFeS~D~EdAekAIe~LNG-~eLdGR~LrVe~AKpr~   92 (800)
                      .+||+|||++.++..+|+.+|...-.-.+-.++-  .-||+||++..  ...|.+|++.++| .++.|+++.|...-++.
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~--k~gyafvd~pd--q~wa~kaie~~sgk~elqGkr~e~~~sv~kk   77 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV--KSGYAFVDCPD--QQWANKAIETLSGKVELQGKRQEVEHSVPKK   77 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceee--ecceeeccCCc--hhhhhhhHHhhchhhhhcCceeeccchhhHH
Confidence            4799999999999999999998751111111110  24899999985  9999999999999 58899999999887653


Q ss_pred             hHHHhhhHHHHhhhhCCCCCCCCCCCCCCCcccCCCCCCCCCcchhhcccccCccceeee----ccCCCCCccccccccc
Q 003717           93 LARLKREWAEDDAQLVNPPVTDSVAPDNKDATRLDTPKKLLDKDKKLNIFFPRLRKVKTL----PFCGTGKHKYSFQRVE  168 (800)
Q Consensus        93 ~~RlkrEraq~rak~~~sp~sD~Vd~~~~kl~is~~Lkksvdesd~LreyFskyGKVKsV----p~pgTGK~KYGF~~ve  168 (800)
                      .+-.+.     +-+  .               +...+.+     +-+..+...||.|..+    +++.+--.        
T Consensus        78 qrsrk~-----Qir--n---------------ippql~w-----evld~Ll~qyg~ve~~eqvnt~~etavv--------  122 (584)
T KOG2193|consen   78 QRSRKI-----QIR--N---------------IPPQLQW-----EVLDSLLAQYGTVENCEQVNTDSETAVV--------  122 (584)
T ss_pred             HHhhhh-----hHh--c---------------CCHHHHH-----HHHHHHHhccCCHhHhhhhccchHHHHH--------
Confidence            222110     000  0               0000111     3455566788887643    22322222        


Q ss_pred             CCCCCcccccccchhhhhhhhccCccccCCCCccccc
Q 003717          169 APPLPKYFCDCEEHSAAFHAAEGKQIHHPAAGQEEIH  205 (800)
Q Consensus       169 ~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n~~q~~i~  205 (800)
                          -+.+..-+.|..|++.+||-.+.+-.-++--|+
T Consensus       123 ----nvty~~~~~~~~ai~kl~g~Q~en~~~k~~YiP  155 (584)
T KOG2193|consen  123 ----NVTYSAQQQHRQAIHKLNGPQLENQHLKVGYIP  155 (584)
T ss_pred             ----HHHHHHHHHHHHHHHhhcchHhhhhhhhcccCc
Confidence                257778888999998888877776554444444

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

Probab=94.07  E-value=0.052  Score=60.07  Aligned_cols=80  Identities=18%  Similarity=0.260  Sum_probs=66.0

Q ss_pred             ccCCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEE--------Eec--cC--CCcEEEEEecCCCHHHHHHHHHhcCCcE
Q 003717           10 VEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVD--------IVR--TK--GRSFGYVDFFPSSHKSLSKLFSTYNGCV   77 (800)
Q Consensus        10 v~qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVr--------VIR--dT--GRGFGFVEFeS~D~EdAekAIe~LNG~e   77 (800)
                      .....+|||-+|+..++..+|.++|.++|.|..-+        +-+  .|  .+|=|.|.|.+  ...|+.|+..+++..
T Consensus        63 ~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D--~~~akaai~~~agkd  140 (351)
T KOG1995|consen   63 KSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYED--PPAAKAAIEWFAGKD  140 (351)
T ss_pred             ccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecC--hhhhhhhhhhhcccc
Confidence            44567999999999999999999999999875421        112  23  36999999996  999999999999999


Q ss_pred             eCCeEEEEEeccch
Q 003717           78 WKGGRLRLERAKEH   91 (800)
Q Consensus        78 LdGR~LrVe~AKpr   91 (800)
                      +.|..|+|..|..+
T Consensus       141 f~gn~ikvs~a~~r  154 (351)
T KOG1995|consen  141 FCGNTIKVSLAERR  154 (351)
T ss_pred             ccCCCchhhhhhhc
Confidence            99999999887544

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

Probab=93.94  E-value=0.12  Score=59.44  Aligned_cols=75  Identities=15%  Similarity=0.174  Sum_probs=59.0

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhhcCCceeE-EEEecc---CCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEecc
Q 003717           14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKA-VDIVRT---KGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAK   89 (800)
Q Consensus        14 rTLFVGNLP~nVTEEDLrelFSqFG~Vks-VrVIRd---TGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~AK   89 (800)
                      -.|=+.+|||.+|+++|.++|+-.-.|.. +.++.+   +..|-|||.|++  .+.|++|+.. |...|+.|-|.|-.+.
T Consensus       104 ~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~s--qe~ae~Al~r-hre~iGhRYIEvF~Ss  180 (510)
T KOG4211|consen  104 GVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFES--QESAEIALGR-HRENIGHRYIEVFRSS  180 (510)
T ss_pred             ceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecC--HHHHHHHHHH-HHHhhccceEEeehhH
Confidence            45677899999999999999998866555 223322   234899999998  9999999864 6788899999998775


Q ss_pred             ch
Q 003717           90 EH   91 (800)
Q Consensus        90 pr   91 (800)
                      ..
T Consensus       181 ~~  182 (510)
T KOG4211|consen  181 RA  182 (510)
T ss_pred             HH
Confidence            44

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

Probab=93.26  E-value=0.27  Score=55.22  Aligned_cols=73  Identities=22%  Similarity=0.207  Sum_probs=62.0

Q ss_pred             EeCCCCCCCHHHHHHhhhcCCceeEEEEeccCCCcEEEEEecCCCHHHHHHHHHhcCCcEeC--CeEEEEEeccchhh
Q 003717           18 VGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWK--GGRLRLERAKEHYL   93 (800)
Q Consensus        18 VGNLP~nVTEEDLrelFSqFG~VksVrVIRdTGRGFGFVEFeS~D~EdAekAIe~LNG~eLd--GR~LrVe~AKpr~~   93 (800)
                      |-|--+.+|-+-|..+.-..|.|.++.|++.++ -.|.|+|++  .+.|++|...|||..|.  -..|+|++|+|..+
T Consensus       127 IlNp~YpItvDVly~Icnp~GkVlRIvIfkkng-VQAmVEFds--v~~AqrAk~alNGADIYsGCCTLKIeyAkP~rl  201 (494)
T KOG1456|consen  127 ILNPQYPITVDVLYTICNPQGKVLRIVIFKKNG-VQAMVEFDS--VEVAQRAKAALNGADIYSGCCTLKIEYAKPTRL  201 (494)
T ss_pred             eecCccccchhhhhhhcCCCCceEEEEEEeccc-eeeEEeech--hHHHHHHHhhcccccccccceeEEEEecCccee
Confidence            345557899999999999999999998886533 379999998  99999999999999885  47999999999744

>smart00361 RRM_1 RNA recognition motif

Probab=93.23  E-value=0.045  Score=46.27  Aligned_cols=51  Identities=12%  Similarity=0.128  Sum_probs=37.9

Q ss_pred             hhhccccc----Cccceeee----ccCCC--CCcc-cccccccCCCCCcccccccchhhhhhhhccCcccc
Q 003717          137 KKLNIFFP----RLRKVKTL----PFCGT--GKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHH  196 (800)
Q Consensus       137 d~LreyFs----kyGKVKsV----p~pgT--GK~K-YGF~~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n  196 (800)
                      ++|+.+|.    .||.|..+    ..+.+  |+++ |||         |.|.+.+++..|+..|||..+.-
T Consensus         3 ~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~f---------V~f~~~~dA~~A~~~l~g~~~~g   64 (70)
T smart00361        3 EDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVY---------ITFERSEDAARAIVDLNGRYFDG   64 (70)
T ss_pred             hhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEE---------EEECCHHHHHHHHHHhCCCEECC
Confidence            56777777    88886543    33444  7666 555         89999999999999999987643

>smart00360 RRM RNA recognition motif

Probab=93.00  E-value=0.071  Score=41.30  Aligned_cols=55  Identities=25%  Similarity=0.423  Sum_probs=40.2

Q ss_pred             CCCCCcchhhcccccCccceeee---ccCCCCCcc-cccccccCCCCCcccccccchhhhhhhhccCcc
Q 003717          130 KKLLDKDKKLNIFFPRLRKVKTL---PFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQI  194 (800)
Q Consensus       130 kksvdesd~LreyFskyGKVKsV---p~pgTGK~K-YGF~~ve~Ps~pV~F~sfEea~aA~eAmNG~~i  194 (800)
                      +..+.. ++|+.+|..||.|..+   +.+.+++++ |+|         +.|.+.+++..|+..++|..+
T Consensus         5 ~~~~~~-~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~---------v~f~~~~~a~~a~~~~~~~~~   63 (71)
T smart00360        5 PPDVTE-EELRELFSKFGKIESVRLVRDKDTGKSKGFAF---------VEFESEEDAEKALEALNGKEL   63 (71)
T ss_pred             CcccCH-HHHHHHHHhhCCEeEEEEEeCCCCCCCCceEE---------EEeCCHHHHHHHHHHcCCCee
Confidence            334444 8899999999986544   334456666 666         889999999999888886555

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

Probab=92.89  E-value=0.058  Score=57.49  Aligned_cols=59  Identities=15%  Similarity=0.184  Sum_probs=48.5

Q ss_pred             CCCCCCcchhhcccccCcccee---eeccCCCCCcc-cccccccCCCCCcccccccchhhhhhhhccCccccC
Q 003717          129 PKKLLDKDKKLNIFFPRLRKVK---TLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHP  197 (800)
Q Consensus       129 Lkksvdesd~LreyFskyGKVK---sVp~pgTGK~K-YGF~~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~  197 (800)
                      |..+..+ ++|.++|..||-|.   .++++.||.+| |+|         |+|.+.++|..|++.+||--+.++
T Consensus       197 Lsed~~E-~dL~eLf~~fg~i~rvylardK~TG~~kGFAF---------VtF~sRddA~rAI~~LnG~gyd~L  259 (270)
T KOG0122|consen  197 LSEDMRE-DDLEELFRPFGPITRVYLARDKETGLSKGFAF---------VTFESRDDAARAIADLNGYGYDNL  259 (270)
T ss_pred             CccccCh-hHHHHHhhccCccceeEEEEccccCcccceEE---------EEEecHHHHHHHHHHccCcccceE
Confidence            3555555 88999999999854   57889999998 555         999999999999999998766654

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

Probab=92.61  E-value=0.14  Score=59.66  Aligned_cols=72  Identities=18%  Similarity=0.270  Sum_probs=56.6

Q ss_pred             CcEEEEeCCCCCCCH--H----HHHHhhhcCCceeEEEEecc--CC-CcEEEEEecCCCHHHHHHHHHhcCCcEeC-CeE
Q 003717           13 QTRIYVGGLGEKVTD--D----DLAKVFSSLGEVKAVDIVRT--KG-RSFGYVDFFPSSHKSLSKLFSTYNGCVWK-GGR   82 (800)
Q Consensus        13 srTLFVGNLP~nVTE--E----DLrelFSqFG~VksVrVIRd--TG-RGFGFVEFeS~D~EdAekAIe~LNG~eLd-GR~   82 (800)
                      ..-|+|-|+|---..  +    -|..+|+++|.|+...++.+  .| +||.|++|.+  ..+|+.|+..|||+.|+ ...
T Consensus        58 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   58 DSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYAS--MRDAKKAVKSLNGKRLDKNHT  135 (698)
T ss_pred             ceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecC--hhhHHHHHHhcccceecccce
Confidence            457899998854332  2    35688999999999888722  33 7999999997  99999999999999886 556


Q ss_pred             EEEE
Q 003717           83 LRLE   86 (800)
Q Consensus        83 LrVe   86 (800)
                      +.|.
T Consensus       136 f~v~  139 (698)
T KOG2314|consen  136 FFVR  139 (698)
T ss_pred             EEee
Confidence            6664

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

Probab=92.53  E-value=0.28  Score=40.58  Aligned_cols=52  Identities=21%  Similarity=0.441  Sum_probs=40.2

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEeccCCCcEEEEEecCCCHHHHHHHH
Q 003717           14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLF   70 (800)
Q Consensus        14 rTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRdTGRGFGFVEFeS~D~EdAekAI   70 (800)
                      +.|-|.|.+....+ .+...|.+||.|..+.+.  ...-+.||.|.+  ..+|++|+
T Consensus         2 ~wI~V~Gf~~~~~~-~vl~~F~~fGeI~~~~~~--~~~~~~~l~y~~--~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAE-EVLEHFASFGEIVDIYVP--ESTNWMYLKYKS--RKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHH-HHHHHHHhcCCEEEEEcC--CCCcEEEEEECC--HHHHHhhC
Confidence            45778888766554 455689999999998774  235689999997  99998885

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

Probab=92.40  E-value=0.2  Score=56.47  Aligned_cols=72  Identities=18%  Similarity=0.305  Sum_probs=55.5

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc---C----CCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEE
Q 003717           14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT---K----GRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLE   86 (800)
Q Consensus        14 rTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd---T----GRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe   86 (800)
                      .-|-|.||++.+|.++++.+|+-.|.|..+.+...   .    ..-.|||.|.+  ...+ .+...|-.+.+-++.|.|-
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d--~~sv-~vaQhLtntvfvdraliv~   84 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLD--SQSV-TVAQHLTNTVFVDRALIVR   84 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccC--Ccce-eHHhhhccceeeeeeEEEE
Confidence            47899999999999999999999999999988732   1    14689999995  4444 4445667777777777665


Q ss_pred             ec
Q 003717           87 RA   88 (800)
Q Consensus        87 ~A   88 (800)
                      .+
T Consensus        85 p~   86 (479)
T KOG4676|consen   85 PY   86 (479)
T ss_pred             ec
Confidence            54

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

Probab=92.32  E-value=0.26  Score=56.90  Aligned_cols=61  Identities=28%  Similarity=0.458  Sum_probs=51.1

Q ss_pred             ccCCcEEEEeCCCCCCCHHHHHHhhh-cCCceeEEEEecc-C---CCcEEEEEecCCCHHHHHHHHHh
Q 003717           10 VEEQTRIYVGGLGEKVTDDDLAKVFS-SLGEVKAVDIVRT-K---GRSFGYVDFFPSSHKSLSKLFST   72 (800)
Q Consensus        10 v~qsrTLFVGNLP~nVTEEDLrelFS-qFG~VksVrVIRd-T---GRGFGFVEFeS~D~EdAekAIe~   72 (800)
                      ++..+|||||+||.-++.++|-.+|. -||.|..|-|=+| .   .+|-|-|+|.+  ..+-.+||.+
T Consensus       367 lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsn--qqsYi~AIsa  432 (520)
T KOG0129|consen  367 IDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSN--QQAYIKAISA  432 (520)
T ss_pred             cCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecc--cHHHHHHHhh
Confidence            45678999999999999999999999 6999998887554 1   37999999997  7777778763

>PF13893 RRM_5: RNA recognition motif

Probab=92.10  E-value=0.071  Score=42.73  Aligned_cols=46  Identities=22%  Similarity=0.434  Sum_probs=35.7

Q ss_pred             hcccccCccceeeeccCCCCCcccccccccCCCCCcccccccchhhhhhhhccCcc
Q 003717          139 LNIFFPRLRKVKTLPFCGTGKHKYSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQI  194 (800)
Q Consensus       139 LreyFskyGKVKsVp~pgTGK~KYGF~~ve~Ps~pV~F~sfEea~aA~eAmNG~~i  194 (800)
                      |..+|++||+|..+...... ..++|         |.|.+.++|..|...+||..+
T Consensus         1 L~~~f~~fG~V~~i~~~~~~-~~~a~---------V~f~~~~~A~~a~~~l~~~~~   46 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK-RGFAF---------VEFASVEDAQKAIEQLNGRQF   46 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-TTEEE---------EEESSHHHHHHHHHHHTTSEE
T ss_pred             ChHHhCCcccEEEEEEEeCC-CCEEE---------EEECCHHHHHHHHHHhCCCEE
Confidence            46789999999876554433 23456         899999999999999999886

(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 ....

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

Probab=92.09  E-value=0.55  Score=46.80  Aligned_cols=80  Identities=25%  Similarity=0.335  Sum_probs=49.4

Q ss_pred             CcEEEEeCCC-----CCCCHH----HHHHhhhcCCceeEEEEeccCCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEE
Q 003717           13 QTRIYVGGLG-----EKVTDD----DLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRL   83 (800)
Q Consensus        13 srTLFVGNLP-----~nVTEE----DLrelFSqFG~VksVrVIRdTGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~L   83 (800)
                      ..+|-|.=+.     ...-++    +|-+.|..||.|.-++++.    +.-+|+|..  -..|.+|+. |+|..++|+.|
T Consensus        27 DaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~----~~mwVTF~d--g~sALaals-~dg~~v~g~~l   99 (146)
T PF08952_consen   27 DATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVG----DTMWVTFRD--GQSALAALS-LDGIQVNGRTL   99 (146)
T ss_dssp             T-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEET----TCEEEEESS--CHHHHHHHH-GCCSEETTEEE
T ss_pred             CceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeC----CeEEEEECc--cHHHHHHHc-cCCcEECCEEE
Confidence            3566666555     112222    6778899999988887764    357899996  788888775 89999999999


Q ss_pred             EEEeccchhhHHHhhh
Q 003717           84 RLERAKEHYLARLKRE   99 (800)
Q Consensus        84 rVe~AKpr~~~RlkrE   99 (800)
                      +|..-.|.+......+
T Consensus       100 ~i~LKtpdW~~~l~~E  115 (146)
T PF08952_consen  100 KIRLKTPDWLKGLEEE  115 (146)
T ss_dssp             EEEE------------
T ss_pred             EEEeCCccHHHHHHHH
Confidence            9999888877655443

; 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=91.86  E-value=0.88  Score=42.55  Aligned_cols=73  Identities=18%  Similarity=0.260  Sum_probs=50.6

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEe-----------ccCCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCe-
Q 003717           14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV-----------RTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGG-   81 (800)
Q Consensus        14 rTLFVGNLP~nVTEEDLrelFSqFG~VksVrVI-----------RdTGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR-   81 (800)
                      .-|.|=+.|.. ....+.++|++||.|.+..-+           ...+...-.|.|.+  ..+|.+|+. .||..|.|. 
T Consensus         7 ~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~--~~~A~rAL~-~NG~i~~g~~   82 (100)
T PF05172_consen    7 TWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDN--PLSAQRALQ-KNGTIFSGSL   82 (100)
T ss_dssp             CEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESS--HHHHHHHHT-TTTEEETTCE
T ss_pred             eEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCC--HHHHHHHHH-hCCeEEcCcE
Confidence            45778888888 445677889999999876411           11356789999998  999999997 599999885 


Q ss_pred             EEEEEeccc
Q 003717           82 RLRLERAKE   90 (800)
Q Consensus        82 ~LrVe~AKp   90 (800)
                      .+-|.++++
T Consensus        83 mvGV~~~~~   91 (100)
T PF05172_consen   83 MVGVKPCDP   91 (100)
T ss_dssp             EEEEEE-HH
T ss_pred             EEEEEEcHH
Confidence            455666643

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.

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

Probab=91.80  E-value=0.17  Score=57.42  Aligned_cols=62  Identities=18%  Similarity=0.297  Sum_probs=53.4

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc-----CC------------CcEEEEEecCCCHHHHHHHHHhcC
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT-----KG------------RSFGYVDFFPSSHKSLSKLFSTYN   74 (800)
Q Consensus        12 qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd-----TG------------RGFGFVEFeS~D~EdAekAIe~LN   74 (800)
                      +.++|.+-|||.+-.-+.|.++|+.+|.|..|+|+.-     ..            +-+|||+|..  .+.|.+|.+.||
T Consensus       230 ~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~--~~~A~KA~e~~~  307 (484)
T KOG1855|consen  230 PSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEE--VEAARKARELLN  307 (484)
T ss_pred             ccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhh--hHHHHHHHHhhc
Confidence            5789999999999999999999999999999999822     11            2489999997  999999999886


Q ss_pred             C
Q 003717           75 G   75 (800)
Q Consensus        75 G   75 (800)
                      -
T Consensus       308 ~  308 (484)
T KOG1855|consen  308 P  308 (484)
T ss_pred             h
Confidence            4

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

Probab=91.51  E-value=0.092  Score=56.17  Aligned_cols=59  Identities=17%  Similarity=0.324  Sum_probs=49.4

Q ss_pred             HHHHHhhh-cCCceeEEEEeccCC---CcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEec
Q 003717           28 DDLAKVFS-SLGEVKAVDIVRTKG---RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERA   88 (800)
Q Consensus        28 EDLrelFS-qFG~VksVrVIRdTG---RGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~A   88 (800)
                      ++|...|+ +||.|..+.|..+.+   +|=.||.|..  .++|++|+..||+..+.|++|..++.
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~--Ee~ae~a~~~lnnRw~~G~pi~ae~~  145 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRS--EEDAEAALEDLNNRWYNGRPIHAELS  145 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhccc--HHHHHHHHHHHcCccccCCcceeeec
Confidence            44555555 899999987764333   7999999998  99999999999999999999999876

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

Probab=91.16  E-value=0.53  Score=56.30  Aligned_cols=72  Identities=13%  Similarity=0.106  Sum_probs=60.6

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEe--ccCC--CcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEe
Q 003717           14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RTKG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLER   87 (800)
Q Consensus        14 rTLFVGNLP~nVTEEDLrelFSqFG~VksVrVI--RdTG--RGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~   87 (800)
                      +-|-+.|+|+.++-+|+.++|..|-.+-.-.++  .+.|  .|-|-|.|++  .++|..|...|++..|..|.|.+.+
T Consensus       868 ~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~nd~G~pTGe~mvAfes--~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  868 RVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFES--QEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             eEEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecC--HHHHHhhhhccccCcccceeEEEEe
Confidence            367899999999999999999999766544334  2344  4899999998  9999999999999999999998764

>PF14259 RRM_6: RNA recognition motif (a

Probab=90.90  E-value=0.12  Score=42.56  Aligned_cols=58  Identities=22%  Similarity=0.399  Sum_probs=42.1

Q ss_pred             CCCCCCcchhhcccccCccceeeeccCC--CCCcc-cccccccCCCCCcccccccchhhhhhhhccCcccc
Q 003717          129 PKKLLDKDKKLNIFFPRLRKVKTLPFCG--TGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHH  196 (800)
Q Consensus       129 Lkksvdesd~LreyFskyGKVKsVp~pg--TGK~K-YGF~~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n  196 (800)
                      ++..++. ++|+.+|..||.|..+....  .|..+ |+|         |.|.+.+++..|+...+|..++.
T Consensus         6 lp~~~~~-~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~---------v~f~~~~~a~~al~~~~~~~~~g   66 (70)
T PF14259_consen    6 LPPSTTE-EDLRNFFSRFGPVEKVRLIKNKDGQSRGFAF---------VEFSSEEDAKRALELLNGKEIDG   66 (70)
T ss_dssp             STTT--H-HHHHHHCTTSSBEEEEEEEESTTSSEEEEEE---------EEESSHHHHHHHHHHHTTEEETT
T ss_pred             CCCCCCH-HHHHHHHHhcCCcceEEEEeeeccccCCEEE---------EEeCCHHHHHHHHHHCCCcEECC
Confidence            4555655 89999999999876554432  25544 666         89999999999999988766643

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 ....

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

Probab=90.62  E-value=0.14  Score=48.98  Aligned_cols=71  Identities=18%  Similarity=0.214  Sum_probs=53.4

Q ss_pred             CcccCCCCCCCCCcchhhcccccCccceee---eccCCCCCcc-cccccccCCCCCcccccccchhhhhhhhccCccccC
Q 003717          122 DATRLDTPKKLLDKDKKLNIFFPRLRKVKT---LPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHP  197 (800)
Q Consensus       122 kl~is~~Lkksvdesd~LreyFskyGKVKs---Vp~pgTGK~K-YGF~~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~  197 (800)
                      .++++ .|...+++ +.|+.+|..||.|..   +.++.+|+.+ |+|         |.|.+.+++..|++.++|..+.. 
T Consensus       117 ~l~v~-nL~~~~~~-~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~---------v~f~~~~~~~~a~~~~~~~~~~~-  184 (306)
T COG0724         117 TLFVG-NLPYDVTE-EDLRELFKKFGPVKRVRLVRDRETGKSRGFAF---------VEFESEESAEKAIEELNGKELEG-  184 (306)
T ss_pred             eEEEe-CCCCCCCH-HHHHHHHHhcCceeEEEeeeccccCccCceEE---------EEecCHHHHHHHHHHcCCCeECC-
Confidence            34444 46777766 999999999999744   4445688887 666         89999999999999999877755 


Q ss_pred             CCCccccch
Q 003717          198 AAGQEEIHD  206 (800)
Q Consensus       198 n~~q~~i~~  206 (800)
                        .-+.|..
T Consensus       185 --~~~~v~~  191 (306)
T COG0724         185 --RPLRVQK  191 (306)
T ss_pred             --ceeEeec
Confidence              3444544

>PLN03120 nucleic acid binding protein; Provisional

Probab=90.45  E-value=0.14  Score=55.08  Aligned_cols=70  Identities=11%  Similarity=0.139  Sum_probs=48.1

Q ss_pred             cccCCCCCCCCCcchhhcccccCccceeeeccCCCCC-cccccccccCCCCCcccccccchhhhhhhhccCccccCCCCc
Q 003717          123 ATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPFCGTGK-HKYSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPAAGQ  201 (800)
Q Consensus       123 l~is~~Lkksvdesd~LreyFskyGKVKsVp~pgTGK-~KYGF~~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n~~q  201 (800)
                      +++++ |...+++ ++|+.||+.||+|..+.....+. .+|||         |.|-+-+++..|+. |||..+.   |..
T Consensus         7 VfVgN-Ls~~tTE-~dLrefFS~~G~I~~V~I~~d~~~~GfAF---------VtF~d~eaAe~All-LnG~~l~---gr~   71 (260)
T PLN03120          7 VKVSN-VSLKATE-RDIKEFFSFSGDIEYVEMQSENERSQIAY---------VTFKDPQGAETALL-LSGATIV---DQS   71 (260)
T ss_pred             EEEeC-CCCCCCH-HHHHHHHHhcCCeEEEEEeecCCCCCEEE---------EEeCcHHHHHHHHH-hcCCeeC---Cce
Confidence            34433 5666766 89999999999998776654332 34666         78888888888884 7776664   455


Q ss_pred             cccchh
Q 003717          202 EEIHDM  207 (800)
Q Consensus       202 ~~i~~~  207 (800)
                      +.|..+
T Consensus        72 V~Vt~a   77 (260)
T PLN03120         72 VTITPA   77 (260)
T ss_pred             EEEEec
Confidence            666543

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

Probab=90.04  E-value=0.33  Score=57.02  Aligned_cols=79  Identities=15%  Similarity=0.214  Sum_probs=64.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHhhhcC-CceeEEEEeccCCCcEEEEEecCCCHHHHHHHHHhcCCcEe---CCeEEEEEe
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSL-GEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVW---KGGRLRLER   87 (800)
Q Consensus        12 qsrTLFVGNLP~nVTEEDLrelFSqF-G~VksVrVIRdTGRGFGFVEFeS~D~EdAekAIe~LNG~eL---dGR~LrVe~   87 (800)
                      ...-|||.||=.-.|.-+|+.++++- |.|... +| ++-+..|||.|.+  .++|...+.+|||..|   +++.|.+.|
T Consensus       443 ~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~-Wm-DkIKShCyV~yss--~eEA~atr~AlhnV~WP~sNPK~L~adf  518 (718)
T KOG2416|consen  443 PSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF-WM-DKIKSHCYVSYSS--VEEAAATREALHNVQWPPSNPKHLIADF  518 (718)
T ss_pred             ccceEeeecccccchHHHHHHHHhhccCchHHH-HH-HHhhcceeEeccc--HHHHHHHHHHHhccccCCCCCceeEeee
Confidence            35679999999999999999999964 555554 43 3346789999998  9999999999999999   578999999


Q ss_pred             ccchhhH
Q 003717           88 AKEHYLA   94 (800)
Q Consensus        88 AKpr~~~   94 (800)
                      +....+.
T Consensus       519 ~~~deld  525 (718)
T KOG2416|consen  519 VRADELD  525 (718)
T ss_pred             cchhHHH
Confidence            8765444

>smart00362 RRM_2 RNA recognition motif

Probab=89.92  E-value=0.21  Score=38.86  Aligned_cols=55  Identities=20%  Similarity=0.384  Sum_probs=40.0

Q ss_pred             CCCCCcchhhcccccCccceeeeccCCC-CCcc-cccccccCCCCCcccccccchhhhhhhhccCcc
Q 003717          130 KKLLDKDKKLNIFFPRLRKVKTLPFCGT-GKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQI  194 (800)
Q Consensus       130 kksvdesd~LreyFskyGKVKsVp~pgT-GK~K-YGF~~ve~Ps~pV~F~sfEea~aA~eAmNG~~i  194 (800)
                      +..++. ++|+.+|..||.|..+..... |.++ |+|         +.|.+.+++..|+..++|..+
T Consensus         8 ~~~~~~-~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~---------v~f~~~~~a~~a~~~~~~~~~   64 (72)
T smart00362        8 PPDVTE-EDLKELFSKFGPIESVKIPKDTGKSKGFAF---------VEFESEEDAEKAIEALNGTKL   64 (72)
T ss_pred             CCcCCH-HHHHHHHHhcCCEEEEEEecCCCCCCceEE---------EEeCCHHHHHHHHHHhCCcEE
Confidence            444544 889999999999775544322 4443 666         899999999999999888665

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

Probab=89.64  E-value=0.83  Score=47.59  Aligned_cols=66  Identities=18%  Similarity=0.316  Sum_probs=57.2

Q ss_pred             hccCCcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEeccCCCcEEEEEecCCCHHHHHHHHHhcCCcEeC
Q 003717            9 EVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWK   79 (800)
Q Consensus         9 Ev~qsrTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRdTGRGFGFVEFeS~D~EdAekAIe~LNG~eLd   79 (800)
                      ..+...++.|.+||...++.+|++.....|.|....+.++   |+|.|+|..  .++...|+..|....+.
T Consensus       111 srrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD---g~GvV~~~r--~eDMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  111 SRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD---GVGVVEYLR--KEDMKYAVRKLDDQKFR  176 (241)
T ss_pred             ccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc---cceeeeeee--hhhHHHHHHhhcccccc
Confidence            3445678999999999999999999999999988877554   699999997  99999999999876664

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=89.39  E-value=0.16  Score=56.00  Aligned_cols=82  Identities=16%  Similarity=0.291  Sum_probs=65.8

Q ss_pred             cEEEEeCCCCCCCHHHHH---HhhhcCCceeEEEEeccC----C---CcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEE
Q 003717           14 TRIYVGGLGEKVTDDDLA---KVFSSLGEVKAVDIVRTK----G---RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRL   83 (800)
Q Consensus        14 rTLFVGNLP~nVTEEDLr---elFSqFG~VksVrVIRdT----G---RGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~L   83 (800)
                      .-+||-+|+..+.++.+.   ++|++||.|..+.+-+++    +   -.-+||+|..  .++|..||...+|..++|+.|
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~--~eda~rci~~v~g~~~dg~~l  155 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEE--EEDADRCIDDVDGFVDDGRAL  155 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccc--hHhhhhHHHHhhhHHhhhhhh
Confidence            457888999887766543   789999999998876543    1   2358999997  899999999999999999999


Q ss_pred             EEEeccchhhHHHh
Q 003717           84 RLERAKEHYLARLK   97 (800)
Q Consensus        84 rVe~AKpr~~~Rlk   97 (800)
                      +..++..+|-....
T Consensus       156 ka~~gttkycs~~l  169 (327)
T KOG2068|consen  156 KASLGTTKYCSFYL  169 (327)
T ss_pred             HHhhCCCcchhHHh
Confidence            98888877655443

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

Probab=88.97  E-value=0.9  Score=49.95  Aligned_cols=60  Identities=20%  Similarity=0.153  Sum_probs=49.4

Q ss_pred             HHHHHhhhcCCceeEEEEeccCC-----CcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEecc
Q 003717           28 DDLAKVFSSLGEVKAVDIVRTKG-----RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAK   89 (800)
Q Consensus        28 EDLrelFSqFG~VksVrVIRdTG-----RGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~AK   89 (800)
                      +++.+..++||.|..|.|.-..+     .---||+|..  .+.|.+|+-.|||..|+||.++..|..
T Consensus       301 de~keEceKyg~V~~viifeip~~p~deavRiFveF~r--~e~aiKA~VdlnGRyFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  301 DETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFER--VESAIKAVVDLNGRYFGGRVVSACFYN  365 (378)
T ss_pred             HHHHHHHHhhcceeeEEEEecCCCccchhheeeeeecc--HHHHHHHHHhcCCceecceeeeheecc
Confidence            46778899999999987762211     2458999997  999999999999999999999887754

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

Probab=88.89  E-value=0.17  Score=53.16  Aligned_cols=49  Identities=20%  Similarity=0.297  Sum_probs=41.4

Q ss_pred             hhhcccccCcccee---eeccCCCCCcc-cccccccCCCCCcccccccchhhhhhhhccCcc
Q 003717          137 KKLNIFFPRLRKVK---TLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQI  194 (800)
Q Consensus       137 d~LreyFskyGKVK---sVp~pgTGK~K-YGF~~ve~Ps~pV~F~sfEea~aA~eAmNG~~i  194 (800)
                      ++|+-.|.+||.|-   +.+++.|+..+ |+|         |-|.+-.++..|++||.|..+
T Consensus        28 d~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaF---------Vrf~~k~daedA~damDG~~l   80 (256)
T KOG4207|consen   28 DDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAF---------VRFHDKRDAEDALDAMDGAVL   80 (256)
T ss_pred             HHHHHHHHHhCcccceecccccccccccceeE---------EEeeecchHHHHHHhhcceee
Confidence            89999999999964   45566788887 777         889999999999999998765

>PLN03121 nucleic acid binding protein; Provisional

Probab=88.45  E-value=0.24  Score=52.76  Aligned_cols=58  Identities=16%  Similarity=0.194  Sum_probs=44.3

Q ss_pred             CCCCCCcchhhcccccCccceeeeccCCCCCcc-cccccccCCCCCcccccccchhhhhhhhccCccccC
Q 003717          129 PKKLLDKDKKLNIFFPRLRKVKTLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHP  197 (800)
Q Consensus       129 Lkksvdesd~LreyFskyGKVKsVp~pgTGK~K-YGF~~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~  197 (800)
                      |...+++ ++|++||+.||+|..+.....++.+ |||         |.|.+.+.+..|+ -++|..|...
T Consensus        13 LS~~tTE-~dLrefFS~~G~I~~V~I~~D~et~gfAf---------VtF~d~~aaetAl-lLnGa~l~d~   71 (243)
T PLN03121         13 LSPKATE-KDVYDFFSHCGAIEHVEIIRSGEYACTAY---------VTFKDAYALETAV-LLSGATIVDQ   71 (243)
T ss_pred             CCCCCCH-HHHHHHHHhcCCeEEEEEecCCCcceEEE---------EEECCHHHHHHHH-hcCCCeeCCc
Confidence            4566656 9999999999998877666555544 555         8899999998888 4888877543

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

Probab=87.74  E-value=0.68  Score=52.35  Aligned_cols=79  Identities=11%  Similarity=0.177  Sum_probs=62.8

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhhcCCc-eeE--EEEe-ccCC--CcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEE
Q 003717           13 QTRIYVGGLGEKVTDDDLAKVFSSLGE-VKA--VDIV-RTKG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLE   86 (800)
Q Consensus        13 srTLFVGNLP~nVTEEDLrelFSqFG~-Vks--VrVI-RdTG--RGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe   86 (800)
                      ..-|-..+||+..+-++|..+|..|.. |.-  |.|+ ...|  .|-|||.|.+  .++|..|+..-+.+...+|.|+|-
T Consensus       280 kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~qGrPSGeAFIqm~n--ae~a~aaaqk~hk~~mk~RYiEvf  357 (508)
T KOG1365|consen  280 KDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNGQGRPSGEAFIQMRN--AERARAAAQKCHKKLMKSRYIEVF  357 (508)
T ss_pred             CCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcCCCCcChhhhhhhhh--hHHHHHHHHHHHHhhcccceEEEe
Confidence            446788999999999999999999976 333  5555 3344  4999999998  899999988877777789999998


Q ss_pred             eccchhh
Q 003717           87 RAKEHYL   93 (800)
Q Consensus        87 ~AKpr~~   93 (800)
                      .+.-..+
T Consensus       358 p~S~eel  364 (508)
T KOG1365|consen  358 PCSVEEL  364 (508)
T ss_pred             eccHHHH
Confidence            7765443

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

Probab=87.38  E-value=0.27  Score=59.49  Aligned_cols=76  Identities=14%  Similarity=0.188  Sum_probs=65.8

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEecc---CCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEecc
Q 003717           13 QTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT---KGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAK   89 (800)
Q Consensus        13 srTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIRd---TGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~AK   89 (800)
                      ...+||.|+|+..|.+.|+.+|..+|.+.+.+++..   ..+|.+||.|.+  ..++.+++..+++..+.-+.+.|..+.
T Consensus       736 K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~y~~--ea~~s~~~~s~d~~~~rE~~~~v~vsn  813 (881)
T KOG0128|consen  736 KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNT--EADASRKVASVDVAGKRENNGEVQVSN  813 (881)
T ss_pred             hhhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccceeccCCC--cchhhhhcccchhhhhhhcCccccccC
Confidence            457999999999999999999999999999987732   347999999998  999999999888888887777777766


Q ss_pred             c
Q 003717           90 E   90 (800)
Q Consensus        90 p   90 (800)
                      |
T Consensus       814 p  814 (881)
T KOG0128|consen  814 P  814 (881)
T ss_pred             C
Confidence            5

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

Probab=86.61  E-value=0.3  Score=53.47  Aligned_cols=62  Identities=24%  Similarity=0.234  Sum_probs=47.4

Q ss_pred             CcccCCCCCCCCCcchhhcccccCcccee---eeccCCCCCcc-cccccccCCCCCcccccccchhhhhhhhccCcc
Q 003717          122 DATRLDTPKKLLDKDKKLNIFFPRLRKVK---TLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQI  194 (800)
Q Consensus       122 kl~is~~Lkksvdesd~LreyFskyGKVK---sVp~pgTGK~K-YGF~~ve~Ps~pV~F~sfEea~aA~eAmNG~~i  194 (800)
                      .+|+.. |+-++++ ..|+.+|..||.|+   .|++.-|||++ |+|         |.|-.--+-..|...+.|+.|
T Consensus       103 TLFv~R-LnydT~E-skLrreF~~YG~IkrirlV~d~vTgkskGYAF---------Ieye~erdm~~AYK~adG~~I  168 (335)
T KOG0113|consen  103 TLFVAR-LNYDTSE-SKLRREFEKYGPIKRIRLVRDKVTGKSKGYAF---------IEYEHERDMKAAYKDADGIKI  168 (335)
T ss_pred             eeeeee-ccccccH-HHHHHHHHhcCcceeEEEeeecccCCccceEE---------EEeccHHHHHHHHHhccCcee
Confidence            455543 4556655 89999999999976   46777899998 999         677777777888888777665

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

Probab=85.94  E-value=0.77  Score=49.53  Aligned_cols=71  Identities=18%  Similarity=0.234  Sum_probs=54.3

Q ss_pred             cEEEEeCCCCCCCHHHHHHhhhcCCceeEEEEec-cC--CCcEEEEEecCCCHHHHHHHHHhcCCc----EeCCeEEEEE
Q 003717           14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVR-TK--GRSFGYVDFFPSSHKSLSKLFSTYNGC----VWKGGRLRLE   86 (800)
Q Consensus        14 rTLFVGNLP~nVTEEDLrelFSqFG~VksVrVIR-dT--GRGFGFVEFeS~D~EdAekAIe~LNG~----eLdGR~LrVe   86 (800)
                      .-|||.||+.-++.+.|.+.|+.||+|....++- +.  +-|-++|.|..  ...|.+|+...+-.    ...|++.-|.
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~eg~v~~~~--k~~a~~a~rr~~~~g~~~~~~~~p~~Ve  109 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAK--KPNARKAARRCREGGFGGTTGGRPVGVE  109 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccccchhhhhc--chhHHHHHHHhccCccccCCCCCccCCC
Confidence            5799999999999999999999999998877763 23  34789999997  77888887765322    3344554444

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

Probab=85.19  E-value=0.46  Score=49.75  Aligned_cols=90  Identities=17%  Similarity=0.139  Sum_probs=60.1

Q ss_pred             CCCCCCCcchhhcccccCc-cceeeecc---CCCCCcc-cccccccCCCCCcccccccchhhhhhhhccCccccCCCCcc
Q 003717          128 TPKKLLDKDKKLNIFFPRL-RKVKTLPF---CGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPAAGQE  202 (800)
Q Consensus       128 ~Lkksvdesd~LreyFsky-GKVKsVp~---pgTGK~K-YGF~~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n~~q~  202 (800)
                      .++..+.+ ..+..||.++ |.|..+++   +-||.+| |||         |.|-+-|.|.-|-+.|| .|+.-  ++-.
T Consensus        56 ~~p~g~~e-~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAF---------VEFEs~eVA~IaAETMN-NYLl~--e~lL  122 (214)
T KOG4208|consen   56 HIPHGFFE-TEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAF---------VEFESEEVAKIAAETMN-NYLLM--EHLL  122 (214)
T ss_pred             ccccchhH-HHHhhhhhhcCCeeEEEEeecccccCCcCceEE---------EEeccHHHHHHHHHHhh-hhhhh--hhee
Confidence            34556666 6677777777 66766555   5799998 999         89999999999999999 56543  2223


Q ss_pred             ccchhhhcCcccchHHHHHHhHHHHHHhhhhccc
Q 003717          203 EIHDMEELGASVINEEELNLMNSVMNKLFERENV  236 (800)
Q Consensus       203 ~i~~~ee~~gsg~~~~e~n~MnsVmnklfeke~v  236 (800)
                      +.+-|.+-+      ...+.|-.|...+|.+..-
T Consensus       123 ~c~vmppe~------~v~~~~~k~~~~~~~~~~~  150 (214)
T KOG4208|consen  123 ECHVMPPEQ------KVEKNLKKVSGTPFKPGKT  150 (214)
T ss_pred             eeEEeCchh------hhhhhhhhhcCCcCCCCCc
Confidence            334344331      1256666677777766543

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

Probab=84.71  E-value=0.89  Score=54.50  Aligned_cols=77  Identities=13%  Similarity=0.060  Sum_probs=62.4

Q ss_pred             CcEEEEeCCCCCCCHHHHHHhhhcCCceeE-EEEe---ccCCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEec
Q 003717           13 QTRIYVGGLGEKVTDDDLAKVFSSLGEVKA-VDIV---RTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERA   88 (800)
Q Consensus        13 srTLFVGNLP~nVTEEDLrelFSqFG~Vks-VrVI---RdTGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~A   88 (800)
                      ..-|||-.||..+++.++-++|...-.|++ +.+-   ++.-++-|||.|..  .+++..|...-..+.++.|.|+|.-.
T Consensus       434 g~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P~~~~~~~afv~F~~--~~a~~~a~~~~~k~y~G~r~irv~si  511 (944)
T KOG4307|consen  434 GGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLPTDLLRPAAFVAFIH--PTAPLTASSVKTKFYPGHRIIRVDSI  511 (944)
T ss_pred             cceEEeccCCccccccchhhhhhhhhhhhheeEeccCCcccccchhhheecc--ccccchhhhcccccccCceEEEeech
Confidence            467999999999999999999998888877 4443   33447999999996  78888888877778888899999865


Q ss_pred             cch
Q 003717           89 KEH   91 (800)
Q Consensus        89 Kpr   91 (800)
                      ...
T Consensus       512 ~~~  514 (944)
T KOG4307|consen  512 ADY  514 (944)
T ss_pred             hhH
Confidence            433

>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=83.95  E-value=1  Score=39.13  Aligned_cols=67  Identities=25%  Similarity=0.501  Sum_probs=39.9

Q ss_pred             EEEEe-CCCCCCCHHHHHHhhhcCCce-----eEEEEeccCCCcEEEEEecCCCHHHHHHHHHhcCCcEeCCeEEEEEec
Q 003717           15 RIYVG-GLGEKVTDDDLAKVFSSLGEV-----KAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERA   88 (800)
Q Consensus        15 TLFVG-NLP~nVTEEDLrelFSqFG~V-----ksVrVIRdTGRGFGFVEFeS~D~EdAekAIe~LNG~eLdGR~LrVe~A   88 (800)
                      +|||. |--..++..+|..++...+.|     -.+.|.    .-|.||+-.   .+.|..++..|++..+.|++|+|+.|
T Consensus         2 rl~in~Gr~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~----~~~S~vev~---~~~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen    2 RLFINVGRKDGLTPRDIVGAICNEAGIPGRDIGRIDIF----DNFSFVEVP---EEVAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             EEEES-SGGGT--HHHHHHHHHTCTTB-GGGEEEEEE-----SS-EEEEE----TT-HHHHHHHHTT--SSS----EEE-
T ss_pred             EEEEEcccccCCCHHHHHHHHHhccCCCHHhEEEEEEe----eeEEEEEEC---HHHHHHHHHHhcCCCCCCeeEEEEEC
Confidence            45553 123467888999888877544     344443    359999998   58999999999999999999999876

; PDB: 2G0C_A 3MOJ_B.

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

Probab=83.03  E-value=0.4  Score=47.83  Aligned_cols=51  Identities=22%  Similarity=0.317  Sum_probs=44.5

Q ss_pred             hhhcccccCccceeeecc---CCCCCcc-cccccccCCCCCcccccccchhhhhhhhccCcccc
Q 003717          137 KKLNIFFPRLRKVKTLPF---CGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHH  196 (800)
Q Consensus       137 d~LreyFskyGKVKsVp~---pgTGK~K-YGF~~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n  196 (800)
                      +++...|..||.||.+.+   +-||..| |+.         |.|...+++.+|++++||+.+..
T Consensus        87 edi~d~F~dyGeiKNihLNLDRRtGy~KGYaL---------vEYet~keAq~A~~~~Ng~~ll~  141 (170)
T KOG0130|consen   87 EDIHDKFADYGEIKNIHLNLDRRTGYVKGYAL---------VEYETLKEAQAAIDALNGAELLG  141 (170)
T ss_pred             HHHHHHHhhcccccceeeccccccccccceee---------eehHhHHHHHHHHHhccchhhhC
Confidence            889999999999998766   4688887 766         78899999999999999988765

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

Probab=82.72  E-value=1.1  Score=49.80  Aligned_cols=57  Identities=16%  Similarity=0.227  Sum_probs=44.0

Q ss_pred             CCCCCCcchhhcccccCccceee--eccCCCCCcccccccccCCCCCcccccccchhhhhhhhccCccc
Q 003717          129 PKKLLDKDKKLNIFFPRLRKVKT--LPFCGTGKHKYSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIH  195 (800)
Q Consensus       129 Lkksvdesd~LreyFskyGKVKs--Vp~pgTGK~KYGF~~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~  195 (800)
                      +++.+.+ .+|+..|.+||+|-.  |-+.+.|-..|||         |.|-..++++.|-++++|-++.
T Consensus       104 IPFrFRd-pDL~aMF~kfG~VldVEIIfNERGSKGFGF---------VTmen~~dadRARa~LHgt~VE  162 (376)
T KOG0125|consen  104 IPFRFRD-PDLRAMFEKFGKVLDVEIIFNERGSKGFGF---------VTMENPADADRARAELHGTVVE  162 (376)
T ss_pred             CCccccC-ccHHHHHHhhCceeeEEEEeccCCCCccce---------EEecChhhHHHHHHHhhcceee
Confidence            5777766 899999999999753  3356677777888         7777778888888888877663

>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=81.99  E-value=4.1  Score=41.85  Aligned_cols=61  Identities=20%  Similarity=0.217  Sum_probs=44.6

Q ss_pred             HHHHHHhhhcCCceeEEEEeccCCCcEEEEEecCCCHHHHHHHHHhcC--CcEeCCeEEEEEeccch
Q 003717           27 DDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYN--GCVWKGGRLRLERAKEH   91 (800)
Q Consensus        27 EEDLrelFSqFG~VksVrVIRdTGRGFGFVEFeS~D~EdAekAIe~LN--G~eLdGR~LrVe~AKpr   91 (800)
                      ...|+++|..|+.+.....++.-+|  ..|.|.+  .+.|..|...|+  +..+.|..|+|.++.+-
T Consensus         9 ~~~l~~l~~~~~~~~~~~~L~sFrR--i~v~f~~--~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~   71 (184)
T PF04847_consen    9 LAELEELFSTYDPPVQFSPLKSFRR--IRVVFES--PESAQRARQLLHWDGTSFNGKRLRVYFGQPT   71 (184)
T ss_dssp             HHHHHHHHHTT-SS-EEEEETTTTE--EEEE-SS--TTHHHHHHHTST--TSEETTEE-EEE----S
T ss_pred             HHHHHHHHHhcCCceEEEEcCCCCE--EEEEeCC--HHHHHHHHHHhcccccccCCCceEEEEcccc
Confidence            4689999999999888777653333  6788887  999999999999  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.

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

Probab=81.44  E-value=0.47  Score=50.38  Aligned_cols=60  Identities=18%  Similarity=0.303  Sum_probs=47.5

Q ss_pred             CCCCCCCCcchhhcccccCccceeeeccC---CCCCcc-cccccccCCCCCcccccccchhhhhhhhccCcccc
Q 003717          127 DTPKKLLDKDKKLNIFFPRLRKVKTLPFC---GTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHH  196 (800)
Q Consensus       127 ~~Lkksvdesd~LreyFskyGKVKsVp~p---gTGK~K-YGF~~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n  196 (800)
                      +.|...+++ .-|...|=.||.|+.|..|   .++||+ |||         |.|--.|++.+|+.-||+..++-
T Consensus        16 GGladeVte-kvLhaAFIPFGDI~dIqiPlDyesqkHRgFgF---------Vefe~aEDAaaAiDNMnesEL~G   79 (298)
T KOG0111|consen   16 GGLADEVTE-KVLHAAFIPFGDIKDIQIPLDYESQKHRGFGF---------VEFEEAEDAAAAIDNMNESELFG   79 (298)
T ss_pred             ccchHHHHH-HHHHhccccccchhhcccccchhcccccceeE---------EEeeccchhHHHhhcCchhhhcc
Confidence            345666756 7788899999998765444   689998 777         88999999999999999877754

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

Probab=80.08  E-value=0.91  Score=47.17  Aligned_cols=61  Identities=20%  Similarity=0.164  Sum_probs=41.6

Q ss_pred             cccCCCCCCCCCcchhhcccccCcccee---eeccCCCCCcccccccccCCCCCcccccccchh---hhhhhhccCcccc
Q 003717          123 ATRLDTPKKLLDKDKKLNIFFPRLRKVK---TLPFCGTGKHKYSFQRVEAPPLPKYFCDCEEHS---AAFHAAEGKQIHH  196 (800)
Q Consensus       123 l~is~~Lkksvdesd~LreyFskyGKVK---sVp~pgTGK~KYGF~~ve~Ps~pV~F~sfEea~---aA~eAmNG~~i~n  196 (800)
                      +++ +.|+..+++ .+|-..|++||.|.   .||++.||++| ||          .|.-.|+..   -|..-+||.-|.-
T Consensus        38 Iyi-ggl~~~LtE-gDil~VFSqyGe~vdinLiRDk~TGKSK-GF----------aFLcYEDQRSTILAVDN~NGiki~g  104 (219)
T KOG0126|consen   38 IYI-GGLPYELTE-GDILCVFSQYGEIVDINLIRDKKTGKSK-GF----------AFLCYEDQRSTILAVDNLNGIKILG  104 (219)
T ss_pred             EEE-CCCcccccC-CcEEEEeeccCceEEEEEEecCCCCccc-ce----------EEEEecCccceEEEEeccCCceecc
Confidence            344 447888877 78889999999954   57999999999 44          233334443   3555667766543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	800
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	2e-12
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	1e-11
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	2e-11
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	2e-11
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	2e-11
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	2e-11
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	2e-11
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	3e-11
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-04
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	3e-11
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	4e-11
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	4e-11
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	5e-11
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	5e-11
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	5e-11
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-11
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-10
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-09
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	1e-10
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	1e-10
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	2e-10
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	2e-10
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	2e-10
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	2e-10
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	2e-10
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	2e-10
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	3e-10
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	3e-10
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-10
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-10
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-10
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	8e-06
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	5e-10
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	5e-10
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	6e-10
1x4e_A	85	RNA binding motif, single-stranded interacting pro	6e-10
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	6e-10
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	7e-10
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	7e-10
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-10
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-06
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	8e-10
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-06
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	9e-10
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	9e-10
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	1e-09
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-09
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-04
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	1e-09
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	1e-09
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	1e-09
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	2e-09
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	2e-09
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	2e-09
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	2e-09
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	2e-09
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-05
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	3e-09
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	3e-09
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	3e-09
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	3e-09
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	3e-09
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	3e-09
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	3e-09
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	3e-07
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-09
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	3e-09
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	3e-09
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	4e-09
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	4e-09
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	4e-09
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	4e-09
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	4e-09
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	5e-09
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	5e-09
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-07
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	6e-09
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	7e-09
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	7e-09
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	8e-09
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	9e-09
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	9e-09
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	1e-08
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	1e-08
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	1e-08
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	1e-08
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	1e-08
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	1e-08
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	1e-08
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	2e-08
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	2e-08
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	2e-08
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	2e-08
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	2e-08
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	3e-08
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-05
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	3e-08
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	3e-05
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	3e-08
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	3e-07
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	4e-08
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	5e-08
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	5e-08
1x5p_A	97	Negative elongation factor E; structure genomics,	5e-08
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	1e-07
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-07
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-06
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-06
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	1e-07
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	2e-07
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	2e-07
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	3e-07
2div_A	99	TRNA selenocysteine associated protein; structural	4e-07
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	4e-07
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	4e-07
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	4e-07
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	8e-07
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	9e-05
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	5e-07
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	5e-07
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	5e-07
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	6e-07
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	9e-07
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	1e-06
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	1e-06
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	2e-06
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	2e-06
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	2e-06
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-06
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	2e-06
1x5o_A	114	RNA binding motif, single-stranded interacting pro	2e-06
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	3e-06
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	5e-06
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-05
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	5e-06
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	5e-06
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	2e-04
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	6e-06
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	7e-06
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	7e-06
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	7e-06
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	8e-06
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	8e-06
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	1e-05
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	1e-05
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-05
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	9e-05
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	2e-05
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-05
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	2e-05
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	2e-05
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	3e-05
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	3e-05
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	3e-05
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	4e-05
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	4e-05
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	5e-05
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	7e-05
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	7e-05
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	8e-05
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	8e-05
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	9e-05
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	1e-04
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	1e-04
2dis_A	109	Unnamed protein product; structural genomics, RRM	1e-04
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	2e-04
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	4e-04
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	4e-04
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	4e-04
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	5e-04
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	6e-04
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	7e-04
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	7e-04
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	8e-04

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 63.0 bits (154), Expect = 2e-12
 Identities = 19/86 (22%), Positives = 39/86 (45%), Gaps = 4/86 (4%)

Query: 5  EAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHK 64
            E    +++R++VG L   +T++++ K+F   G+   V I + KG  FG++     +  
Sbjct: 7  GGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG--FGFIRL--ETRT 62

Query: 65 SLSKLFSTYNGCVWKGGRLRLERAKE 90
                   +    +G +LR+  A  
Sbjct: 63 LAEIAKVELDNMPLRGKQLRVRFACH 88

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 61.6 bits (150), Expect = 1e-11
 Identities = 20/87 (22%), Positives = 39/87 (44%), Gaps = 7/87 (8%)

Query: 8  AEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RTKGRS--FGYVDFFPSSH 63
           E +   ++++GGL  +  +  L  VF   G +  V ++  RT  +S  F ++ F   + 
Sbjct: 2  VEADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRT-SKSRGFAFITF--ENP 58

Query: 64 KSLSKLFSTYNGCVWKGGRLRLERAKE 90
                    NG    G  +++E+AK+
Sbjct: 59 ADAKNAAKDMNGKSLHGKAIKVEQAKK 85

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 60.3 bits (147), Expect = 2e-11
 Identities = 23/93 (24%), Positives = 38/93 (40%), Gaps = 6/93 (6%)

Query: 1  MEKKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK-GRS--FGYVD 57
          +E     +E      +++G L    +  +L    S L     + +V  + G +  FGYVD
Sbjct: 5  LEDPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVD 64

Query: 58 FFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKE 90
          F   S + L K      G    G  ++LE+ K 
Sbjct: 65 F--ESAEDLEKALE-LTGLKVFGNEIKLEKPKG 94

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 60.4 bits (147), Expect = 2e-11
 Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 3/76 (3%)

Query: 15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYN 74
          ++YVG LG      +L + FS  G ++ V I R     F +V+F     +         +
Sbjct: 2  KVYVGNLGTGAGKGELERAFSYYGPLRTVWIAR-NPPGFAFVEF--EDPRDAEDAVRGLD 58

Query: 75 GCVWKGGRLRLERAKE 90
          G V  G R+R+E +  
Sbjct: 59 GKVICGSRVRVELSTG 74

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 60.0 bits (146), Expect = 2e-11
 Identities = 21/86 (24%), Positives = 39/86 (45%), Gaps = 5/86 (5%)

Query: 6  AEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK-GRS--FGYVDFFPSS 62
            A+ E    ++VG L  +V ++ L ++F   G +  V I + + G+   FG+V F    
Sbjct: 9  FPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCF--KH 66

Query: 63 HKSLSKLFSTYNGCVWKGGRLRLERA 88
           +S+S   +  NG    G  + +   
Sbjct: 67 PESVSYAIALLNGIRLYGRPINVSGP 92

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 60.4 bits (147), Expect = 2e-11
 Identities = 18/86 (20%), Positives = 37/86 (43%), Gaps = 4/86 (4%)

Query: 7  EAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRS--FGYVDFFPSSHK 64
                  R++V  +  +  D DL ++F   G++  V+I+  +  S  FG+V F   +  
Sbjct: 9  SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTF--ENSA 66

Query: 65 SLSKLFSTYNGCVWKGGRLRLERAKE 90
             +     +G V +G ++ +  A  
Sbjct: 67 DADRAREKLHGTVVEGRKIEVNNATA 92

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 60.4 bits (147), Expect = 2e-11
 Identities = 18/82 (21%), Positives = 38/82 (46%), Gaps = 4/82 (4%)

Query: 11  EEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRS--FGYVDFFPSSHKSLSK 68
            +  R++V  +  +  D DL ++F   G++  V+I+  +  S  FG+V F   +     +
Sbjct: 27  SQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTF--ENSADADR 84

Query: 69  LFSTYNGCVWKGGRLRLERAKE 90
                +G V +G ++ +  A  
Sbjct: 85  AREKLHGTVVEGRKIEVNNATA 106

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 63.9 bits (156), Expect = 3e-11
 Identities = 23/85 (27%), Positives = 39/85 (45%), Gaps = 4/85 (4%)

Query: 4  KEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSH 63
          K  E    ++ R++VG L   +T++D  ++F   GE   V I R +G  FG++     S 
Sbjct: 13 KPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRG--FGFIRL--ESR 68

Query: 64 KSLSKLFSTYNGCVWKGGRLRLERA 88
                 +  +G + K   LR+  A
Sbjct: 69 TLAEIAKAELDGTILKSRPLRIRFA 93

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 42.8 bits (101), Expect = 2e-04
 Identities = 15/72 (20%), Positives = 29/72 (40%), Gaps = 5/72 (6%)

Query: 14  TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVR-TKGRS--FGYVDFFPSSHKSLSKLF 70
             + V  L   V+++ L + FS  G V+   +V   +GR+   G+V+F  ++     K  
Sbjct: 97  AALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEF--AAKPPARKAL 154

Query: 71  STYNGCVWKGGR 82
                  +    
Sbjct: 155 ERCGDGAFLLTT 166

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 59.9 bits (146), Expect = 3e-11
 Identities = 19/89 (21%), Positives = 33/89 (37%), Gaps = 6/89 (6%)

Query: 6  AEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RTKGRS--FGYVDFFPS 61
          +  +V+    + V  L  + + D L +VF   G V  V I           F +V F   
Sbjct: 6  SGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRF--H 63

Query: 62 SHKSLSKLFSTYNGCVWKGGRLRLERAKE 90
            +      +  +G    G  LR++ A+ 
Sbjct: 64 DRRDAQDAEAAMDGAELDGRELRVQVARY 92

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 59.2 bits (144), Expect = 4e-11
 Identities = 18/80 (22%), Positives = 36/80 (45%), Gaps = 4/80 (5%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RTKGRSFGYVDFFPSSHKSLSKLFS 71
            +YVG L   VT+  + ++FS +G  K+  ++   T    + +V+F    H+  +   +
Sbjct: 16 RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEF--YEHRDAAAALA 73

Query: 72 TYNGCVWKGGRLRLERAKEH 91
            NG    G  +++  A   
Sbjct: 74 AMNGRKILGKEVKVNWATTP 93

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 59.6 bits (145), Expect = 4e-11
 Identities = 21/90 (23%), Positives = 34/90 (37%), Gaps = 5/90 (5%)

Query: 2   EKKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK-GRS--FGYVDF 58
                 A VE   ++ V  L   V+D D+ ++F+  G +K   +   + GRS     V F
Sbjct: 18  SGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHF 77

Query: 59  FPSSHKSLSKLFSTYNGCVWKGGRLRLERA 88
                    K    YNG    G  + ++  
Sbjct: 78  --ERKADALKAMKQYNGVPLDGRPMNIQLV 105

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 59.7 bits (145), Expect = 5e-11
 Identities = 19/92 (20%), Positives = 32/92 (34%), Gaps = 5/92 (5%)

Query: 2   EKKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK-GRS--FGYVDF 58
                   VE   ++ V  L   V+D D+ ++F+  G +K   +   + GRS     V F
Sbjct: 24  SGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHF 83

Query: 59  FPSSHKSLSKLFSTYNGCVWKGGRLRLERAKE 90
                    K    Y G    G  + ++    
Sbjct: 84  --ERRADALKAMKQYKGVPLDGRPMDIQLVAS 113

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 59.2 bits (144), Expect = 5e-11
 Identities = 23/87 (26%), Positives = 41/87 (47%), Gaps = 6/87 (6%)

Query: 8  AEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RTKGRS--FGYVDFFPSSH 63
              ++ +++VGGL     +  L +VFS  G++  V +V  R   RS  FG+V F   + 
Sbjct: 7  GMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTF--ENI 64

Query: 64 KSLSKLFSTYNGCVWKGGRLRLERAKE 90
                    NG    G ++R+++A +
Sbjct: 65 DDAKDAMMAMNGKSVDGRQIRVDQAGK 91

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 58.8 bits (143), Expect = 5e-11
 Identities = 15/82 (18%), Positives = 38/82 (46%), Gaps = 5/82 (6%)

Query: 12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK-GRS--FGYVDFFPSSHKSLSK 68
          E+ ++++ GL    T ++L ++  + G VK + +V  + G+     YV++   +    S+
Sbjct: 16 EKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEY--ENESQASQ 73

Query: 69 LFSTYNGCVWKGGRLRLERAKE 90
               +G   K   +++  +  
Sbjct: 74 AVMKMDGMTIKENIIKVAISNS 95

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 58.9 bits (143), Expect = 6e-11
 Identities = 16/78 (20%), Positives = 30/78 (38%), Gaps = 4/78 (5%)

Query: 13  QTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFST 72
            T  Y+G +    T+ DL  +F + G +        KG    ++ +   +H+  +     
Sbjct: 27  VTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKG--CCFIKY--DTHEQAAVCIVA 82

Query: 73  YNGCVWKGGRLRLERAKE 90
                ++G  LR    KE
Sbjct: 83  LANFPFQGRNLRTGWGKE 100

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 59.9 bits (146), Expect = 1e-10
 Identities = 20/90 (22%), Positives = 33/90 (36%), Gaps = 7/90 (7%)

Query: 3   KKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRS--FGYVDFFP 60
           K     +V     +    L   +T+D+L +VF    E++   +V   G+S    Y++F  
Sbjct: 89  KGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIR---LVSQDGKSKGIAYIEF-- 143

Query: 61  SSHKSLSKLFSTYNGCVWKGGRLRLERAKE 90
            S     K      G    G  + L    E
Sbjct: 144 KSEADAEKNLEEKQGAEIDGRSVSLYYTGE 173

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 57.2 bits (139), Expect = 1e-09
 Identities = 22/92 (23%), Positives = 35/92 (38%), Gaps = 6/92 (6%)

Query: 3  KKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV-RTKGRS--FGYVDFF 59
               +E      +++G L    +  +L    S L     + +V    G +  FGYVDF 
Sbjct: 3  HMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDF- 61

Query: 60 PSSHKSLSKLFSTYNGCVWKGGRLRLERAKEH 91
            S + L K      G    G  ++LE+ K  
Sbjct: 62 -ESAEDLEKALE-LTGLKVFGNEIKLEKPKGR 91

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 58.1 bits (141), Expect = 1e-10
 Identities = 20/79 (25%), Positives = 39/79 (49%), Gaps = 4/79 (5%)

Query: 12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFS 71
          +   +Y GG+   +TD  + + FS  G++  + +   KG  + +V F  S+H+S +    
Sbjct: 24 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG--YSFVRF--STHESAAHAIV 79

Query: 72 TYNGCVWKGGRLRLERAKE 90
          + NG   +G  ++    KE
Sbjct: 80 SVNGTTIEGHVVKCYWGKE 98

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 58.1 bits (141), Expect = 1e-10
 Identities = 21/78 (26%), Positives = 35/78 (44%), Gaps = 3/78 (3%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK-GRSFGYVDFFPSSHKSLSKLFST 72
           RIYVG L   +   D+  VF   G ++ +D+   + G  F +V+F     +        
Sbjct: 23 CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEF--EDPRDAEDAVYG 80

Query: 73 YNGCVWKGGRLRLERAKE 90
           +G  + G RLR+E  + 
Sbjct: 81 RDGYDYDGYRLRVEFPRS 98

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 57.7 bits (140), Expect = 2e-10
 Identities = 23/88 (26%), Positives = 40/88 (45%), Gaps = 6/88 (6%)

Query: 8  AEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RTKGRS--FGYVDFFPSSH 63
          +E  +   +YVGGL EKV++  L ++F   G V    +   R  G+   +G+V+F   S 
Sbjct: 10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEF--LSE 67

Query: 64 KSLSKLFSTYNGCVWKGGRLRLERAKEH 91
          +         +     G  +R+ +A  H
Sbjct: 68 EDADYAIKIMDMIKLYGKPIRVNKASAH 95

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

 Score = 57.7 bits (140), Expect = 2e-10
 Identities = 20/93 (21%), Positives = 39/93 (41%), Gaps = 10/93 (10%)

Query: 1   MEKKEAEAEVEEQ----TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYV 56
           + +       +E     TR++V      V + +L ++F   G +K V I+   G  F +V
Sbjct: 15  VPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--NG--FAFV 70

Query: 57  DFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAK 89
           +F     +S +K     +G  +    L +  +K
Sbjct: 71  EF--EEAESAAKAIEEVHGKSFANQPLEVVYSK 101

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 57.3 bits (139), Expect = 2e-10
 Identities = 20/92 (21%), Positives = 34/92 (36%), Gaps = 7/92 (7%)

Query: 1  MEKKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRS--FGYVDF 58
          +E      +V     +    L   +T+D+L +VF    E++   +V   G+S    Y++F
Sbjct: 4  LEDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIR---LVSQDGKSKGIAYIEF 60

Query: 59 FPSSHKSLSKLFSTYNGCVWKGGRLRLERAKE 90
             S     K      G    G  + L    E
Sbjct: 61 --KSEADAEKNLEEKQGAEIDGRSVSLYYTGE 90

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 57.2 bits (139), Expect = 2e-10
 Identities = 20/84 (23%), Positives = 37/84 (44%), Gaps = 6/84 (7%)

Query: 11 EEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RTKGRS--FGYVDFFPSSHKSL 66
             + +YVG L   +T+D L  +F   G++  + ++     GRS  +G++ F  S  +  
Sbjct: 3  SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITF--SDSECA 60

Query: 67 SKLFSTYNGCVWKGGRLRLERAKE 90
           +     NG    G  +R+    E
Sbjct: 61 RRALEQLNGFELAGRPMRVGHVTE 84

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 59.1 bits (143), Expect = 2e-10
 Identities = 24/93 (25%), Positives = 35/93 (37%), Gaps = 6/93 (6%)

Query: 2   EKKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RTKGRS--FGYVD 57
                  +VE  T + V  L  + + D L +VF   G V  V I   R    S  F +V 
Sbjct: 59  HHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVR 118

Query: 58  FFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKE 90
           F     +         +G V  G  LR++ A+ 
Sbjct: 119 F--HDKRDAEDAMDAMDGAVLDGRELRVQMARY 149

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 56.8 bits (138), Expect = 2e-10
 Identities = 18/82 (21%), Positives = 36/82 (43%), Gaps = 7/82 (8%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK---GRS--FGYVDFFPSSHKSLSK 68
          T++++G L   VT D + ++FS+ G++K +D+   +     S  + YV+F   +     K
Sbjct: 5  TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEF--ENPDEAEK 62

Query: 69 LFSTYNGCVWKGGRLRLERAKE 90
               +G    G  +       
Sbjct: 63 ALKHMDGGQIDGQEITATAVLA 84

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 56.9 bits (138), Expect = 3e-10
 Identities = 25/80 (31%), Positives = 42/80 (52%), Gaps = 10/80 (12%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFF--PSSHKSLSKLFS 71
          TR++VGGLG   +   LA+ F   G ++ +D V+  G SF Y+ +    ++  + +K+  
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVK--GDSFAYIQYESLDAAQAACAKM-- 73

Query: 72 TYNGCVWKGG--RLRLERAK 89
             G    G   RLR++ AK
Sbjct: 74 --RGFPLGGPDRRLRVDFAK 91

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 59.1 bits (143), Expect = 3e-10
 Identities = 19/92 (20%), Positives = 32/92 (34%), Gaps = 5/92 (5%)

Query: 2   EKKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK-GRS--FGYVDF 58
                   VE   ++ V  L   V+D D+ ++F+  G +K   +   + GRS     V F
Sbjct: 77  SGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHF 136

Query: 59  FPSSHKSLSKLFSTYNGCVWKGGRLRLERAKE 90
                    K    Y G    G  + ++    
Sbjct: 137 --ERRADALKAMKQYKGVPLDGRPMDIQLVAS 166

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 56.8 bits (138), Expect = 3e-10
 Identities = 17/84 (20%), Positives = 36/84 (42%), Gaps = 6/84 (7%)

Query: 11 EEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RTKGRS--FGYVDFFPSSHKSL 66
              R++V  L    +++DL K+FS+ G +  +         +   F +V F     +  
Sbjct: 6  SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTF--MFPEHA 63

Query: 67 SKLFSTYNGCVWKGGRLRLERAKE 90
           K ++  +G V++G  L +  +  
Sbjct: 64 VKAYAEVDGQVFQGRMLHVLPSTI 87

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 56.0 bits (136), Expect = 4e-10
 Identities = 19/82 (23%), Positives = 31/82 (37%), Gaps = 8/82 (9%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RTKGRS--FGYVDFFPSSHKSLSKL 69
            ++VG L   V D+ L   F       +  ++     G S  +G+V F  +S       
Sbjct: 2  FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSF--TSQDDAQNA 59

Query: 70 FSTYNGCVWKGGR-LRLERAKE 90
            +  G     GR LR+  A +
Sbjct: 60 MDSMQG-QDLNGRPLRINWAAK 80

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 58.3 bits (142), Expect = 4e-10
 Identities = 16/76 (21%), Positives = 35/76 (46%), Gaps = 5/76 (6%)

Query: 16 IYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK-GRS--FGYVDFFPSSHKSLSKLFST 72
          +YVG L + +T+D L + F   G +  + I+  K  ++  + +V++        +    T
Sbjct: 3  LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEY--HQSHDANIALQT 60

Query: 73 YNGCVWKGGRLRLERA 88
           NG   +   +++  A
Sbjct: 61 LNGKQIENNIVKINWA 76

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 46.0 bits (110), Expect = 8e-06
 Identities = 18/81 (22%), Positives = 31/81 (38%), Gaps = 12/81 (14%)

Query: 15  RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVR--TKGRS--FGYVDF--FPSSHKSLSK 68
            ++VG L   V D+ L   F       +  ++     G S  +G+V F     +  ++  
Sbjct: 89  NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 148

Query: 69  LFSTYNGCVWKGGR-LRLERA 88
           +     G     GR LR+  A
Sbjct: 149 M----QG-QDLNGRPLRINWA 164

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 56.1 bits (136), Expect = 5e-10
 Identities = 24/86 (27%), Positives = 35/86 (40%), Gaps = 6/86 (6%)

Query: 8  AEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RTKGRS--FGYVDFFPSSH 63
          A  +    + V GL    T+ DL +VFS  G +  V IV  +   RS  F +V F   + 
Sbjct: 10 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF--ENV 67

Query: 64 KSLSKLFSTYNGCVWKGGRLRLERAK 89
              +     NG    G R+R+    
Sbjct: 68 DDAKEAKERANGMELDGRRIRVSGPS 93

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 56.1 bits (136), Expect = 5e-10
 Identities = 20/89 (22%), Positives = 34/89 (38%), Gaps = 6/89 (6%)

Query: 6  AEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RTKGRS--FGYVDFFPS 61
          +      +  +YVGGL E+V D  L   F   G++  + I       +   F +V+F   
Sbjct: 5  SSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF--E 62

Query: 62 SHKSLSKLFSTYNGCVWKGGRLRLERAKE 90
            +  +      N     G  +R+  AK 
Sbjct: 63 LAEDAAAAIDNMNESELFGRTIRVNLAKP 91

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 57.1 bits (138), Expect = 6e-10
 Identities = 25/94 (26%), Positives = 36/94 (38%), Gaps = 6/94 (6%)

Query: 1   MEKKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RTKGRS--FGYV 56
           M       +VE  T + V  L  + + D L +VF   G V  V I   R    S  F +V
Sbjct: 35  MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 94

Query: 57  DFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKE 90
            F     +         +G V  G  LR++ A+ 
Sbjct: 95  RF--HDKRDAEDAMDAMDGAVLDGRELRVQMARY 126

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 55.2 bits (134), Expect = 6e-10
 Identities = 16/82 (19%), Positives = 32/82 (39%), Gaps = 6/82 (7%)

Query: 12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RTKGRS--FGYVDFFPSSHKSLS 67
            + +Y+ GL    TD DL K+    G++ +   +  +T  +   +G+VDF   S  +  
Sbjct: 4  GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDF--DSPSAAQ 61

Query: 68 KLFSTYNGCVWKGGRLRLERAK 89
          K  +       +    +     
Sbjct: 62 KAVTALKASGVQAQMAKQSGPS 83

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 55.7 bits (135), Expect = 6e-10
 Identities = 16/100 (16%), Positives = 34/100 (34%), Gaps = 6/100 (6%)

Query: 2   EKKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPS 61
                     E   + +  L    T++ L +VF     +K       K + + +++F  +
Sbjct: 4   GSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEF--A 61

Query: 62  SHKSLSKLFSTYNGCVWKGGRLRLERAKEHYLARLKREWA 101
           S +   +  ++ N    +G  +RLE        R      
Sbjct: 62  SFEDAKEALNSCNKREIEGRAIRLELQGP----RGSPNSG 97

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 55.2 bits (134), Expect = 7e-10
 Identities = 20/83 (24%), Positives = 33/83 (39%), Gaps = 6/83 (7%)

Query: 11 EEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RTKGRS--FGYVDFFPSSHKSL 66
            +  +YVGGL E+V D  L   F   G++  + I       +   F +V+F     +  
Sbjct: 5  TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF--ELAEDA 62

Query: 67 SKLFSTYNGCVWKGGRLRLERAK 89
          +      N     G  +R+  AK
Sbjct: 63 AAAIDNMNESELFGRTIRVNLAK 85

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 55.8 bits (135), Expect = 7e-10
 Identities = 22/94 (23%), Positives = 41/94 (43%), Gaps = 8/94 (8%)

Query: 3  KKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK---GRS--FGYVD 57
                + +  ++I V  +  +    ++ ++FS+ GE+K V + +     G    FG+VD
Sbjct: 5  SSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVD 64

Query: 58 FFPSSHKSLSKLFST-YNGCVWKGGRLRLERAKE 90
          F   + +   K F+   +     G RL LE A  
Sbjct: 65 F--ITKQDAKKAFNALCHSTHLYGRRLVLEWADS 96

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 61.8 bits (149), Expect = 8e-10
 Identities = 71/484 (14%), Positives = 142/484 (29%), Gaps = 169/484 (34%)

Query: 157 TGKHKYSFQ---RVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPAAGQEEIHDMEELGAS 213
           TG+H+Y ++    V        F DC+                         D++++  S
Sbjct: 11  TGEHQYQYKDILSVFEDAFVDNF-DCK-------------------------DVQDMPKS 44

Query: 214 VINEEELNLMNSVMNKLFERENVSNAG--LSGTELTNYERNSYNFIGDLQIGGNEVDSVA 271
           ++++EE+       + +   ++  +    L  T L+  E     F+ ++         + 
Sbjct: 45  ILSKEEI-------DHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEV---------LR 88

Query: 272 DEYNLVINAVSGGNNRMVLSRCQEKTTILPTNKKLTLSEARTSKDRSAQSL-----PREQ 326
             Y  +++ +         +  ++     P+       E R       Q        R Q
Sbjct: 89  INYKFLMSPIK--------TEQRQ-----PSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQ 135

Query: 327 KKNDL------LRSKKRKSLHNDEILM--------AASPLDDMNVQTNMNKPSTPLATQH 372
               L      LR  K   +      +        A        VQ  M           
Sbjct: 136 PYLKLRQALLELRPAKNVLIDG----VLGSGKTWVALDVCLSYKVQCKM----------- 180

Query: 373 AETDSGVRKSTASHSWSQKMSWKALVGDKDSRAFSVSNILPS-----DAS-TEEADNGIN 426
              D  +        W   ++    +    +   +V  +L       D + T  +D+  N
Sbjct: 181 ---DFKI-------FW---LN----LK-NCNSPETVLEMLQKLLYQIDPNWTSRSDHSSN 222

Query: 427 SFEELNFDENESDDLMINVVSKKKPKMAL-----SSSQKWE-------TTSTTYRKSVSN 474
               ++  + E   L+    SK      L      +++ W           TT  K V++
Sbjct: 223 IKLRIHSIQAELRRLL---KSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTD 279

Query: 475 E-DNNTTKDRPIQQEKSTLPSKKKRKSVIDDESDK------NKSVHTVPETDGCAQTYTE 527
                TT    +     TL           DE         +     +P           
Sbjct: 280 FLSAATTTHISLDHHSMTL---------TPDEVKSLLLKYLDCRPQDLPR---------- 320

Query: 528 SQMPTG-PQLVEPESVVEQSISDHSESKKPSQRVVIGSKGND-ESSVSNVLPDNSAKEEQ 585
            ++ T  P+ +   S++ +SI D   +    + V         ESS++ + P     E +
Sbjct: 321 -EVLTTNPRRL---SIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPA----EYR 372

Query: 586 RVFD 589
           ++FD
Sbjct: 373 KMFD 376

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 53.3 bits (127), Expect = 3e-07
 Identities = 67/443 (15%), Positives = 130/443 (29%), Gaps = 124/443 (27%)

Query: 371 QHAETDSGVRKSTASHSWSQKMS--WKALVGDKDSRAFSVSNILPSDASTEEADNGINSF 428
            H + ++G  +    + +   +S    A V + D +   V ++  S  S EE D+ I S 
Sbjct: 5   HHMDFETGEHQ----YQYKDILSVFEDAFVDNFDCK--DVQDMPKSILSKEEIDHIIMSK 58

Query: 429 EELNFDENESDDLMINVVSKKKPKM-------ALSSSQKW--------------ETTSTT 467
                D       +   +  K+ +M        L  + K+               T    
Sbjct: 59  -----DAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYI 113

Query: 468 YRKSVSNEDNNTTKDRPIQQEKSTLPSKKKRKSVIDDESDKNKSVH-------TVPETDG 520
            ++     DN       + + +   P  K R+++++    KN  +        T    D 
Sbjct: 114 EQRDRLYNDNQVFAKYNVSRLQ---PYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDV 170

Query: 521 CAQTYTESQMPTG------PQLVEPESVVEQ-------------SISDHS-------ESK 554
           C     + +M              PE+V+E              S SDHS        S 
Sbjct: 171 CLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSI 230

Query: 555 KPSQRVVIGSKGNDESSVSNVLPDNSAKEEQRVFD--CPDEPLGST-DSKNQNSLARN-- 609
           +   R ++ SK  +   +  VL +    +    F+  C    L +T   +  + L+    
Sbjct: 231 QAELRRLLKSKPYENCLL--VLLNVQNAKAWNAFNLSCK--ILLTTRFKQVTDFLSAATT 286

Query: 610 -----ENLEGKLAETESVEVPAKAQPSKSNTAPNKSGKGS----------------SWFQ 648
                ++    L   E   +  K    +    P +    +                +W  
Sbjct: 287 THISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATW-- 344

Query: 649 KSPWTQLVNEDNSSF---SITQISPGIT---------FKKH-DVPKTQLG--------KE 687
              W  +  +  ++    S+  + P            F     +P   L          +
Sbjct: 345 -DNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSD 403

Query: 688 VANPNDKKSSKSVGQAGSKPITC 710
           V    +K    S+ +   K  T 
Sbjct: 404 VMVVVNKLHKYSLVEKQPKESTI 426

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 49.9 bits (118), Expect = 4e-06
 Identities = 60/493 (12%), Positives = 121/493 (24%), Gaps = 159/493 (32%)

Query: 4   KEAEAEVEEQTRIYV---GGLG------EKVTDDDLAKVFS------SLGEVKAVDIVRT 48
           ++A  E+     + +    G G      +      +           +L    + + V  
Sbjct: 141 RQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLE 200

Query: 49  KGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKEHYLARLKREWAE------ 102
             +        P+         +          +LR+   +      L+R          
Sbjct: 201 MLQKL-LYQIDPNWTSRSDHSSNI---------KLRIHSIQA----ELRRLLKSKPYENC 246

Query: 103 ----DDAQ--------------LV---NPPVTDSVAPDNKDATRLDTPKKLLDKDKKLNI 141
                + Q              L+      VTD ++        LD     L  D+  ++
Sbjct: 247 LLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSL 306

Query: 142 F----------FPRLRKVKTLPF----CGTGKHKYS-----FQRVEAPPLPKYFCDC--- 179
                       PR   + T P                   ++ V    L          
Sbjct: 307 LLKYLDCRPQDLPR-EVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNV 365

Query: 180 ---EEHSAAFHA----AEGKQIHHPAA----------GQEEIHDMEEL-GASVIN----- 216
               E+   F           I  P              + +  + +L   S++      
Sbjct: 366 LEPAEYRKMFDRLSVFPPSAHI--PTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKE 423

Query: 217 ----------------EEELNLMNSVMNKLFERENVSNAGLSGTELTNYERNSYNFIGD- 259
                           E E  L  S+++     +   +  L    L  Y    Y+ IG  
Sbjct: 424 STISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQY---FYSHIGHH 480

Query: 260 LQIGGNEVDSVADEYNL----------VINAVSGGNNRMVLSRCQEKTTILPTNKKLTLS 309
           L+   +      +   L          +   +     R   +      +IL      TL 
Sbjct: 481 LKNIEH-----PERMTLFRMVFLDFRFLEQKI-----RHDSTAWNASGSILN-----TLQ 525

Query: 310 EARTSKDRSAQSLPR-EQKKNDLLRSKKRKSLHNDEILMAASPLDDMNVQTNMNKPSTPL 368
           + +  K     + P+ E+  N +L       L   E  +  S   D+ ++  +      +
Sbjct: 526 QLKFYKPYICDNDPKYERLVNAIL-----DFLPKIEENLICSKYTDL-LRIALMAEDEAI 579

Query: 369 ATQHAETDSGVRK 381
                E    V++
Sbjct: 580 ---FEEAHKQVQR 589

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 58.1 bits (141), Expect = 8e-10
 Identities = 19/62 (30%), Positives = 32/62 (51%), Gaps = 4/62 (6%)

Query: 1  MEKKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK--GRS--FGYV 56
          M K E+  E E+  ++++GGL  + TD+ L   F   G +    ++R     RS  FG+V
Sbjct: 1  MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFV 60

Query: 57 DF 58
           +
Sbjct: 61 TY 62

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 48.8 bits (117), Expect = 1e-06
 Identities = 21/92 (22%), Positives = 38/92 (41%), Gaps = 7/92 (7%)

Query: 1   MEKKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RTKGRS--FGYV 56
            E  +         +I+VGG+ E   +  L   F   G+++ ++I+  R  G+   F +V
Sbjct: 92  REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFV 151

Query: 57  DFFPSSHKSLSKLFSTYNGCVWKGGRLRLERA 88
            F    H S+ K+       V  G    + +A
Sbjct: 152 TF--DDHDSVDKIVIQKYHTV-NGHNCEVRKA 180

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 55.8 bits (135), Expect = 9e-10
 Identities = 21/80 (26%), Positives = 34/80 (42%), Gaps = 5/80 (6%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK-GRS--FGYVDFFPSSHKSLSKLF 70
          + ++V  L  KV    L +VFS  G V   DI+  K G+S   G V F         +  
Sbjct: 16 STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTF--EQSIEAVQAI 73

Query: 71 STYNGCVWKGGRLRLERAKE 90
          S +NG +     + ++  + 
Sbjct: 74 SMFNGQLLFDRPMHVKMDER 93

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 55.0 bits (133), Expect = 9e-10
 Identities = 19/77 (24%), Positives = 41/77 (53%), Gaps = 5/77 (6%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSK-LFST 72
          T +YVGGLG+ +T+ DL   F   GE++ + +V+ +     ++ F  ++ ++       +
Sbjct: 13 TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQ--CAFIQF--ATRQAAEVAAEKS 68

Query: 73 YNGCVWKGGRLRLERAK 89
          +N  +  G RL ++  +
Sbjct: 69 FNKLIVNGRRLNVKWGR 85

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 54.8 bits (133), Expect = 1e-09
 Identities = 19/84 (22%), Positives = 36/84 (42%), Gaps = 7/84 (8%)

Query: 11 EEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK--GRS--FGYVDFFPSSHKSL 66
           +   IYVG +    T ++L   F   G V  V I+  K  G    F Y++F   S K  
Sbjct: 4  ADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEF---SDKES 60

Query: 67 SKLFSTYNGCVWKGGRLRLERAKE 90
           +     +  +++G ++++   + 
Sbjct: 61 VRTSLALDESLFRGRQIKVIPKRT 84

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 56.8 bits (138), Expect = 1e-09
 Identities = 21/81 (25%), Positives = 44/81 (54%), Gaps = 6/81 (7%)

Query: 13 QTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK--GRS--FGYVDFFPSSHKSLSK 68
          +T + V  L + +T ++   +F S+GE+++  +VR K  G+S  +G+V++     K   K
Sbjct: 2  KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNY--IDPKDAEK 59

Query: 69 LFSTYNGCVWKGGRLRLERAK 89
            +T NG   +   +++  A+
Sbjct: 60 AINTLNGLRLQTKTIKVSYAR 80

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 42.6 bits (101), Expect = 1e-04
 Identities = 17/77 (22%), Positives = 29/77 (37%), Gaps = 6/77 (7%)

Query: 9   EVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK--GRS--FGYVDFFPSSHK 64
                  +YV GL + +T  +L ++FS  G +    I+  +  G S   G++ F      
Sbjct: 84  ASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRF--DKRI 141

Query: 65  SLSKLFSTYNGCVWKGG 81
              +     NG    G 
Sbjct: 142 EAEEAIKGLNGQKPSGA 158

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 54.6 bits (132), Expect = 1e-09
 Identities = 17/81 (20%), Positives = 33/81 (40%), Gaps = 5/81 (6%)

Query: 11 EEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLF 70
              ++Y+G L   VT DDL ++F       A  ++   G  + +VD+         +  
Sbjct: 6  SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSG--YAFVDY--PDQNWAIRAI 61

Query: 71 STYNGCV-WKGGRLRLERAKE 90
           T +G V   G  + ++ +  
Sbjct: 62 ETLSGKVELHGKIMEVDYSVS 82

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 54.5 bits (132), Expect = 1e-09
 Identities = 14/77 (18%), Positives = 32/77 (41%), Gaps = 6/77 (7%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTY 73
          T+++VG +    T+ +L   F   G V   DIV+     + +V       +   +     
Sbjct: 11 TKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD----YAFVHM--ERAEDAVEAIRGL 64

Query: 74 NGCVWKGGRLRLERAKE 90
          +   ++G R+ ++ +  
Sbjct: 65 DNTEFQGKRMHVQLSTS 81

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 54.9 bits (133), Expect = 1e-09
 Identities = 18/89 (20%), Positives = 38/89 (42%), Gaps = 10/89 (11%)

Query: 8  AEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK--GRS--FGYVDFFPSSH 63
             ++   I V  L E   + DL ++F   G +  + + + K  G+S  F ++ F     
Sbjct: 10 RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRED 69

Query: 64 --KSLSKLFSTYNGCVWKGGRLRLERAKE 90
            ++++ +    +G  +    L +E AK 
Sbjct: 70 AARAIAGV----SGFGYDHLILNVEWAKP 94

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 56.0 bits (135), Expect = 2e-09
 Identities = 18/77 (23%), Positives = 34/77 (44%), Gaps = 3/77 (3%)

Query: 14  TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTY 73
            ++YVG LG      +L + F   G +++V + R     F +V+F     +  +      
Sbjct: 74  CKVYVGNLGNNGNKTELERAFGYYGPLRSVWVAR-NPPGFAFVEF--EDPRDAADAVREL 130

Query: 74  NGCVWKGGRLRLERAKE 90
           +G    G R+R+E +  
Sbjct: 131 DGRTLCGCRVRVELSNG 147

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 54.6 bits (132), Expect = 2e-09
 Identities = 17/86 (19%), Positives = 35/86 (40%), Gaps = 9/86 (10%)

Query: 12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVR-----TKGRS--FGYVDFFPSSHK 64
            + +++  L    T++ L  VFS +G +K+  I +         S  FG+V++     +
Sbjct: 4  GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEY--KKPE 61

Query: 65 SLSKLFSTYNGCVWKGGRLRLERAKE 90
             K      G    G +L +  ++ 
Sbjct: 62 QAQKALKQLQGHTVDGHKLEVRISER 87

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 55.5 bits (134), Expect = 2e-09
 Identities = 21/90 (23%), Positives = 38/90 (42%), Gaps = 6/90 (6%)

Query: 5   EAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RTKGRS--FGYVDFFP 60
           +   E +    + V  +   V +  L ++F   G +++V IV  R   +S  +G+V F  
Sbjct: 34  QMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKF-- 91

Query: 61  SSHKSLSKLFSTYNGCVWKGGRLRLERAKE 90
            S  S  +  +  NG      RL++  A  
Sbjct: 92  QSGSSAQQAIAGLNGFNILNKRLKVALAAS 121

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 54.6 bits (132), Expect = 2e-09
 Identities = 21/81 (25%), Positives = 38/81 (46%), Gaps = 6/81 (7%)

Query: 14  TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RTKGRS--FGYVDFFPSSHKSLSKL 69
            R+YVG L   +T+D L  +F   G ++++ ++     GRS  +G++ F  S  +   K 
Sbjct: 27  MRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITF--SDSECAKKA 84

Query: 70  FSTYNGCVWKGGRLRLERAKE 90
               NG    G  +++    E
Sbjct: 85  LEQLNGFELAGRPMKVGHVTE 105

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 56.4 bits (137), Expect = 2e-09
 Identities = 21/82 (25%), Positives = 38/82 (46%), Gaps = 6/82 (7%)

Query: 12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK--GRS--FGYVDFFPSSHKSLS 67
            T + V  L + +TD +L  +F ++G +    I+R    G S  + +VDF  +S     
Sbjct: 2  SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDF--TSEMDSQ 59

Query: 68 KLFSTYNGCVWKGGRLRLERAK 89
          +     NG   +  RL++  A+
Sbjct: 60 RAIKVLNGITVRNKRLKVSYAR 81

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 45.3 bits (108), Expect = 1e-05
 Identities = 22/82 (26%), Positives = 36/82 (43%), Gaps = 6/82 (7%)

Query: 8   AEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK--GRS--FGYVDFFPSSH 63
            E  + T +YV  L   +TDD L  +F   G +   +I+R K  GR     +V +  +  
Sbjct: 84  GESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRY--NKR 141

Query: 64  KSLSKLFSTYNGCVWKGGRLRL 85
           +   +  S  N  + +GG   L
Sbjct: 142 EEAQEAISALNNVIPEGGSQPL 163

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 54.7 bits (132), Expect = 3e-09
 Identities = 17/96 (17%), Positives = 35/96 (36%), Gaps = 8/96 (8%)

Query: 3   KKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RTKGRS--FGYVDF 58
                ++V E   +++  L     ++ L +V    G++K V +V       S    +  F
Sbjct: 5   SSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQF 64

Query: 59  FPSSH--KSLSKL--FSTYNGCVWKGGRLRLERAKE 90
                  K L+     +   G    G +L+++ A  
Sbjct: 65  MTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVT 100

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 54.2 bits (131), Expect = 3e-09
 Identities = 14/81 (17%), Positives = 34/81 (41%), Gaps = 6/81 (7%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK--GRS--FGYVDFFPSSHKSLSKL 69
            +Y+G +    T++ +  + S++G V  + ++     GRS  + +++F     +S +  
Sbjct: 3  RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEF--RDLESSASA 60

Query: 70 FSTYNGCVWKGGRLRLERAKE 90
              NG       L+   +  
Sbjct: 61 VRNLNGYQLGSRFLKCGYSSN 81

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 54.2 bits (131), Expect = 3e-09
 Identities = 18/87 (20%), Positives = 39/87 (44%), Gaps = 6/87 (6%)

Query: 8  AEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK--GRS--FGYVDFFPSSH 63
          A       ++VG +  + T++ L  +FS +G V +  +V  +  G+   +G+ ++     
Sbjct: 3  AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEY--QDQ 60

Query: 64 KSLSKLFSTYNGCVWKGGRLRLERAKE 90
          ++        NG  + G  LR++ A  
Sbjct: 61 ETALSAMRNLNGREFSGRALRVDNAAS 87

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 55.1 bits (133), Expect = 3e-09
 Identities = 24/94 (25%), Positives = 37/94 (39%), Gaps = 6/94 (6%)

Query: 1   MEKKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RTKGRS--FGYV 56
                  A  +    + V GL    T+ DL +VFS  G +  V IV  +   RS  F +V
Sbjct: 34  SRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFV 93

Query: 57  DFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKE 90
            F   +     +     NG    G R+R++ +  
Sbjct: 94  YF--ENVDDAKEAKERANGMELDGRRIRVDFSIT 125

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 54.4 bits (131), Expect = 3e-09
 Identities = 23/100 (23%), Positives = 44/100 (44%), Gaps = 8/100 (8%)

Query: 3  KKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSF---GYVDFF 59
          +   + +V+ ++ +Y+ G     T DD+ +     G+V  + + RT  ++F    +V F 
Sbjct: 2  RWILKNDVKNRS-VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVF- 59

Query: 60 PSSHKSLSKLFSTYNGCVWKGGRLRLERAKEHYLARLKRE 99
            S +S  K F    G  +K   L +    + Y A+   E
Sbjct: 60 -DSIESAKK-FVETPGQKYKETDLLILFKDD-YFAKKNEE 96

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 53.8 bits (130), Expect = 3e-09
 Identities = 17/77 (22%), Positives = 31/77 (40%), Gaps = 6/77 (7%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTY 73
           +I+VG +    T  +L  +F   G V   D+V    + + +V              +  
Sbjct: 10 WKIFVGNVSAACTSQELRSLFERRGRVIECDVV----KDYAFVHM--EKEADAKAAIAQL 63

Query: 74 NGCVWKGGRLRLERAKE 90
          NG   KG R+ +E + +
Sbjct: 64 NGKEVKGKRINVELSTK 80

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 56.9 bits (138), Expect = 3e-09
 Identities = 24/92 (26%), Positives = 46/92 (50%), Gaps = 8/92 (8%)

Query: 4   KEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVR--TKGRS--FGYVDFF 59
            +   E     RIYV  + + ++DDD+  VF + G++K+  + R  T G+   +G++++ 
Sbjct: 116 DQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEY- 174

Query: 60  PSSHKSLSKLFSTYNGCVWKGGR-LRLERAKE 90
               +S     S+ N     GG+ LR+ +A  
Sbjct: 175 -EKAQSSQDAVSSMNL-FDLGGQYLRVGKAVT 204

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 51.2 bits (123), Expect = 3e-07
 Identities = 11/54 (20%), Positives = 29/54 (53%), Gaps = 4/54 (7%)

Query: 9  EVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RTKGRS--FGYVDF 58
           +   +R+YVG +  ++ +D + + F+  G +K++D+       +   F +V++
Sbjct: 24 ALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEY 77

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 53.7 bits (130), Expect = 3e-09
 Identities = 19/79 (24%), Positives = 28/79 (35%), Gaps = 4/79 (5%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRS--FGYVDFFPSSHKSLSKLFS 71
           +I+V  L    T   L   F+  G V   DI    G+S   G V F   S +   +   
Sbjct: 9  CQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKF--ESPEVAERACR 66

Query: 72 TYNGCVWKGGRLRLERAKE 90
            NG    G  + +   + 
Sbjct: 67 MMNGMKLSGREIDVRIDRN 85

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 53.7 bits (130), Expect = 3e-09
 Identities = 20/84 (23%), Positives = 32/84 (38%), Gaps = 8/84 (9%)

Query: 13 QTRIYVGGLGEKVTDDDLAKVFSSLG--EVKAVDIV--RTKGRS--FGYVDFFPSSHKSL 66
          +  +Y+G L    TD+DL +   SLG  ++  +     R  G+S  F  V     S  S 
Sbjct: 1  RIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGV--GSEASS 58

Query: 67 SKLFSTYNGCVWKGGRLRLERAKE 90
           KL          G    +  + +
Sbjct: 59 KKLMDLLPKRELHGQNPVVTPSNK 82

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 53.8 bits (130), Expect = 3e-09
 Identities = 19/80 (23%), Positives = 39/80 (48%), Gaps = 7/80 (8%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK-GRS--FGYVDFFPSSHKSLSKLF 70
            ++VGG+  ++ + ++   F+  G VK V I+  + G S  +G+V F   +   + K+ 
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSF--YNDVDVQKIV 67

Query: 71 STYNGCVWKGGRLRLERAKE 90
             +   + G +L+L  A  
Sbjct: 68 E--SQINFHGKKLKLGPAIR 85

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 54.2 bits (131), Expect = 4e-09
 Identities = 18/92 (19%), Positives = 37/92 (40%), Gaps = 7/92 (7%)

Query: 3   KKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK--GRS--FGYVDF 58
                 E  +   ++   L  ++   DL   FS++G+V+ V I+  +   RS    YV+F
Sbjct: 15  VDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEF 74

Query: 59  FPSSHKSLSKLFSTYNGCVWKGGRLRLERAKE 90
                +S+        G    G  + ++ ++ 
Sbjct: 75  --CEIQSVPLAIG-LTGQRLLGVPIIVQASQA 103

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 54.8 bits (132), Expect = 4e-09
 Identities = 15/61 (24%), Positives = 25/61 (40%), Gaps = 4/61 (6%)

Query: 2   EKKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RTKGRS--FGYVD 57
               +      +  +YVGGL E+V D  L   F   G++  + I       +   F +V+
Sbjct: 52  GSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 111

Query: 58  F 58
           F
Sbjct: 112 F 112

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 53.8 bits (130), Expect = 4e-09
 Identities = 17/83 (20%), Positives = 36/83 (43%), Gaps = 6/83 (7%)

Query: 12  EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RTKGRS--FGYVDFFPSSHKSLS 67
           E   ++V G+ E+ T++D+   F+  GE+K + +   R  G    +  V++   ++K   
Sbjct: 22  EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY--ETYKEAQ 79

Query: 68  KLFSTYNGCVWKGGRLRLERAKE 90
                 NG    G  + ++    
Sbjct: 80  AAMEGLNGQDLMGQPISVDWCFV 102

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 55.2 bits (133), Expect = 4e-09
 Identities = 18/92 (19%), Positives = 40/92 (43%), Gaps = 6/92 (6%)

Query: 2   EKKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RTKGRS--FGYVD 57
           + +E E  +++   +YVG L    T++ + ++FS  G++K + +   + K  +  F +V+
Sbjct: 28  DNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVE 87

Query: 58  FFPSSHKSLSKLFSTYNGCVWKGGRLRLERAK 89
           +   S           NG       +R +   
Sbjct: 88  Y--YSRADAENAMRYINGTRLDDRIIRTDWDA 117

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 53.0 bits (128), Expect = 4e-09
 Identities = 13/77 (16%), Positives = 33/77 (42%), Gaps = 6/77 (7%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTY 73
           ++++G L  + T+ ++  +F   G+V   DI+    +++G+V        +        
Sbjct: 9  VKLFIGNLPREATEQEIRSLFEQYGKVLECDII----KNYGFVHI--EDKTAAEDAIRNL 62

Query: 74 NGCVWKGGRLRLERAKE 90
          +     G  + +E +K 
Sbjct: 63 HHYKLHGVNINVEASKN 79

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 54.0 bits (130), Expect = 5e-09
 Identities = 18/94 (19%), Positives = 39/94 (41%), Gaps = 7/94 (7%)

Query: 1   MEKKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK--GRS--FGYV 56
                 E +  ++  +YVG +    T  DL   FSS G +  + I+  K  G    + Y+
Sbjct: 24  QPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYI 83

Query: 57  DFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKE 90
           +F   + ++        +  V++G  +++   + 
Sbjct: 84  EF---AERNSVDAAVAMDETVFRGRTIKVLPKRT 114

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 55.8 bits (135), Expect = 5e-09
 Identities = 18/82 (21%), Positives = 41/82 (50%), Gaps = 8/82 (9%)

Query: 14  TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVR--TKGRS--FGYVDFFPSSHKSLSKL 69
            ++++GGL   + DD + ++ +S G +KA ++V+    G S  + + ++         + 
Sbjct: 115 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEY--VDINVTDQA 172

Query: 70  FSTYNGCVWKGGR-LRLERAKE 90
            +  NG +  G + L ++RA  
Sbjct: 173 IAGLNG-MQLGDKKLLVQRASV 193

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 51.2 bits (123), Expect = 2e-07
 Identities = 34/200 (17%), Positives = 73/200 (36%), Gaps = 44/200 (22%)

Query: 15  RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT---------KGRSFGYVDFFPSSHKS 65
           R+YVG +   +T++ +   F++   +  +              + ++F +++F   S   
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEF--RSVDE 63

Query: 66  LSKLFSTYNGCVWKGGRLRLERAKEHYLARLKREWAEDDAQLVNPPVTDSVAPDNKDATR 125
            ++  + ++G +++G  L++ R               ++  +  P V  +V P       
Sbjct: 64  TTQAMA-FDGIIFQGQSLKIRRPH----DYQPLPGMSENPSVYVPGVVSTVVP------- 111

Query: 126 LDTPKKL--------LDKDKKLNIF--FPRLRKVKTLPFCGTGKHK-YSFQRVEAPPLPK 174
            D+  KL        L+ D+   +   F  L+    +    TG  K Y+F   E      
Sbjct: 112 -DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAF--CE------ 162

Query: 175 YFCDCEEHSAAFHAAEGKQI 194
            + D      A     G Q+
Sbjct: 163 -YVDINVTDQAIAGLNGMQL 181

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 52.6 bits (127), Expect = 6e-09
 Identities = 20/81 (24%), Positives = 34/81 (41%), Gaps = 8/81 (9%)

Query: 15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK--GRS--FGYVDFFPSSHKSLSKLF 70
           ++VG L  ++T   +A  F+  G +    +V+    G+S  +G+V F   +        
Sbjct: 8  HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSF--FNKWDAENAI 65

Query: 71 STYNGCVWKGGR-LRLERAKE 90
              G  W GGR +R   A  
Sbjct: 66 QQMGG-QWLGGRQIRTNWATR 85

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 52.6 bits (127), Expect = 7e-09
 Identities = 18/85 (21%), Positives = 34/85 (40%), Gaps = 6/85 (7%)

Query: 8  AEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RTKGRS--FGYVDFFPSSH 63
               ++ +YV  L   +T++DL ++FS  G+V  V I+  +   +S    ++ F     
Sbjct: 11 GLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILF--LDK 68

Query: 64 KSLSKLFSTYNGCVWKGGRLRLERA 88
           S        N     G  ++   A
Sbjct: 69 DSAQNCTRAINNKQLFGRVIKASIA 93

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 52.7 bits (127), Expect = 7e-09
 Identities = 18/78 (23%), Positives = 39/78 (50%), Gaps = 7/78 (8%)

Query: 14 TRIYVGGL-GEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFST 72
          +R+++G L  + V+ +DL ++FS  G +  ++I       FG++ F   + +S+      
Sbjct: 23 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNA----FGFIQF--DNPQSVRDAIEX 76

Query: 73 YNGCVWKGGRLRLERAKE 90
           +  +  G +L LE +  
Sbjct: 77 ESQEMNFGKKLILEVSSS 94

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 53.0 bits (128), Expect = 8e-09
 Identities = 23/91 (25%), Positives = 36/91 (39%), Gaps = 7/91 (7%)

Query: 3  KKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAV-DIVRTKGRS--FGYVDFF 59
               A  +    ++V GL E  T++ L + F      + V D  R  G S  FG+VDF 
Sbjct: 5  SSGPNARSQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTD--RETGSSKGFGFVDF- 61

Query: 60 PSSHKSLSKLFSTYNGCVWKGGRLRLERAKE 90
           +S +               G ++ L+ AK 
Sbjct: 62 -NSEEDAKAAKEAMEDGEIDGNKVTLDWAKP 91

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Length = 126

 Score = 53.5 bits (129), Expect = 9e-09
 Identities = 16/92 (17%), Positives = 37/92 (40%), Gaps = 6/92 (6%)

Query: 3   KKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK--GRS--FGYVDF 58
            +       E   ++V G+ E+ T++D+   F+  GE+K + +   +  G    +  V++
Sbjct: 12  DEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 71

Query: 59  FPSSHKSLSKLFSTYNGCVWKGGRLRLERAKE 90
              ++K         NG    G  + ++    
Sbjct: 72  --ETYKEAQAAMEGLNGQDLMGQPISVDWCFV 101

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 52.8 bits (127), Expect = 1e-08
 Identities = 18/78 (23%), Positives = 32/78 (41%), Gaps = 7/78 (8%)

Query: 14 TRIYVGGLG-EKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFST 72
          +R+++G L    V   D+  +FS  G V    +     + + +V +  S+ +        
Sbjct: 28 SRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH----KGYAFVQY--SNERHARAAVLG 81

Query: 73 YNGCVWKGGRLRLERAKE 90
           NG V  G  L +  A E
Sbjct: 82 ENGRVLAGQTLDINMAGE 99

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 52.2 bits (126), Expect = 1e-08
 Identities = 18/80 (22%), Positives = 40/80 (50%), Gaps = 7/80 (8%)

Query: 12 EQTRIYVGGL-GEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLF 70
           ++R+++G L  + V+ +DL ++FS  G +  ++I       FG++ F   + +S+    
Sbjct: 9  PKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNA----FGFIQF--DNPQSVRDAI 62

Query: 71 STYNGCVWKGGRLRLERAKE 90
             +  +  G +L LE +  
Sbjct: 63 ECESQEMNFGKKLILEVSSS 82

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 52.7 bits (127), Expect = 1e-08
 Identities = 20/83 (24%), Positives = 33/83 (39%), Gaps = 10/83 (12%)

Query: 14  TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RTKGRS--FGYVDF--FPSSHKSLS 67
             +Y+  L  +VT+ DL  +F+   E K   I      GR     ++ F     + ++L 
Sbjct: 26  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 85

Query: 68  KLFSTYNGCVWKGGRLRLERAKE 90
            +    NG    G  L +E  K 
Sbjct: 86  LV----NGYKLYGKILVIEFGKN 104

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 52.2 bits (126), Expect = 1e-08
 Identities = 20/80 (25%), Positives = 38/80 (47%), Gaps = 7/80 (8%)

Query: 15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RTKGRS--FGYVDFFPSSHKSLSKLF 70
           IYVG L    T + + ++FS  G+V  V ++  R   +   FG+V+      +S+S+  
Sbjct: 3  NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEM---QEESVSEAI 59

Query: 71 STYNGCVWKGGRLRLERAKE 90
          +  +   + G  +R+  A  
Sbjct: 60 AKLDNTDFMGRTIRVTEANP 79

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 52.3 bits (126), Expect = 1e-08
 Identities = 20/100 (20%), Positives = 37/100 (37%), Gaps = 14/100 (14%)

Query: 1  MEKKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVK--------AVDIVRTK--G 50
          M          +   I+V GLGE VT + +A  F  +G +K         +++   +  G
Sbjct: 1  MGHHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETG 60

Query: 51 RS--FGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERA 88
          +      V F      S       ++G  + G  +++  A
Sbjct: 61 KLKGEATVSFD--DPPSAKAAIDWFDGKEFSGNPIKVSFA 98

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 52.7 bits (127), Expect = 1e-08
 Identities = 17/83 (20%), Positives = 36/83 (43%), Gaps = 6/83 (7%)

Query: 12  EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RTKGRS--FGYVDFFPSSHKSLS 67
           E   ++V  + E+  +D++ + F   GE+K + +   R  G S  +  V++   +HK   
Sbjct: 25  EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEY--ETHKQAL 82

Query: 68  KLFSTYNGCVWKGGRLRLERAKE 90
                 NG    G  ++++    
Sbjct: 83  AAKEALNGAEIMGQTIQVDWCFV 105

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 52.2 bits (126), Expect = 1e-08
 Identities = 23/79 (29%), Positives = 38/79 (48%), Gaps = 4/79 (5%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRS--FGYVDFFPSSHKSLSKLFS 71
            +YV  L + + D+ L K FS  G + +  ++   GRS  FG+V F  SS +  +K  +
Sbjct: 16 VNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCF--SSPEEATKAVT 73

Query: 72 TYNGCVWKGGRLRLERAKE 90
            NG +     L +  A+ 
Sbjct: 74 EMNGRIVATKPLYVALAQR 92

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 51.9 bits (125), Expect = 2e-08
 Identities = 15/83 (18%), Positives = 34/83 (40%), Gaps = 4/83 (4%)

Query: 7  EAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSL 66
          E  +     +YV  L    +++ + K F+++       + + +   + +V F  S+ +  
Sbjct: 9  EDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD--YAFVHF--SNREDA 64

Query: 67 SKLFSTYNGCVWKGGRLRLERAK 89
           +     NG V  G  + +  AK
Sbjct: 65 VEAMKALNGKVLDGSPIEVTLAK 87

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 52.4 bits (126), Expect = 2e-08
 Identities = 20/85 (23%), Positives = 35/85 (41%), Gaps = 8/85 (9%)

Query: 11 EEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK--GRS--FGYVDFFPSSHKSL 66
               ++VG L  ++T +D+   F+  G +    +V+    G+S  +G+V F   +    
Sbjct: 13 SNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSF--FNKWDA 70

Query: 67 SKLFSTYNGCVWKGGR-LRLERAKE 90
                  G  W GGR +R   A  
Sbjct: 71 ENAIQQMGG-QWLGGRQIRTNWATR 94

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 52.4 bits (126), Expect = 2e-08
 Identities = 13/81 (16%), Positives = 28/81 (34%), Gaps = 3/81 (3%)

Query: 11 EEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT-KGRSFGYVDFFPSSHKSLSKL 69
          E    +Y+  L  K+T +++  +F   G ++ + +  T + R   YV +           
Sbjct: 6  EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVY--EDIFDAKNA 63

Query: 70 FSTYNGCVWKGGRLRLERAKE 90
              +G       L +     
Sbjct: 64 VDHLSGFNVSNRYLVVLYYNA 84

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103

 Score = 51.5 bits (124), Expect = 2e-08
 Identities = 17/76 (22%), Positives = 32/76 (42%), Gaps = 6/76 (7%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTY 73
            ++V  L   VT++ L K FS  G+++ V  +    + + ++ F         K     
Sbjct: 12 KVLFVRNLANTVTEEILEKAFSQFGKLERVKKL----KDYAFIHF--DERDGAVKAMEEM 65

Query: 74 NGCVWKGGRLRLERAK 89
          NG   +G  + +  AK
Sbjct: 66 NGKDLEGENIEIVFAK 81

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Length = 165

 Score = 53.3 bits (128), Expect = 2e-08
 Identities = 17/93 (18%), Positives = 38/93 (40%), Gaps = 6/93 (6%)

Query: 2   EKKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK--GRS--FGYVD 57
           E +       E   ++V  + E+  +D++ + F   GE+K + +   +  G S  +  V+
Sbjct: 61  ELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVE 120

Query: 58  FFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKE 90
           +   +HK         NG    G  ++++    
Sbjct: 121 Y--ETHKQALAAKEALNGAEIMGQTIQVDWCFV 151

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 54.2 bits (131), Expect = 3e-08
 Identities = 23/85 (27%), Positives = 36/85 (42%), Gaps = 6/85 (7%)

Query: 8  AEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK--GRS--FGYVDFFPSSH 63
          A       +YVG L   VT+  L + FS  G + ++ + R     RS  + YV+F     
Sbjct: 10 APSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNF--QQP 67

Query: 64 KSLSKLFSTYNGCVWKGGRLRLERA 88
              +   T N  V KG  +R+  +
Sbjct: 68 ADAERALDTMNFDVIKGKPVRIMWS 92

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 46.1 bits (110), Expect = 1e-05
 Identities = 17/81 (20%), Positives = 38/81 (46%), Gaps = 10/81 (12%)

Query: 14  TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRS--FGYVDF--FPSSHKSLSKL 69
             I++  L + + +  L   FS+ G + +  +V  +  S  +G+V F    ++ +++ K+
Sbjct: 104 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKM 163

Query: 70  FSTYNGCVWKGGR-LRLERAK 89
               NG +    R + + R K
Sbjct: 164 ----NG-MLLNDRKVFVGRFK 179

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 53.0 bits (128), Expect = 3e-08
 Identities = 18/85 (21%), Positives = 42/85 (49%), Gaps = 8/85 (9%)

Query: 9   EVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVR--TKGRS--FGYVDFFPSSHK 64
            +    ++++GGL   + DD + ++ +S G +KA ++V+    G S  + + ++      
Sbjct: 90  PLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEY--VDIN 147

Query: 65  SLSKLFSTYNGCVWKGGR-LRLERA 88
              +  +  NG +  G + L ++RA
Sbjct: 148 VTDQAIAGLNG-MQLGDKKLLVQRA 171

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 44.1 bits (105), Expect = 3e-05
 Identities = 8/53 (15%), Positives = 24/53 (45%), Gaps = 9/53 (16%)

Query: 15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT---------KGRSFGYVDF 58
          R+YVG +   +T++ +   F++   +  +              + ++F +++F
Sbjct: 6  RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEF 58

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 52.9 bits (128), Expect = 3e-08
 Identities = 17/52 (32%), Positives = 30/52 (57%), Gaps = 4/52 (7%)

Query: 11 EEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK--GRS--FGYVDF 58
          +E  ++++GGL    T+D+L + F   G V  + I++    GRS  FG++ F
Sbjct: 1  KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSF 52

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 49.8 bits (120), Expect = 3e-07
 Identities = 19/84 (22%), Positives = 42/84 (50%), Gaps = 7/84 (8%)

Query: 9   EVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RTKGRS--FGYVDFFPSSHK 64
           E ++  +I+VGG+G  V   +  + FS  G +    ++  +  G+S  FG+V +   S  
Sbjct: 83  EQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTY--DSAD 140

Query: 65  SLSKLFSTYNGCVWKGGRLRLERA 88
           ++ ++        +K  ++ ++RA
Sbjct: 141 AVDRVCQN-KFIDFKDRKIEIKRA 163

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 51.2 bits (123), Expect = 4e-08
 Identities = 13/102 (12%), Positives = 30/102 (29%), Gaps = 8/102 (7%)

Query: 13  QTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK--GRS--FGYVDFFPSSHKSLSK 68
              +    L + V +  L  +    GEV+ V+I+      +      V F  +S +   +
Sbjct: 6   LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLF--TSTRGAKE 63

Query: 69  LFSTYNGCVWKGGRLRLERAKEHYLARLKREWAEDDAQLVNP 110
                +     G  +  +        +  + +         P
Sbjct: 64  TVKNLHLTSVMGNIIHAQLDI--KGQQRMKYYELIVNGSYTP 103

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 50.9 bits (122), Expect = 5e-08
 Identities = 22/98 (22%), Positives = 41/98 (41%), Gaps = 18/98 (18%)

Query: 7  EAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKA--------VDIV--RTKGRS--FG 54
          E +  +   I+V GLGE VT + +A  F  +G +K         +++   R  G+     
Sbjct: 1  EQDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEA 60

Query: 55 YVDFF--PSSHKSLSKLFSTYNGCVWKGGRLRLERAKE 90
           V F   PS+  ++       +G  + G  +++  A  
Sbjct: 61 TVSFDDPPSAKAAIDWF----DGKEFSGNPIKVSFATR 94

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

 Score = 50.6 bits (121), Expect = 5e-08
 Identities = 15/77 (19%), Positives = 27/77 (35%), Gaps = 3/77 (3%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTY 73
            +YVG L       DL +    LG V  + +     R   ++ +      +  +  S  
Sbjct: 20 ADVYVGNLPRDARVSDLKRALRELGSV-PLRLTWQGPRRRAFLHY--PDSAAAQQAVSCL 76

Query: 74 NGCVWKGGRLRLERAKE 90
           G       LR+  A++
Sbjct: 77 QGLRLGTDTLRVALARQ 93

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 50.4 bits (121), Expect = 5e-08
 Identities = 14/80 (17%), Positives = 32/80 (40%), Gaps = 6/80 (7%)

Query: 11 EEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLF 70
           +   +YV G    +T   L   FS  G +  + +   +     +V +     +S  +  
Sbjct: 13 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRN--CAFVTY--EKMESADQAV 66

Query: 71 STYNGCVWKGGRLRLERAKE 90
          +  NG   +  +L++  A++
Sbjct: 67 AELNGTQVESVQLKVNIARK 86

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 49.6 bits (119), Expect = 1e-07
 Identities = 25/92 (27%), Positives = 39/92 (42%), Gaps = 8/92 (8%)

Query: 3  KKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK--GRS--FGYVDF 58
              E   E     YVG L       D+  +F  L  +++V +VR K   +   F YV+F
Sbjct: 5  SSGKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEF 63

Query: 59 FPSSHKSLSKLFSTYNGCVWKGGRLRLERAKE 90
                SL +   TY+G +     LR++ A+ 
Sbjct: 64 --DEVDSLKEAL-TYDGALLGDRSLRVDIAEG 92

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 53.1 bits (128), Expect = 1e-07
 Identities = 12/79 (15%), Positives = 29/79 (36%), Gaps = 6/79 (7%)

Query: 14  TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK--GRS--FGYVDFFPSSHKSLSKL 69
             + V  L   +T     ++    G ++   +V ++  G+S  +G+ ++      S ++ 
Sbjct: 96  ALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEY--MKKDSAARA 153

Query: 70  FSTYNGCVWKGGRLRLERA 88
            S   G       L +   
Sbjct: 154 KSDLLGKPLGPRTLYVHWT 172

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 50.0 bits (120), Expect = 1e-06
 Identities = 14/104 (13%), Positives = 37/104 (35%), Gaps = 8/104 (7%)

Query: 4   KEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSH 63
           +  E +   + +I + GL   VT+ ++  + S    +K   + + KG    +V     + 
Sbjct: 13  EHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYKG--TAFVTL--LNG 67

Query: 64  KSLSKLFSTYNGCVWKGGRLRLERAKEH---YLARLKREWAEDD 104
           +      + ++    +   L ++         +A L     +  
Sbjct: 68  EQAEAAINAFHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQ 111

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 50.0 bits (120), Expect = 1e-06
 Identities = 12/94 (12%), Positives = 29/94 (30%), Gaps = 6/94 (6%)

Query: 1   MEKKEAEAEVEEQTRIYVGGLGEKVTDDD-LAKVFSSLGEVKAVDIVR-TKGRS--FGYV 56
            +  +    +     + V  L     D D L +  S++       +     G+   F  +
Sbjct: 172 TDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVL 231

Query: 57  DFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKE 90
           ++   + +   +     +G    G  LR+     
Sbjct: 232 EY--ETAEMAEEAQQQADGLSLGGSHLRVSFCAP 263

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 49.2 bits (118), Expect = 1e-07
 Identities = 20/81 (24%), Positives = 33/81 (40%), Gaps = 9/81 (11%)

Query: 15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVR---TKGRS--FGYVDFFPSSHKSLSKL 69
            ++G L   VT++ + + F     + AV + R      R   FGY +F      SL   
Sbjct: 21 TAFLGNLPYDVTEESIKEFFRG-LNISAVRLPREPSNPERLKGFGYAEF--EDLDSLLSA 77

Query: 70 FSTYNGCVWKGGRLRLERAKE 90
           S  N       R+R++ A +
Sbjct: 78 LS-LNEESLGNRRIRVDVADQ 97

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 48.8 bits (117), Expect = 2e-07
 Identities = 19/81 (23%), Positives = 33/81 (40%), Gaps = 9/81 (11%)

Query: 15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV---RTKGRS--FGYVDFFPSSHKSLSKL 69
            ++G L   VT++ + + F  L  + AV +        R   FGY +F      SL   
Sbjct: 17 TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEF--EDLDSLLSA 73

Query: 70 FSTYNGCVWKGGRLRLERAKE 90
            + N       R+R++ A +
Sbjct: 74 L-SLNEESLGNKRIRVDVADQ 93

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 48.9 bits (117), Expect = 2e-07
 Identities = 22/101 (21%), Positives = 38/101 (37%), Gaps = 14/101 (13%)

Query: 2   EKKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV----------RTKGR 51
                  E  + + IYV GL + VT DDLA  F   G VK               +  G+
Sbjct: 4   GSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGK 63

Query: 52  S--FGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKE 90
                 V +      +       ++G  ++G +L++  A++
Sbjct: 64  PKGDATVSYE--DPPTAKAAVEWFDGKDFQGSKLKVSLARK 102

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 48.0 bits (115), Expect = 3e-07
 Identities = 15/55 (27%), Positives = 28/55 (50%), Gaps = 1/55 (1%)

Query: 4  KEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDF 58
          + +       ++++VG   E +T ++L + F   GEV  V I +   R+F +V F
Sbjct: 2  RGSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPK-PFRAFAFVTF 55

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 48.1 bits (115), Expect = 4e-07
 Identities = 19/91 (20%), Positives = 40/91 (43%), Gaps = 11/91 (12%)

Query: 8  AEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGE-VKAVDIVRTK--GRS--FGYVDFFPSS 62
                  +++G L   + ++ +++ F+++GE V +V I+R +  G    + +V+F  + 
Sbjct: 4  GSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEF--AD 61

Query: 63 HKSLSKLFSTYNGCVWKGG----RLRLERAK 89
            +  K     NG    G     R +L  A 
Sbjct: 62 LATAEKCLHKINGKPLPGATPAKRFKLNYAT 92

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score = 50.9 bits (121), Expect = 4e-07
 Identities = 22/93 (23%), Positives = 37/93 (39%), Gaps = 8/93 (8%)

Query: 12  EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV----RTKGRS--FGYVDFFPSSHKS 65
           ++  +Y+G L    TD+DL +   SLG    ++I     R  G+S  F  V     S  S
Sbjct: 67  KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGV--GSEAS 124

Query: 66  LSKLFSTYNGCVWKGGRLRLERAKEHYLARLKR 98
             KL          G    +    + +L++ + 
Sbjct: 125 SKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEM 157

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 49.5 bits (118), Expect = 4e-07
 Identities = 23/98 (23%), Positives = 38/98 (38%), Gaps = 8/98 (8%)

Query: 4   KEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV----RTKGRS--FGYVD 57
                    +  +YVG      TD  L +V  S+G    V++     R  G+S  +  V 
Sbjct: 46  YTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVV 105

Query: 58  FFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKEHYLAR 95
              +S  S+ KL     G V  G ++ +  A    L++
Sbjct: 106 V--ASENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQ 141

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 51.5 bits (124), Expect = 4e-07
 Identities = 12/93 (12%), Positives = 30/93 (32%), Gaps = 6/93 (6%)

Query: 1   MEKKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT----KGRSFGYV 56
           + + E       +  +++       T  ++  +   +  V     + +      R F Y+
Sbjct: 105 VGQNEIIVSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYI 164

Query: 57  DFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAK 89
           D   +S +         NG   +G  L  + + 
Sbjct: 165 DV--TSKEDARYCVEKLNGLKIEGYTLVTKVSN 195

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 50.8 bits (122), Expect = 8e-07
 Identities = 15/107 (14%), Positives = 38/107 (35%), Gaps = 7/107 (6%)

Query: 2   EKKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRS--FGYVDFF 59
           +  EA     E T + V  L +    + + K F   G +  VD+  +  ++  F  ++F 
Sbjct: 30  KANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEF- 88

Query: 60  PSSHKSLSKLFSTYNGCVWKGGRLRLERAKEH--YLARLKREWAEDD 104
            + +       +  +  V     + +    E   ++      + + +
Sbjct: 89  -ARYDGALAAITKTHK-VVGQNEIIVSHLTECTLWMTNFPPSYTQRN 133

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 44.2 bits (105), Expect = 9e-05
 Identities = 13/94 (13%), Positives = 34/94 (36%), Gaps = 9/94 (9%)

Query: 2   EKKEAEAEVEEQTRIYVGGLGEKVTDDD-LAKVFSSLGEVKAVDIVR---TKGRS--FGY 55
           + K  ++   E   I +  L  ++ D++ L + F   G ++ ++I         +    +
Sbjct: 199 KSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAF 258

Query: 56  VDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAK 89
           + F   +  S  +     N  +     + +  A 
Sbjct: 259 MVF--ENKDSAERALQM-NRSLLGNREISVSLAD 289

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 48.0 bits (115), Expect = 5e-07
 Identities = 16/80 (20%), Positives = 38/80 (47%), Gaps = 8/80 (10%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRS--FGYVDF--FPSSHKSLSKL 69
            I++  L + + +  L   FS+ G + +  +V  +  S  +G+V F    ++ +++ K+
Sbjct: 6  GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKM 65

Query: 70 FSTYNGCVWKGGRLRLERAK 89
              NG +    ++ + R K
Sbjct: 66 ----NGMLLNDRKVFVGRFK 81

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 47.7 bits (114), Expect = 5e-07
 Identities = 15/63 (23%), Positives = 27/63 (42%), Gaps = 3/63 (4%)

Query: 15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDF--FPSSHKSLSKLFST 72
           ++V G    V    L++ F + G V +V + + KG  F  V+     +    LS+   +
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGV-FAIVEMGDVGAREAVLSQSQHS 68

Query: 73 YNG 75
            G
Sbjct: 69 LGG 71

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

 Score = 47.4 bits (113), Expect = 5e-07
 Identities = 11/83 (13%), Positives = 30/83 (36%), Gaps = 3/83 (3%)

Query: 9  EVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKG-RSFGYVDFFPSSHKSLS 67
          + +   ++ +  +   +  + L  +    G V++ + V T    +   V +  SS     
Sbjct: 11 KRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTY--SSKDQAR 68

Query: 68 KLFSTYNGCVWKGGRLRLERAKE 90
          +     NG   +   L++    +
Sbjct: 69 QALDKLNGFQLENFTLKVAYIPD 91

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 46.8 bits (112), Expect = 6e-07
 Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 1/48 (2%)

Query: 11 EEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDF 58
             + ++VG     +T+D+L + FS  G+V  V I +   R+F +V F
Sbjct: 3  SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-PFRAFAFVTF 49

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 46.8 bits (112), Expect = 9e-07
 Identities = 20/60 (33%), Positives = 31/60 (51%), Gaps = 4/60 (6%)

Query: 3  KKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK--GRS--FGYVDF 58
              +  V++ + + V GL  K T+ DL + FS+ GEV  V + +    G S  FG+V F
Sbjct: 5  SSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRF 64

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 46.8 bits (112), Expect = 1e-06
 Identities = 14/57 (24%), Positives = 27/57 (47%), Gaps = 4/57 (7%)

Query: 6  AEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RTKGRS--FGYVDF 58
          + +   +  +I+VGG+     + +L + F   G V  V ++    K R   FG++ F
Sbjct: 3  SGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITF 59

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 46.7 bits (111), Expect = 1e-06
 Identities = 13/76 (17%), Positives = 25/76 (32%), Gaps = 5/76 (6%)

Query: 15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYN 74
          R+ V GL    +  DL       G+V   D+ R      G V+F     + ++      +
Sbjct: 17 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR---DGTGVVEF--VRKEDMTYAVRKLD 71

Query: 75 GCVWKGGRLRLERAKE 90
             ++         + 
Sbjct: 72 NTKFRSHEGETAYIRV 87

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 46.1 bits (110), Expect = 2e-06
 Identities = 19/79 (24%), Positives = 33/79 (41%), Gaps = 7/79 (8%)

Query: 15 RIYVGGLGEKVTDDDLAKVFSSL-GEVKAVDIVRTK-GRS--FGYVDFFPSSHKSLSKLF 70
           ++VG L   V D  L + F  +    +   +V  + G S  +G+V F  +      +  
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKF--TDELEQKRAL 68

Query: 71 STYNGCVWKGGR-LRLERA 88
          +   G V  G + +RL  A
Sbjct: 69 TECQGAVGLGSKPVRLSVA 87

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 45.2 bits (108), Expect = 2e-06
 Identities = 12/58 (20%), Positives = 28/58 (48%), Gaps = 6/58 (10%)

Query: 15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RTKGRS--FGYVDFFPSSHKSLSK 68
          +I+VGGL     ++ + + F   GEV+++++       +   F ++ F     + + K
Sbjct: 1  KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITF--KEEEPVKK 56

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 45.8 bits (109), Expect = 2e-06
 Identities = 14/89 (15%), Positives = 28/89 (31%), Gaps = 12/89 (13%)

Query: 11 EEQTRIYVGGLGEKVTDDDLAKVFSSLG--EVKAVDIVRTK--GRS--FGYVDFFPSSHK 64
               I +  +      D +    S      V  + +++ K   ++  F +V    SS  
Sbjct: 7  HHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQL--SSAM 64

Query: 65 SLSKLFSTYNGCVWK----GGRLRLERAK 89
            S+L              G  + ++ AK
Sbjct: 65 DASQLLQILQSLHPPLKIDGKTIGVDFAK 93

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 46.0 bits (109), Expect = 2e-06
 Identities = 19/107 (17%), Positives = 29/107 (27%), Gaps = 7/107 (6%)

Query: 14  TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTY 73
           T I    L       ++ + FS  G +  V +          V+F         K F   
Sbjct: 11  TVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGI--TAIVEFL--EPLEARKAFRHL 66

Query: 74  NGCVWKGGRLRLERAKEHYLARLKREWAEDDAQLVNPPVTDSVAPDN 120
               +    L LE A             + D+Q   P       P +
Sbjct: 67  AYSKFHHVPLYLEWAPIG---VFGAAPQKKDSQHEQPAEKAESGPSS 110

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 45.7 bits (109), Expect = 2e-06
 Identities = 25/99 (25%), Positives = 44/99 (44%), Gaps = 9/99 (9%)

Query: 6  AEAEVEEQTRIYVGGLGEKVTDDDLAK----VFSSLGEVKAVDIVRT-KGRSFGYVDFFP 60
          A  E      IY+  L EK+  D+L K    +FS  G++  + + R+ K R   +V F  
Sbjct: 1  AVPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIF-- 58

Query: 61 SSHKSLSKLFSTYNGCVWKGGRLRLERAK--EHYLARLK 97
              S +    +  G  +    +R++ AK     +A++K
Sbjct: 59 KEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMK 97

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 46.1 bits (110), Expect = 2e-06
 Identities = 12/61 (19%), Positives = 26/61 (42%), Gaps = 4/61 (6%)

Query: 2  EKKEAEAEVEEQ-TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK-GRS--FGYVD 57
           + +   + E+  T +Y+  L   + + +L  +    G+V +  I+R   G S   G+  
Sbjct: 13 VQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFAR 72

Query: 58 F 58
           
Sbjct: 73 M 73

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

 Score = 45.8 bits (109), Expect = 3e-06
 Identities = 21/80 (26%), Positives = 33/80 (41%), Gaps = 6/80 (7%)

Query: 14  TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK--GRS--FGYVDFFPSSHKSLSKL 69
             +++  L ++ TD DLA  F   G V +  +   K    S  FG+V F   +  S    
Sbjct: 41  CNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSF--DNPDSAQVA 98

Query: 70  FSTYNGCVWKGGRLRLERAK 89
               NG      RL+++  K
Sbjct: 99  IKAMNGFQVGTKRLKVQLKK 118

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

 Score = 46.8 bits (112), Expect = 5e-06
 Identities = 13/84 (15%), Positives = 35/84 (41%), Gaps = 8/84 (9%)

Query: 12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVR------TKGRSFGYVDFFPSSHKS 65
          +  +++VG +    ++ DL ++F   G V  ++++R       + +   +V F   + K+
Sbjct: 2  DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTF--YTRKA 59

Query: 66 LSKLFSTYNGCVWKGGRLRLERAK 89
            +  +  +      G     + K
Sbjct: 60 ALEAQNALHNMKVLPGMHHPIQMK 83

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

 Score = 45.7 bits (109), Expect = 1e-05
 Identities = 17/61 (27%), Positives = 34/61 (55%), Gaps = 6/61 (9%)

Query: 4   KEAEAEVEEQ---TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK-GRS--FGYVD 57
           K A++E        ++++G + +K T++D+  +FSS G+++   I+R   G S    +V 
Sbjct: 83  KPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVT 142

Query: 58  F 58
           F
Sbjct: 143 F 143

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 45.2 bits (107), Expect = 5e-06
 Identities = 13/76 (17%), Positives = 25/76 (32%), Gaps = 5/76 (6%)

Query: 15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYN 74
          R+ V GL    +  DL       G+V   D+ R      G V+F     + ++      +
Sbjct: 18 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR---DGTGVVEF--VRKEDMTYAVRKLD 72

Query: 75 GCVWKGGRLRLERAKE 90
             ++         + 
Sbjct: 73 NTKFRSHEGETAYIRV 88

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 47.2 bits (112), Expect = 5e-06
 Identities = 34/194 (17%), Positives = 59/194 (30%), Gaps = 25/194 (12%)

Query: 16  IYVGGLG-EKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYN 74
           + V  L  E+VT   L  +F   G+V+ V I+  K +    V    +         S  N
Sbjct: 6   LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-KENALVQM--ADGNQAQLAMSHLN 62

Query: 75  GCVWKGGRLRLERAKEHYLARLKR--EWAEDDAQLVNPPVTDSVAPDNKDATRLDTPKKL 132
           G    G  +R+  +K   +   +   E         N P+     P +K+   +  P   
Sbjct: 63  GHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSAT 122

Query: 133 L---------DKDKKLNIFFPRLRKVKTLPFCGTGKHKYSFQRVEAPPLPKYFCDCEEHS 183
           L          ++    +F      VK   F    + K +   ++           EE  
Sbjct: 123 LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDR-KMAL--IQ-------MGSVEEAV 172

Query: 184 AAFHAAEGKQIHHP 197
            A        +   
Sbjct: 173 QALIDLHNHDLGEN 186

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 42.6 bits (100), Expect = 2e-04
 Identities = 16/77 (20%), Positives = 32/77 (41%), Gaps = 3/77 (3%)

Query: 14  TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSK-LFST 72
             +++  +   V+++DL  +FSS G V        K R    +     S +   + L   
Sbjct: 121 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQM--GSVEEAVQALIDL 178

Query: 73  YNGCVWKGGRLRLERAK 89
           +N  + +   LR+  +K
Sbjct: 179 HNHDLGENHHLRVSFSK 195

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 45.0 bits (107), Expect = 6e-06
 Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 4/58 (6%)

Query: 5  EAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RTKGRS--FGYVDF 58
              +    T+I+VGGL    TD  L K F   G+++   ++  R  G+S  +G+V  
Sbjct: 9  HGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTM 66

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 43.6 bits (104), Expect = 7e-06
 Identities = 16/48 (33%), Positives = 25/48 (52%), Gaps = 4/48 (8%)

Query: 15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RTKGRS--FGYVDF 58
          +I+VGGL    T +D+   F   G+V    ++  +T  R   FG+V F
Sbjct: 1  KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTF 48

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 44.5 bits (106), Expect = 7e-06
 Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 4/61 (6%)

Query: 2  EKKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK--GRS--FGYVD 57
                +  +E  +++VGGL    T + L   FS  GEV    I++ K   +S  FG+V 
Sbjct: 5  SSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVK 64

Query: 58 F 58
          F
Sbjct: 65 F 65

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 44.6 bits (106), Expect = 7e-06
 Identities = 15/62 (24%), Positives = 32/62 (51%), Gaps = 4/62 (6%)

Query: 1  MEKKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK--GRS--FGYV 56
          +  +  + E E+  ++++GGL  + T++ L   +   G++    ++R     RS  FG+V
Sbjct: 15 VPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFV 74

Query: 57 DF 58
           F
Sbjct: 75 TF 76

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 43.7 bits (104), Expect = 8e-06
 Identities = 19/57 (33%), Positives = 27/57 (47%), Gaps = 4/57 (7%)

Query: 6  AEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK--GRS--FGYVDF 58
          A    E+  +++VGGL    +  DL   F+  GEV    I      GRS  FG++ F
Sbjct: 4  ASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILF 60

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 44.2 bits (105), Expect = 8e-06
 Identities = 12/56 (21%), Positives = 29/56 (51%), Gaps = 3/56 (5%)

Query: 6  AEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVR-TKGRS--FGYVDF 58
          +E+      +++VG L ++ +++D+ ++F   G +    ++R   G S    +V F
Sbjct: 8  SESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKF 63

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 43.8 bits (104), Expect = 1e-05
 Identities = 14/83 (16%), Positives = 25/83 (30%), Gaps = 6/83 (7%)

Query: 11 EEQTRIYVGGLGEKVTDDDLAKVFSSLGEVK-AVDIVR-TKGRS--FGYVDFFPSSHKSL 66
             T I V  +   V+ D++   F     +  +V +    KG       V F   S    
Sbjct: 13 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAF--ESRDEA 70

Query: 67 SKLFSTYNGCVWKGGRLRLERAK 89
          +      N       +++L    
Sbjct: 71 TAAVIDLNDRPIGSRKVKLVLGS 93

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 44.1 bits (104), Expect = 1e-05
 Identities = 14/91 (15%), Positives = 44/91 (48%), Gaps = 5/91 (5%)

Query: 16  IYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNG 75
           I++  L   VT+ ++  +    G+V  + +++ K ++F  ++   +++  ++  + T   
Sbjct: 19  IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVN--YYTSVT 76

Query: 76  CVWKGGRLRLERAKEHYLARLKREWAEDDAQ 106
            V +G  + ++ +       LK + + + A+
Sbjct: 77  PVLRGQPIYIQFSNHK---ELKTDSSPNQAR 104

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 46.1 bits (109), Expect = 1e-05
 Identities = 33/194 (17%), Positives = 59/194 (30%), Gaps = 25/194 (12%)

Query: 16  IYVGGLG-EKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYN 74
           + V  L  E+VT   L  +F   G+V+ V I+  K +    V    +         S  N
Sbjct: 37  LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-KENALVQM--ADGNQAQLAMSHLN 93

Query: 75  GCVWKGGRLRLERAKEHYLARLKREWAEDDA--QLVNPPVTDSVAPDNKDATRLDTPKKL 132
           G    G  +R+  +K   +   +    +        N P+     P +K+   +  P   
Sbjct: 94  GHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSAT 153

Query: 133 L---------DKDKKLNIFFPRLRKVKTLPFCGTGKHKYSFQRVEAPPLPKYFCDCEEHS 183
           L          ++    +F      VK   F    + K +   ++           EE  
Sbjct: 154 LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDR-KMAL--IQ-------MGSVEEAV 203

Query: 184 AAFHAAEGKQIHHP 197
            A        +   
Sbjct: 204 QALIDLHNHDLGEN 217

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 43.8 bits (103), Expect = 9e-05
 Identities = 16/77 (20%), Positives = 32/77 (41%), Gaps = 3/77 (3%)

Query: 14  TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSK-LFST 72
             +++  +   V+++DL  +FSS G V        K R    +     S +   + L   
Sbjct: 152 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQM--GSVEEAVQALIDL 209

Query: 73  YNGCVWKGGRLRLERAK 89
           +N  + +   LR+  +K
Sbjct: 210 HNHDLGENHHLRVSFSK 226

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 43.7 bits (103), Expect = 2e-05
 Identities = 15/77 (19%), Positives = 27/77 (35%), Gaps = 3/77 (3%)

Query: 15  RIYVGGLGEKVTDDDLAKVFSSLG-EVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTY 73
           RI +  L E  +  DL  +      E     +        G ++F   S + L +     
Sbjct: 30  RITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEF--PSEEILVEALERL 87

Query: 74  NGCVWKGGRLRLERAKE 90
           N   ++G  + +ER   
Sbjct: 88  NNIEFRGSVITVERDDN 104

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 46.0 bits (108), Expect = 2e-05
 Identities = 24/98 (24%), Positives = 40/98 (40%), Gaps = 7/98 (7%)

Query: 6  AEAEVEEQTRIYVGGLGEKVTDDDLAK----VFSSLGEVKAVDIVRT-KGRSFGYVDFFP 60
          A  E      IY+  L EK+  D+L K    +FS  G++  + + R+ K R   +V F  
Sbjct: 2  AVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIF-- 59

Query: 61 SSHKSLSKLFSTYNGCVWKGGRLRLERAKEHYLARLKR 98
              S +    +  G  +    +R++ AK       K 
Sbjct: 60 KEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKM 97

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 43.5 bits (103), Expect = 2e-05
 Identities = 17/80 (21%), Positives = 34/80 (42%), Gaps = 6/80 (7%)

Query: 14  TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK--GRS--FGYVDFFPSSHKSLSKL 69
             +++  L ++  D DL ++F   G V +  +   K    S  FG+V +   +  S    
Sbjct: 26  ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSY--DNPVSAQAA 83

Query: 70  FSTYNGCVWKGGRLRLERAK 89
             + NG      RL+++  +
Sbjct: 84  IQSMNGFQIGMKRLKVQLKR 103

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 42.7 bits (101), Expect = 2e-05
 Identities = 14/82 (17%), Positives = 25/82 (30%), Gaps = 6/82 (7%)

Query: 11 EEQTRIYVGGLGEKVTDDDLAKVFSSLGEVK-AVDIVRT-KGRS--FGYVDFFPSSHKSL 66
             T I V  +   V+ D++   F     +  +V +    KG       V F   S    
Sbjct: 13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAF--ESRDEA 70

Query: 67 SKLFSTYNGCVWKGGRLRLERA 88
          +      N       +++L   
Sbjct: 71 TAAVIDLNDRPIGSRKVKLSGP 92

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score = 43.1 bits (102), Expect = 3e-05
 Identities = 6/52 (11%), Positives = 25/52 (48%), Gaps = 4/52 (7%)

Query: 11 EEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK--GRS--FGYVDF 58
           +  ++++G +   + + DL  +F   G++  + +++ +  G      ++ +
Sbjct: 11 HDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTY 62

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 42.1 bits (100), Expect = 3e-05
 Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 4/48 (8%)

Query: 15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK--GRS--FGYVDF 58
          ++++GGL  + T + L + F   GEVK   ++R     RS  FG+V F
Sbjct: 2  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 49

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 42.0 bits (99), Expect = 3e-05
 Identities = 18/84 (21%), Positives = 37/84 (44%), Gaps = 16/84 (19%)

Query: 15 RIYVGGLGEKVTDDDLAKVFS-----------SLGEVKAVDIVRTKGRSFGYVDFFPSSH 63
          R+YVG +   +T++ +   F+               V AV I + K   F +++F     
Sbjct: 8  RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN--FAFLEFRSVDE 65

Query: 64 KSLSKLFSTYNGCVWKGGRLRLER 87
           + +  F   +G +++G  L++ R
Sbjct: 66 TTQAMAF---DGIIFQGQSLKIRR 86

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 42.6 bits (100), Expect = 4e-05
 Identities = 15/78 (19%), Positives = 31/78 (39%), Gaps = 7/78 (8%)

Query: 1  MEKKEAEAEVEEQTR---IYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVD 57
          + + E    V   T+   +  GGLG  V+ + L  V    G V    ++    + + +  
Sbjct: 12 LLRHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVD--ALLMPPNKPYSFAR 69

Query: 58 FFPSSHKSLSKLFSTYNG 75
          +   + +   + + T NG
Sbjct: 70 Y--RTTEESKRAYVTLNG 85

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 42.1 bits (99), Expect = 4e-05
 Identities = 10/71 (14%), Positives = 27/71 (38%), Gaps = 2/71 (2%)

Query: 16 IYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNG 75
          +++ GL + V + DL +     G +  V ++  K ++    +    +  +++      N 
Sbjct: 24 VHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYA--ADNQ 81

Query: 76 CVWKGGRLRLE 86
              G    + 
Sbjct: 82 IYIAGHPAFVN 92

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 42.9 bits (101), Expect = 5e-05
 Identities = 22/98 (22%), Positives = 38/98 (38%), Gaps = 11/98 (11%)

Query: 1   MEKKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKA------VDIVRTK-GRS- 52
           +    +    E   RIYV  L + V + DL  +F    +  +       DI   K GR  
Sbjct: 33  LSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMK 92

Query: 53  -FGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAK 89
              ++     + K+ +K     NG V  G  + ++ A+
Sbjct: 93  GQAFIGL--PNEKAAAKALKEANGYVLFGKPMVVQFAR 128

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 41.7 bits (98), Expect = 7e-05
 Identities = 12/74 (16%), Positives = 28/74 (37%), Gaps = 2/74 (2%)

Query: 16 IYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNG 75
          ++V GL E V + DL +     G +  V ++  K ++    +   S+ + ++        
Sbjct: 18 VHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFA--ADVP 75

Query: 76 CVWKGGRLRLERAK 89
              G +     + 
Sbjct: 76 VYIAGQQAFFNYST 89

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 41.9 bits (99), Expect = 7e-05
 Identities = 17/56 (30%), Positives = 27/56 (48%), Gaps = 4/56 (7%)

Query: 7  EAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK--GRS--FGYVDF 58
                  ++++GGL  + T + L + F   GEVK   ++R     RS  FG+V F
Sbjct: 19 SHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 74

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 41.8 bits (98), Expect = 8e-05
 Identities = 14/91 (15%), Positives = 44/91 (48%), Gaps = 5/91 (5%)

Query: 16  IYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNG 75
           I++  L   VT+ ++  +    G+V  + +++ K ++F  ++   +++  ++  + T   
Sbjct: 34  IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVN--YYTSVT 91

Query: 76  CVWKGGRLRLERAKEHYLARLKREWAEDDAQ 106
            V +G  + ++ +       LK + + + A+
Sbjct: 92  PVLRGQPIYIQFSNHK---ELKTDSSPNQAR 119

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

 Score = 42.2 bits (99), Expect = 8e-05
 Identities = 13/108 (12%), Positives = 36/108 (33%), Gaps = 7/108 (6%)

Query: 1   MEKKEAEAEVEEQTRIYVGGLGEKVTDDDLAK----VFSSLGEVKAVDIVRT-KGRSFGY 55
            +        E    + +  +  +V  + L      + SS G++  + +  +       Y
Sbjct: 17  PDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAY 76

Query: 56  VDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKEHYLARLKREWAED 103
           + F  ++ +S       + G  ++G  L +  ++       +    E 
Sbjct: 77  IVF--ATQESAQAFVEAFQGYPFQGNPLVITFSETPQSQVAEDGSLEH 122

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 40.9 bits (96), Expect = 9e-05
 Identities = 9/76 (11%), Positives = 25/76 (32%), Gaps = 5/76 (6%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTY 73
          + I V  L +     ++  +      +K   + R K     +V     + +        +
Sbjct: 6  SGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDRNKR--TAFVTL--LNGEQAQNAIQMF 60

Query: 74 NGCVWKGGRLRLERAK 89
          +   ++G  L ++   
Sbjct: 61 HQYSFRGKDLIVQLQP 76

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 42.1 bits (99), Expect = 1e-04
 Identities = 14/59 (23%), Positives = 24/59 (40%), Gaps = 2/59 (3%)

Query: 2  EKKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRS--FGYVDF 58
             E   +      +++ GL  K T++D+   FS L  V+    +   GR      V+F
Sbjct: 35 GDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEF 93

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 41.0 bits (96), Expect = 1e-04
 Identities = 7/74 (9%), Positives = 34/74 (45%), Gaps = 2/74 (2%)

Query: 16 IYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNG 75
          +++  L  +VT+ ++  +    G+V  + +++ K ++F  +    ++   ++  + +   
Sbjct: 18 LHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVN--YYSAVT 75

Query: 76 CVWKGGRLRLERAK 89
             +   + ++ + 
Sbjct: 76 PHLRNQPIYIQYSN 89

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 41.3 bits (97), Expect = 1e-04
 Identities = 19/109 (17%), Positives = 46/109 (42%), Gaps = 16/109 (14%)

Query: 11  EEQTRIYVGGLGEKVTDDDLAKVFSSLGE-VKAVDIVR-----TKGRSFGYVDFFPSSHK 64
               R+++GG+ +    +++ +  + + E V  V +        K R F +V++   SH+
Sbjct: 6   SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEY--ESHR 63

Query: 65  SLSKLFSTY-NGCVWKGGR-LRLERAKEHYLARLKREWAEDDAQLVNPP 111
           + +        G +   G  + ++ A+       + +  ED  + V+ P
Sbjct: 64  AAAMARRKLMPGRIQLWGHQIAVDWAEP------EIDVDEDVMETVSGP 106

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 40.3 bits (95), Expect = 2e-04
 Identities = 15/75 (20%), Positives = 32/75 (42%), Gaps = 12/75 (16%)

Query: 15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV---RTKGRS--FGYVDF--FPSSHKSLS 67
           I++G L  ++ +  L   FS+ G +     +      G S  + +++F  F +S  ++ 
Sbjct: 7  GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66

Query: 68 KLFSTYNGCVWKGGR 82
           +    NG  +   R
Sbjct: 67 AM----NG-QYLCNR 76

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 40.2 bits (94), Expect = 4e-04
 Identities = 12/94 (12%), Positives = 34/94 (36%), Gaps = 7/94 (7%)

Query: 1   MEKKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVK-AVDIVRTK-GRS--FGYV 56
            ++  + +  E    +Y+ GL  +  +  +   F  L  V+ ++ I     G++   G+V
Sbjct: 13  QKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFV 72

Query: 57  DFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKE 90
           +F   +           +        +++    +
Sbjct: 73  EF--RNEADYKAALC-RHKQYMGNRFIQVHPITK 103

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 40.0 bits (93), Expect = 4e-04
 Identities = 9/80 (11%), Positives = 26/80 (32%), Gaps = 8/80 (10%)

Query: 15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKG------RSFGYVDFF--PSSHKSL 66
          +++VGGL   + +D++   F   G +      + +       + + ++ F    S    +
Sbjct: 10 KVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALI 69

Query: 67 SKLFSTYNGCVWKGGRLRLE 86
                            ++
Sbjct: 70 DACLEEDGKLYLCVSSPTIK 89

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 39.3 bits (92), Expect = 4e-04
 Identities = 20/99 (20%), Positives = 37/99 (37%), Gaps = 14/99 (14%)

Query: 16  IYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK-GRS--FGYVDFFPSSHKSLSKLFST 72
           + V G+     ++D+   F  L  V AV +++   GR+   G V F   S +   +    
Sbjct: 19  VSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKF--LSPQDTFEALK- 74

Query: 73  YNGCVWKGGRLRLERAKEHYLARLKREWAEDDAQLVNPP 111
            N  +     + +  A E       R+W      + + P
Sbjct: 75  RNRMLMIQRYVEVSPATE-------RQWVAAGGHITSGP 106

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 39.9 bits (93), Expect = 5e-04
 Identities = 12/62 (19%), Positives = 24/62 (38%), Gaps = 4/62 (6%)

Query: 1  MEKKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEV-KAVDIVRTK-GRS--FGYV 56
          M +    A+      + + GL    T +++ + FS L  V   + +     G+     +V
Sbjct: 30 MGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFV 89

Query: 57 DF 58
           F
Sbjct: 90 QF 91

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 39.3 bits (92), Expect = 6e-04
 Identities = 7/60 (11%), Positives = 19/60 (31%), Gaps = 4/60 (6%)

Query: 3  KKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVK-AVDIVRTK-GRS--FGYVDF 58
                    +   ++  +   +T  D+ +    +   + AV ++    G+      V F
Sbjct: 5  SSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQF 64

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 40.6 bits (94), Expect = 7e-04
 Identities = 21/86 (24%), Positives = 36/86 (41%), Gaps = 7/86 (8%)

Query: 13  QTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSF---GYVDFFPSSHKSLSKL 69
              +Y+ G     T DD+ +     G+V  + + RT  ++F    +V F   S +S  K 
Sbjct: 109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVF--DSIESAKK- 165

Query: 70  FSTYNGCVWKGGRLRLERAKEHYLAR 95
           F    G  +K   L +    + Y A+
Sbjct: 166 FVETPGQKYKETDLLILFKDD-YFAK 190

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 39.1 bits (91), Expect = 7e-04
 Identities = 16/87 (18%), Positives = 31/87 (35%), Gaps = 12/87 (13%)

Query: 16  IYVGGLGEKVTDDDLAK---VFSSLGEVKAVDIVRTKG-------RSFGYVDFFPSSHKS 65
           ++V GL +++ D ++ K    F   G++  V I  +          +  YV +     + 
Sbjct: 18  VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTY--IRSED 75

Query: 66  LSKLFSTYNGCVWKGGRLRLERAKEHY 92
             +     N  V  G  L+       Y
Sbjct: 76  ALRAIQCVNNVVVDGRTLKASLGTTKY 102

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 40.5 bits (94), Expect = 8e-04
 Identities = 15/79 (18%), Positives = 34/79 (43%), Gaps = 4/79 (5%)

Query: 16 IYVGGLG-EKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYN 74
          + V GL   K+  D +  VF   G V+ V  +++K      V+   +   ++ +  +  N
Sbjct: 7  LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-PGAAMVEM--ADGYAVDRAITHLN 63

Query: 75 GCVWKGGRLRLERAKEHYL 93
               G ++ +  +K+  +
Sbjct: 64 NNFMFGQKMNVCVSKQPAI 82

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

No hit with probability above 80.00

---

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	800
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	1e-08
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	1e-08
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	1e-08
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	3e-08
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	3e-08
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	5e-08
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	6e-08
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	7e-08
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-07
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-07
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	2e-07
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	3e-07
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	6e-07
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	7e-07
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	1e-06
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	1e-06
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-06
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	2e-06
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	5e-06
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	5e-06
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	7e-06
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	7e-06
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-05
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	1e-05
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	1e-05
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	1e-05
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	1e-05
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	1e-05
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	2e-05
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	2e-05
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	2e-05
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	2e-05
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	4e-05
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	8e-05
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	9e-05
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	1e-04
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-04
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	2e-04
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	2e-04
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	2e-04
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	2e-04
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	3e-04
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	3e-04
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	3e-04
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-04
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-04
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	6e-04
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	7e-04
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	0.001
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	0.001
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	0.001
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	0.001
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	0.001
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	0.002
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	0.002
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	0.002
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	0.003

>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 = 50.8 bits (121), Expect = 1e-08
 Identities = 14/77 (18%), Positives = 32/77 (41%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTY 73
            I++  L + + +  L   FS+ G + +  +V  +  S GY      + ++  +     
Sbjct: 9  GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKM 68

Query: 74 NGCVWKGGRLRLERAKE 90
          NG +    ++ + R K 
Sbjct: 69 NGMLLNDRKVFVGRFKS 85

>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 = 51.1 bits (122), Expect = 1e-08
 Identities = 20/89 (22%), Positives = 40/89 (44%), Gaps = 8/89 (8%)

Query: 8  AEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRS-----FGYVDFFPSS 62
           + +  ++I V  +  +    ++ ++FS+ GE+K V + +    +     FG+VDF   +
Sbjct: 3  PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDF--IT 60

Query: 63 HKSLSK-LFSTYNGCVWKGGRLRLERAKE 90
           +   K   +  +     G RL LE A  
Sbjct: 61 KQDAKKAFNALCHSTHLYGRRLVLEWADS 89

>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 = 50.4 bits (120), Expect = 1e-08
 Identities = 20/78 (25%), Positives = 36/78 (46%), Gaps = 2/78 (2%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--KGRSFGYVDFFPSSHKSLSKLFS 71
          T + V  L + +TD +L  +F ++G +    I+R    G S+GY     +S     +   
Sbjct: 3  TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 62

Query: 72 TYNGCVWKGGRLRLERAK 89
            NG   +  RL++  A+
Sbjct: 63 VLNGITVRNKRLKVSYAR 80

>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 = 49.5 bits (118), Expect = 3e-08
 Identities = 13/75 (17%), Positives = 26/75 (34%), Gaps = 1/75 (1%)

Query: 15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFP-SSHKSLSKLFSTY 73
          ++ V  L   V+D D+ ++F+  G +K   +   +                   K    Y
Sbjct: 2  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQY 61

Query: 74 NGCVWKGGRLRLERA 88
          NG    G  + ++  
Sbjct: 62 NGVPLDGRPMNIQLV 76

>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 = 50.1 bits (119), Expect = 3e-08
 Identities = 19/80 (23%), Positives = 31/80 (38%), Gaps = 1/80 (1%)

Query: 11 EEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLF 70
              RIYVG L   +   D+  VF   G ++ +D+   +G        F    +      
Sbjct: 12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEF-EDPRDAEDAV 70

Query: 71 STYNGCVWKGGRLRLERAKE 90
             +G  + G RLR+E  + 
Sbjct: 71 YGRDGYDYDGYRLRVEFPRS 90

>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 = 48.8 bits (116), Expect = 5e-08
 Identities = 21/76 (27%), Positives = 33/76 (43%), Gaps = 2/76 (2%)

Query: 16 IYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVR--TKGRSFGYVDFFPSSHKSLSKLFSTY 73
          +YVG L   VT+  L + FS  G + ++ + R     RS GY            +   T 
Sbjct: 3  LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 62

Query: 74 NGCVWKGGRLRLERAK 89
          N  V KG  +R+  ++
Sbjct: 63 NFDVIKGKPVRIMWSQ 78

>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 = 48.5 bits (115), Expect = 6e-08
 Identities = 17/81 (20%), Positives = 34/81 (41%), Gaps = 9/81 (11%)

Query: 16 IYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKG-------RSFGYVDFFPSSHKSLSK 68
          +++  L    T++ L  VFS +G +K+  I + K          FG+V++     +   K
Sbjct: 1  LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEY--KKPEQAQK 58

Query: 69 LFSTYNGCVWKGGRLRLERAK 89
                G    G +L +  ++
Sbjct: 59 ALKQLQGHTVDGHKLEVRISE 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 = 48.8 bits (116), Expect = 7e-08
 Identities = 18/79 (22%), Positives = 35/79 (44%), Gaps = 4/79 (5%)

Query: 12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFS 71
          +   +Y GG+   +TD  + + FS  G++  + +   KG SF       S+  ++  +  
Sbjct: 17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSV-- 74

Query: 72 TYNGCVWKGGRLRLERAKE 90
            NG   +G  ++    KE
Sbjct: 75 --NGTTIEGHVVKCYWGKE 91

>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 = 47.4 bits (112), Expect = 2e-07
 Identities = 11/84 (13%), Positives = 34/84 (40%), Gaps = 8/84 (9%)

Query: 15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK-------GRSFGYVDFFPSSHKSLS 67
          R+YVG +   +T++ +   F++   +  +              +   +      S    +
Sbjct: 3  RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 68 KLFSTYNGCVWKGGRLRLERAKEH 91
          +    ++G +++G  L++ R  ++
Sbjct: 63 QAM-AFDGIIFQGQSLKIRRPHDY 85

>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 = 47.3 bits (112), Expect = 2e-07
 Identities = 17/87 (19%), Positives = 36/87 (41%), Gaps = 6/87 (6%)

Query: 7  EAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVK----AVDIVRTKGRSFGYVDFFPSS 62
          E  +++   +YVG L    T++ + ++FS  G++K     +D ++     F +V++   S
Sbjct: 1  EKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEY--YS 58

Query: 63 HKSLSKLFSTYNGCVWKGGRLRLERAK 89
                     NG       +R +   
Sbjct: 59 RADAENAMRYINGTRLDDRIIRTDWDA 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 = 46.9 bits (111), Expect = 2e-07
 Identities = 21/81 (25%), Positives = 35/81 (43%), Gaps = 8/81 (9%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK----GRSFGYVDFFPSSHKSLSKL 69
          T +YV  L   +TDD L  +F   G +   +I+R K     R   +V +  +  +   + 
Sbjct: 7  TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRY--NKREEAQEA 64

Query: 70 FSTYNGCVWKGG--RLRLERA 88
           S  N  + +GG   L +  A
Sbjct: 65 ISALNNVIPEGGSQPLSVRLA 85

>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 = 46.7 bits (110), Expect = 3e-07
 Identities = 15/78 (19%), Positives = 28/78 (35%), Gaps = 3/78 (3%)

Query: 16 IYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT---KGRSFGYVDFFPSSHKSLSKLFST 72
          I++G L  ++ +  L   FS+ G +     +      G S GY     +S  +       
Sbjct: 1  IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 73 YNGCVWKGGRLRLERAKE 90
           NG       + +  A +
Sbjct: 61 MNGQYLCNRPITVSYAFK 78

>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 = 45.7 bits (108), Expect = 6e-07
 Identities = 17/83 (20%), Positives = 38/83 (45%), Gaps = 4/83 (4%)

Query: 7  EAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSL 66
          E    +++R++VG L   +T++++ K+F   G+   V I +   + FG++     +    
Sbjct: 2  EKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD--KGFGFIRL--ETRTLA 57

Query: 67 SKLFSTYNGCVWKGGRLRLERAK 89
                 +    +G +LR+  A 
Sbjct: 58 EIAKVELDNMPLRGKQLRVRFAC 80

>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 = 45.8 bits (108), Expect = 7e-07
 Identities = 18/90 (20%), Positives = 30/90 (33%), Gaps = 3/90 (3%)

Query: 1  MEKKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFP 60
          +E      +V     +    L   +T+D+L +VF    +   + +V   G+S G      
Sbjct: 4  LEDPCTSKKVRAARTLLAKNLSFNITEDELKEVFE---DALEIRLVSQDGKSKGIAYIEF 60

Query: 61 SSHKSLSKLFSTYNGCVWKGGRLRLERAKE 90
           S     K      G    G  + L    E
Sbjct: 61 KSEADAEKNLEEKQGAEIDGRSVSLYYTGE 90

>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 = 45.4 bits (107), Expect = 1e-06
 Identities = 19/86 (22%), Positives = 34/86 (39%), Gaps = 2/86 (2%)

Query: 8  AEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFP--SSHKS 65
          +E  +   +YVGGL EKV++  L ++F   G V    + + +         F    S + 
Sbjct: 4  SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEED 63

Query: 66 LSKLFSTYNGCVWKGGRLRLERAKEH 91
                  +     G  +R+ +A  H
Sbjct: 64 ADYAIKIMDMIKLYGKPIRVNKASAH 89

>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 = 45.1 bits (106), Expect = 1e-06
 Identities = 15/80 (18%), Positives = 34/80 (42%)

Query: 11 EEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLF 70
              R++V  +  +  D DL ++F   G++  V+I+  +  S G+      +     +  
Sbjct: 9  STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAR 68

Query: 71 STYNGCVWKGGRLRLERAKE 90
             +G V +G ++ +  A  
Sbjct: 69 EKLHGTVVEGRKIEVNNATA 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 = 44.9 bits (106), Expect = 2e-06
 Identities = 15/78 (19%), Positives = 34/78 (43%), Gaps = 7/78 (8%)

Query: 14 TRIYVGGLG-EKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFST 72
          +R+++G L    V   D+  +FS  G++    +     + F +V +   + ++     + 
Sbjct: 16 SRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH----KGFAFVQY--VNERNARAAVAG 69

Query: 73 YNGCVWKGGRLRLERAKE 90
           +G +  G  L +  A E
Sbjct: 70 EDGRMIAGQVLDINLAAE 87

>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 = 44.2 bits (104), Expect = 2e-06
 Identities = 13/84 (15%), Positives = 35/84 (41%), Gaps = 5/84 (5%)

Query: 7  EAEVEEQTR-IYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKS 65
          + +     + +YV  L    +++ + K F+++       + + +  +F +      + ++
Sbjct: 1  DEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEA 60

Query: 66 LSKLFSTYNGCVWKGGRLRLERAK 89
          +  L    NG V  G  + +  AK
Sbjct: 61 MKAL----NGKVLDGSPIEVTLAK 80

>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 = 43.2 bits (101), Expect = 5e-06
 Identities = 8/78 (10%), Positives = 21/78 (26%), Gaps = 2/78 (2%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGEVK--AVDIVRTKGRSFGYVDFFPSSHKSLSKLFS 71
            +++       T  ++  +   +  V             S  +     +S +       
Sbjct: 2  CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 61

Query: 72 TYNGCVWKGGRLRLERAK 89
            NG   +G  L  + + 
Sbjct: 62 KLNGLKIEGYTLVTKVSN 79

>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 = 43.1 bits (101), Expect = 5e-06
 Identities = 17/76 (22%), Positives = 34/76 (44%), Gaps = 5/76 (6%)

Query: 15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYN 74
          ++Y+G L   VT DDL ++F       A  ++   G  + +VD+         +   T +
Sbjct: 3  KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSG--YAFVDY--PDQNWAIRAIETLS 58

Query: 75 GCVWKGGR-LRLERAK 89
          G V   G+ + ++ + 
Sbjct: 59 GKVELHGKIMEVDYSV 74

>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 = 43.5 bits (102), Expect = 7e-06
 Identities = 13/81 (16%), Positives = 27/81 (33%), Gaps = 3/81 (3%)

Query: 11 EEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK-GRSFGYVDFFPSSHKSLSKL 69
          E    +Y+  L  K+T +++  +F   G ++ + +  T   R   YV +           
Sbjct: 5  EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVY--EDIFDAKNA 62

Query: 70 FSTYNGCVWKGGRLRLERAKE 90
              +G       L +     
Sbjct: 63 CDHLSGFNVCNRYLVVLYYNA 83

>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 = 42.3 bits (99), Expect = 7e-06
 Identities = 15/80 (18%), Positives = 36/80 (45%), Gaps = 6/80 (7%)

Query: 11 EEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLF 70
           +   +YV G    +T   L   FS  G +  + +   +  +F   +   S+ +++++L 
Sbjct: 3  RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAEL- 59

Query: 71 STYNGCVWKGGRLRLERAKE 90
             NG   +  +L++  A++
Sbjct: 60 ---NGTQVESVQLKVNIARK 76

>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 = 42.3 bits (99), Expect = 1e-05
 Identities = 15/79 (18%), Positives = 38/79 (48%), Gaps = 6/79 (7%)

Query: 15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVR----TKGRSFGYVDFFPSSHKSLSKLF 70
          ++++GGL   + DD + ++ +S G +KA ++V+       + + + ++         +  
Sbjct: 3  KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEY--VDINVTDQAI 60

Query: 71 STYNGCVWKGGRLRLERAK 89
          +  NG      +L ++RA 
Sbjct: 61 AGLNGMQLGDKKLLVQRAS 79

>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 = 42.3 bits (99), Expect = 1e-05
 Identities = 16/81 (19%), Positives = 34/81 (41%)

Query: 9  EVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSK 68
          +  +   +YVG L   VT+  + ++FS +G  K+  ++     +  Y       H+  + 
Sbjct: 4  DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAA 63

Query: 69 LFSTYNGCVWKGGRLRLERAK 89
            +  NG    G  +++  A 
Sbjct: 64 ALAAMNGRKILGKEVKVNWAT 84

>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 = 42.3 bits (99), Expect = 1e-05
 Identities = 16/81 (19%), Positives = 34/81 (41%), Gaps = 2/81 (2%)

Query: 11 EEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKG--RSFGYVDFFPSSHKSLSK 68
          ++   I V  L E   + DL ++F   G +  + + + K   +S G+        +  ++
Sbjct: 6  DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAAR 65

Query: 69 LFSTYNGCVWKGGRLRLERAK 89
            +  +G  +    L +E AK
Sbjct: 66 AIAGVSGFGYDHLILNVEWAK 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 = 42.4 bits (99), Expect = 1e-05
 Identities = 17/81 (20%), Positives = 34/81 (41%), Gaps = 2/81 (2%)

Query: 12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEV--KAVDIVRTKGRSFGYVDFFPSSHKSLSKL 69
          E   ++V  + E+  +D++ + F   GE+    +++ R  G S GY      +HK     
Sbjct: 6  EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 65

Query: 70 FSTYNGCVWKGGRLRLERAKE 90
              NG    G  ++++    
Sbjct: 66 KEALNGAEIMGQTIQVDWCFV 86

>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 = 42.7 bits (100), Expect = 1e-05
 Identities = 22/100 (22%), Positives = 42/100 (42%), Gaps = 14/100 (14%)

Query: 1  MEK-------KEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK---- 49
          MEK       +  + E E+  ++++GGL  + T++ L   +   G++    ++R      
Sbjct: 1  MEKTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKR 60

Query: 50 GRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAK 89
           R FG+V F  SS   +    +        G  +  +RA 
Sbjct: 61 SRGFGFVTF--SSMAEVDAAMAA-RPHSIDGRVVEPKRAV 97

>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 = 42.3 bits (99), Expect = 1e-05
 Identities = 16/91 (17%), Positives = 34/91 (37%), Gaps = 7/91 (7%)

Query: 3  KKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVR----TKGRSFGYVDF 58
                E  +   ++   L  ++   DL   FS++G+V+ V I+      + +   YV+F
Sbjct: 8  VDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEF 67

Query: 59 FPSSHKSLSKLFSTYNGCVWKGGRLRLERAK 89
                    L     G    G  + ++ ++
Sbjct: 68 ---CEIQSVPLAIGLTGQRLLGVPIIVQASQ 95

>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 = 41.6 bits (97), Expect = 2e-05
 Identities = 18/79 (22%), Positives = 36/79 (45%), Gaps = 2/79 (2%)

Query: 13 QTRIYVGGLGEKVTDDDLAKVFSSLGEV--KAVDIVRTKGRSFGYVDFFPSSHKSLSKLF 70
          +T + V  L + +T ++   +F S+GE+    +   +  G+S GY        K   K  
Sbjct: 2  KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61

Query: 71 STYNGCVWKGGRLRLERAK 89
          +T NG   +   +++  A+
Sbjct: 62 NTLNGLRLQTKTIKVSYAR 80

>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 = 41.2 bits (96), Expect = 2e-05
 Identities = 15/75 (20%), Positives = 27/75 (36%), Gaps = 2/75 (2%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGEVK--AVDIVRTKGRSFGYVDFFPSSHKSLSKLFS 71
            +YV GL + +T  +L ++FS  G +    + + +  G S G             +   
Sbjct: 7  ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 66

Query: 72 TYNGCVWKGGRLRLE 86
            NG    G    + 
Sbjct: 67 GLNGQKPSGATEPIT 81

>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 = 41.7 bits (97), Expect = 2e-05
 Identities = 22/92 (23%), Positives = 37/92 (40%), Gaps = 10/92 (10%)

Query: 9  EVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV----------RTKGRSFGYVDF 58
          E  + + IYV GL + VT DDLA  F   G VK               +  G+  G    
Sbjct: 4  EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATV 63

Query: 59 FPSSHKSLSKLFSTYNGCVWKGGRLRLERAKE 90
                +       ++G  ++G +L++  A++
Sbjct: 64 SYEDPPTAKAAVEWFDGKDFQGSKLKVSLARK 95

>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 = 41.2 bits (96), Expect = 2e-05
 Identities = 18/84 (21%), Positives = 33/84 (39%), Gaps = 7/84 (8%)

Query: 9  EVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK----GRSFGYVDFFPSSHK 64
          E E+  ++++GGL  + TD+ L   F   G +    ++R       R FG+V +   +  
Sbjct: 2  EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY---ATV 58

Query: 65 SLSKLFSTYNGCVWKGGRLRLERA 88
                         G  +  +RA
Sbjct: 59 EEVDAAMNARPHKVDGRVVEPKRA 82

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.3 bits (94), Expect = 4e-05
 Identities = 18/78 (23%), Positives = 34/78 (43%), Gaps = 7/78 (8%)

Query: 15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK--GRSFG--YVDFFPSSHKSLSKLF 70
          ++++GGL  + T + L + F   GEVK   ++R     RS G  +V F       + K+ 
Sbjct: 2  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF--MDQAGVDKVL 59

Query: 71 STYNGCVWKGGRLRLERA 88
          +  +        +  + A
Sbjct: 60 A-QSRHELDSKTIDPKVA 76

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.6 bits (92), Expect = 8e-05
 Identities = 12/48 (25%), Positives = 25/48 (52%), Gaps = 4/48 (8%)

Query: 15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKG----RSFGYVDF 58
          +I+VGGL     ++ + + F   GEV+++++         R F ++ F
Sbjct: 1  KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITF 48

>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 = 40.0 bits (93), Expect = 9e-05
 Identities = 17/78 (21%), Positives = 29/78 (37%), Gaps = 4/78 (5%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTY 73
           RI V  L   VT D L ++FS  G V  +       +    + +  +   S      + 
Sbjct: 8  LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQY--ADPVSAQHAKLSL 65

Query: 74 NGCVW--KGGRLRLERAK 89
          +G         LR++ +K
Sbjct: 66 DGQNIYNACCTLRIDFSK 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 = 39.3 bits (91), Expect = 1e-04
 Identities = 22/81 (27%), Positives = 34/81 (41%), Gaps = 6/81 (7%)

Query: 13 QTRIYVGGLGEKVTDDDLAKVFSSLGEVK----AVDIVRTKGRSFGYVDFFPSSHKSLSK 68
          +  +YVGGL E+V D  L   F   G++      +D    K R F +V+F     +  + 
Sbjct: 5  KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF--ELAEDAAA 62

Query: 69 LFSTYNGCVWKGGRLRLERAK 89
               N     G  +R+  AK
Sbjct: 63 AIDNMNESELFGRTIRVNLAK 83

>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 = 39.3 bits (91), Expect = 2e-04
 Identities = 17/81 (20%), Positives = 36/81 (44%), Gaps = 6/81 (7%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK----GRSFGYVDFFPSSHKSLSKL 69
           R++V  L    +++DL K+FS+ G +  +           + F +V F     +   K 
Sbjct: 9  GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTF--MFPEHAVKA 66

Query: 70 FSTYNGCVWKGGRLRLERAKE 90
          ++  +G V++G  L +  +  
Sbjct: 67 YAEVDGQVFQGRMLHVLPSTI 87

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.9 bits (90), Expect = 2e-04
 Identities = 12/92 (13%), Positives = 35/92 (38%), Gaps = 5/92 (5%)

Query: 7  EAEVEEQTRIYVGGLGE-KVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKS 65
          +  VE +  +++      K     L ++    G +    I+     +F  +     +  +
Sbjct: 2  KGRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAA 61

Query: 66 LSKLFSTYNGCVWKGGRLRLERAKEHYLARLK 97
          +   + T    +  G  +R+  ++++   R+K
Sbjct: 62 VD--YYTTTPALVFGKPVRVHLSQKY--KRIK 89

>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 = 41.1 bits (95), Expect = 2e-04
 Identities = 15/72 (20%), Positives = 31/72 (43%), Gaps = 2/72 (2%)

Query: 9  EVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK--GRSFGYVDFFPSSHKSL 66
          E E+  ++++GGL  + TD+ L   F   G +    ++R     RS G+     ++ + +
Sbjct: 2  EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 61

Query: 67 SKLFSTYNGCVW 78
              +     V 
Sbjct: 62 DAAMNARPHKVD 73

>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 = 38.9 bits (90), Expect = 2e-04
 Identities = 17/87 (19%), Positives = 34/87 (39%), Gaps = 2/87 (2%)

Query: 6  AEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEV--KAVDIVRTKGRSFGYVDFFPSSH 63
          ++ E  E   +++  L ++  D DL ++F   G V    V I +    S  +      + 
Sbjct: 11 SQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNP 70

Query: 64 KSLSKLFSTYNGCVWKGGRLRLERAKE 90
           S      + NG      RL+++  + 
Sbjct: 71 VSAQAAIQSMNGFQIGMKRLKVQLKRS 97

>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 = 39.0 bits (90), Expect = 2e-04
 Identities = 20/82 (24%), Positives = 30/82 (36%), Gaps = 2/82 (2%)

Query: 11 EEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RTKGRSFGYVDFFPSSHKSLSK 68
          E    +Y+  L  +VT+ DL  +F+   E K   I      GR  G       + +   +
Sbjct: 16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQ 75

Query: 69 LFSTYNGCVWKGGRLRLERAKE 90
               NG    G  L +E  K 
Sbjct: 76 ALHLVNGYKLYGKILVIEFGKN 97

>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 = 37.9 bits (87), Expect = 3e-04
 Identities = 11/75 (14%), Positives = 25/75 (33%), Gaps = 1/75 (1%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTY 73
          T + V  L +    + + K F   G +  VD+  +  ++F +      +    +    T 
Sbjct: 1  TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFA-RIEFARYDGALAAITK 59

Query: 74 NGCVWKGGRLRLERA 88
             V     + +   
Sbjct: 60 THKVVGQNEIIVSHL 74

>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 = 38.3 bits (88), Expect = 3e-04
 Identities = 13/83 (15%), Positives = 29/83 (34%), Gaps = 8/83 (9%)

Query: 10 VEEQTRIYVGGLGEKVTDDDLAKVF---SSLGEVKAVDIVRTKGRSF-----GYVDFFPS 61
          V ++  ++V GL +++ D ++ K        G++  V I  +   +              
Sbjct: 5  VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYI 64

Query: 62 SHKSLSKLFSTYNGCVWKGGRLR 84
            +   +     N  V  G  L+
Sbjct: 65 RSEDALRAIQCVNNVVVDGRTLK 87

>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 = 37.8 bits (87), Expect = 3e-04
 Identities = 20/78 (25%), Positives = 30/78 (38%), Gaps = 6/78 (7%)

Query: 11 EEQTRIYVGGLGEKVTDDDLAKVFSSLGEVK----AVDIVRTKGRSFGYVDFFPSSHKSL 66
          +    + V GL    T+ DL +VFS  G +       D    + R F +V F   +    
Sbjct: 7  DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF--ENVDDA 64

Query: 67 SKLFSTYNGCVWKGGRLR 84
           +     NG    G R+R
Sbjct: 65 KEAKERANGMELDGRRIR 82

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.7 bits (87), Expect = 4e-04
 Identities = 22/78 (28%), Positives = 35/78 (44%), Gaps = 7/78 (8%)

Query: 15 RIYVGGLGEKVTDDDLAKVFSSLGEV----KAVDIVRTKGRSFGYVDFFPSSHKSLSKLF 70
          ++++GGL    T  DL   FS  GEV      +D +  + R FG+V F     +S+ K+ 
Sbjct: 1  KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLF--KESESVDKVM 58

Query: 71 STYNGCVWKGGRLRLERA 88
                   G  +  +RA
Sbjct: 59 DQ-KEHKLNGKVIDPKRA 75

>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 = 37.7 bits (87), Expect = 6e-04
 Identities = 11/89 (12%), Positives = 29/89 (32%), Gaps = 5/89 (5%)

Query: 1   MEKKEAEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT---KGRSFGYVD 57
              + A+      + + +    ++  ++   ++    GEV+ +++            YV 
Sbjct: 15  NSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVK 74

Query: 58  FFPSSHKSLSKLFSTYNGCVWKGGRLRLE 86
           F     +   K     N   + G  +  E
Sbjct: 75  F--RREEDAEKAVIDLNNRWFNGQPIHAE 101

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.2 bits (86), Expect = 6e-04
 Identities = 11/66 (16%), Positives = 24/66 (36%), Gaps = 5/66 (7%)

Query: 12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDF--FPSSHKSLSKL 69
          + T + V G  +      L   F+  G +    +  T    + ++ +     + K+LSK 
Sbjct: 3  DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNTGN--WMHIRYQSKLQARKALSKD 59

Query: 70 FSTYNG 75
             +  
Sbjct: 60 GRIFGE 65

>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 = 37.0 bits (85), Expect = 7e-04
 Identities = 13/79 (16%), Positives = 29/79 (36%), Gaps = 9/79 (11%)

Query: 15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFF-----PSSHKSLSKL 69
          +I+VGGL    T +D+   F   G+V    ++  K  +      F         + + ++
Sbjct: 1  KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 70 FSTYNGCVWKGGRLRLERA 88
              +        +  ++A
Sbjct: 61 ----HFHEINNKMVECKKA 75

>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 = 37.0 bits (85), Expect = 0.001
 Identities = 15/80 (18%), Positives = 28/80 (35%), Gaps = 3/80 (3%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGE---VKAVDIVRTKGRSFGYVDFFPSSHKSLSKLF 70
            IY+  L EK+  D+L K   ++          +V    +  G          S +   
Sbjct: 4  HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 63

Query: 71 STYNGCVWKGGRLRLERAKE 90
           +  G  +    +R++ AK 
Sbjct: 64 RSMQGFPFYDKPMRIQYAKT 83

>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 = 36.5 bits (84), Expect = 0.001
 Identities = 19/77 (24%), Positives = 36/77 (46%), Gaps = 5/77 (6%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTY 73
          + ++VG     +T+D+L + FS  G+V  V I +   R+F +V F  +  +    L    
Sbjct: 6  SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF-RAFAFVTF--ADDQIAQSLCG-- 60

Query: 74 NGCVWKGGRLRLERAKE 90
             + KG  + +  A+ 
Sbjct: 61 EDLIIKGISVHISNAEP 77

>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 = 36.5 bits (83), Expect = 0.001
 Identities = 16/83 (19%), Positives = 31/83 (37%), Gaps = 2/83 (2%)

Query: 8  AEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK-GRSFGYVDFFPSSHKSL 66
          +E      +++G L    +  +L    S L     + +V  + G +  +      S + L
Sbjct: 8  SESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDL 67

Query: 67 SKLFSTYNGCVWKGGRLRLERAK 89
           K      G    G  ++LE+ K
Sbjct: 68 EKAL-ELTGLKVFGNEIKLEKPK 89

>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 = 36.2 bits (83), Expect = 0.001
 Identities = 11/77 (14%), Positives = 22/77 (28%), Gaps = 2/77 (2%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTK--GRSFGYVDFFPSSHKSLSKLFS 71
          T I V  +   V+ D++   F     +     ++    G   G       S    +    
Sbjct: 10 TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 69

Query: 72 TYNGCVWKGGRLRLERA 88
            N       +++L   
Sbjct: 70 DLNDRPIGSRKVKLVLG 86

>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 = 36.6 bits (84), Expect = 0.001
 Identities = 21/78 (26%), Positives = 39/78 (50%), Gaps = 6/78 (7%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTY 73
          TR++VGGLG   +   LA+ F   G ++ +D V+    ++   +   ++  + +K+    
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKM---- 73

Query: 74 NGCVWKGG--RLRLERAK 89
           G    G   RLR++ AK
Sbjct: 74 RGFPLGGPDRRLRVDFAK 91

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.3 bits (83), Expect = 0.002
 Identities = 21/83 (25%), Positives = 37/83 (44%), Gaps = 6/83 (7%)

Query: 12 EQTRIYVGGLGEKVTDDDLAKVFSSLG----EVKAVDIVRTKGRSFGYVDFFPSSHKSLS 67
          ++ +++VGGL     +  L +VFS  G     V   D    + R FG+V F   +     
Sbjct: 4  DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTF--ENIDDAK 61

Query: 68 KLFSTYNGCVWKGGRLRLERAKE 90
                NG    G ++R+++A +
Sbjct: 62 DAMMAMNGKSVDGRQIRVDQAGK 84

>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 = 36.2 bits (83), Expect = 0.002
 Identities = 10/82 (12%), Positives = 33/82 (40%), Gaps = 6/82 (7%)

Query: 14 TRIYVGGLGEKVTDDDLAKVFSSLG----EVKAVDIVRTKGRSFGYVDFFPSSHKSLSKL 69
           R+++GG+ +    +++ +  + +     +V        K ++ G+      SH++ +  
Sbjct: 2  CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 61

Query: 70 FSTYNG--CVWKGGRLRLERAK 89
                      G ++ ++ A+
Sbjct: 62 RRKLMPGRIQLWGHQIAVDWAE 83

>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 = 36.5 bits (83), Expect = 0.002
 Identities = 14/97 (14%), Positives = 25/97 (25%), Gaps = 4/97 (4%)

Query: 14  TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTY 73
           T I    L       ++ + FS  G +  V +      +         + K+   L    
Sbjct: 11  TVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHL---- 66

Query: 74  NGCVWKGGRLRLERAKEHYLARLKREWAEDDAQLVNP 110
               +    L LE A         ++      Q    
Sbjct: 67  AYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEK 103

>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 = 35.9 bits (82), Expect = 0.003
 Identities = 22/107 (20%), Positives = 41/107 (38%), Gaps = 8/107 (7%)

Query: 8   AEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKA--VDIVRTKGRSFGYVDFFPSSHKS 65
           A       ++VG +  + T++ L  +FS +G V +  +   R  G+  GY        ++
Sbjct: 3   AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQET 62

Query: 66  LSKLFSTYNGCVWKGGRLRLERAKEHYLARLKREWAEDDAQLVNPPV 112
                   NG  + G  LR++ A        ++   E  +     PV
Sbjct: 63  ALSAMRNLNGREFSGRALRVDNAAS------EKNKEELKSLGTGAPV 103

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	800
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.83
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.73
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.72
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.71
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.71
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.7
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.7
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.69
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.69
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.69
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.69
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.69
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.69
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.69
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.68
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.68
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.68
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.68
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.67
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.67
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.66
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.66
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.66
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.66
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.66
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.65
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.65
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.65
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.65
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.65
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.64
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.63
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.63
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.63
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.63
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.63
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.63
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.62
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.62
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.62
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.62
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.62
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.62
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.61
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.61
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.61
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.61
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.6
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.6
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.59
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.59
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.58
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.58
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.58
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.57
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.57
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.57
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.56
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.56
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.56
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.56
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.55
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.55
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.55
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.55
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.55
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.55
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.54
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.52
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.51
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.5
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.5
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.5
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.49
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.49
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.48
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.48
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.48
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.44
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.43
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.43
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.36
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.3
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.27
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
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.17
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.91
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	97.82
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	97.8
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	97.75
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	97.69
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	97.67
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	97.66
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	97.65
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	97.63
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	97.62
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	97.59
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	97.58
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	97.58
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	97.56
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	97.52
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	97.5
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	97.46
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	97.43
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	97.42
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	97.41
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	97.41
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	97.39
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	97.39
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	97.39
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	97.37
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	97.37
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	97.31
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	97.3
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	97.29
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	97.25
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	97.2
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	97.17
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	97.16
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	97.11
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	97.1
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	97.03
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	97.02
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	96.98
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	96.98
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	96.96
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	96.81
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	96.78
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	96.74
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	96.68
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	96.68
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	96.67
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	96.64
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	96.61
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	96.61
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	96.6
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	96.53
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	96.48
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	96.46
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	96.46
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	96.44
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	96.43
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	96.4
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	96.36
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	96.34
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	96.31
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	96.29
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	96.27
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	96.25
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	96.18
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	96.11
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	96.11
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	95.95
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	95.9
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	95.86
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	95.86
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	95.85
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	95.83
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	95.81
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	95.8
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	95.76
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	95.65
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	95.41
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	95.39
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	95.07
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	94.97
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	94.44
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	94.34
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	94.27
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	94.01
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	92.02
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	91.7
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	89.83
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	89.26
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	83.44

>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=99.83  E-value=2.1e-20  Score=138.64  Aligned_cols=165  Identities=18%  Similarity=0.274  Sum_probs=124.2

Q ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC--CC--CCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEE
Q ss_conf             057849999079988998899985303896249999656--99--76799993689988999999845994767937799
Q 003717           10 VEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--KG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRL   85 (800)
Q Consensus        10 v~q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd--TG--RGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkV   85 (800)
                      .++.++|||||||+.+++++|+++|++||.|..+.++++  ++  +|||||+|.+  .++|.+|+.. ++..+.++.+.+
T Consensus         3 p~~~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~--~~~a~~a~~~-~~~~~~~~~~~~   79 (183)
T d1u1qa_           3 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYAT--VEEVDAAMNA-RPHKVDGRVVEP   79 (183)
T ss_dssp             CHHHHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESS--HHHHHHHHHT-CSCEETTEECEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEEECCCCCCCCCCEECCCCC--HHHHHHHHHH-CCCCCCCCCHHH
T ss_conf             8889789997989989899999999873987899864112478855743220488--8999999984-577641110233


Q ss_pred             EECCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCEE---EECCCCCCCCC-
Q ss_conf             74240136887654888865217999989889999873347998888885200001146764236---60158999721-
Q 003717           86 ERAKEHYLARLKREWAEDDAQLVNPPVTDSVAPDNKDATRLDTPKKLLDKDKKLNIFFPRLRKVK---TLPFCGTGKHK-  161 (800)
Q Consensus        86 e~AkPk~l~R~krErkeakakk~~sp~sDsvd~q~pkl~is~~Lk~svsesd~LreyFskyGKVK---sVp~kgTGK~K-  161 (800)
                      ....+.....       .          .........+++.+ |+..+++ +.|+.+|..||.|.   +++++.+|+.+ 
T Consensus        80 ~~~~~~~~~~-------~----------~~~~~~~~~i~V~~-lp~~~te-~~L~~~f~~~G~v~~~~i~~~~~~~~~~g  140 (183)
T d1u1qa_          80 KRAVSREDSQ-------R----------PGAHLTVKKIFVGG-IKEDTEE-HHLRDYFEQYGKIEVIEIMTDRGSGKKRG  140 (183)
T ss_dssp             EECCCTTGGG-------S----------TTTTCCCSEEEEEC-CCTTCCH-HHHHHHHGGGSCEEEEEEEECTTTCCEEE
T ss_pred             HHHHHCCCCC-------C----------CCCCCCCCEEEECC-CCCCCCH-HHHHHHHCCCCCEEEEEEECCCCCCCCCE
T ss_conf             3322112311-------0----------11345642358816-7776789-99965431588653223300266685010


Q ss_pred             CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCHHHH
Q ss_conf             111333689999643441021235464146810268998632102110
Q 003717          162 YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPAAGQEEIHDMEE  209 (800)
Q Consensus       162 YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n~~q~~i~~~ee  209 (800)
                      |+|         |.|.+.+++..|+. +++.   ..+|.++.|+.+.+
T Consensus       141 ~~f---------V~f~~~e~A~~Al~-~~~~---~~~G~~i~V~~A~~  175 (183)
T d1u1qa_         141 FAF---------VTFDDHDSVDKIVI-QKYH---TVNGHNCEVRKALS  175 (183)
T ss_dssp             EEE---------EEESCHHHHHHHHT-SSCE---EETTEEEEEEECCC
T ss_pred             EEE---------EEECCHHHHHHHHH-HCCC---EECCEEEEEEECCC
T ss_conf             599---------99789999999998-5999---09997979996688

>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=99.73  E-value=1.3e-17  Score=121.76  Aligned_cols=81  Identities=23%  Similarity=0.366  Sum_probs=73.2

Q ss_pred             HCCCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC--CC--CCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEE
Q ss_conf             0057849999079988998899985303896249999656--99--7679999368998899999984599476793779
Q 003717            9 EVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--KG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLR   84 (800)
Q Consensus         9 Ev~q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd--TG--RGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLk   84 (800)
                      +....++|||||||+++++++|+++|++||.|.++.|+++  ++  ||||||+|.+  .++|..|+..|||..|+||+|+
T Consensus        38 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~--~~~A~~Ai~~lng~~~~gr~l~  115 (139)
T d1u6fa1          38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQS--GSSAQQAIAGLNGFNILNKRLK  115 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESS--HHHHHHHHHHTTTEECSSCEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEECC--HHHHHHHHHHHCCCEECCEEEE
T ss_conf             99999889996979889999999999765003221111221111122203689799--9999999998489888998889


Q ss_pred             EEECCCH
Q ss_conf             9742401
Q 003717           85 LERAKEH   91 (800)
Q Consensus        85 Ve~AkPk   91 (800)
                      |.+|+++
T Consensus       116 V~~a~~~  122 (139)
T d1u6fa1         116 VALAASG  122 (139)
T ss_dssp             EEESSCC
T ss_pred             EEECCCC
T ss_conf             9876888

>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=99.72  E-value=3.2e-17  Score=119.34  Aligned_cols=80  Identities=21%  Similarity=0.432  Sum_probs=73.9

Q ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC--CCCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEEC
Q ss_conf             57849999079988998899985303896249999656--9976799993689988999999845994767937799742
Q 003717           11 EEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--KGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERA   88 (800)
Q Consensus        11 ~q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd--TGRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~A   88 (800)
                      ...++|||+|||+.+++++|+++|++||+|..|.++++  ..+|||||+|.+  .++|.+|+..|||..|+||+|+|++|
T Consensus         9 ~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~--~~~a~~Ai~~l~~~~~~g~~l~V~~A   86 (93)
T d2cq3a1           9 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFEN--SADADRAREKLHGTVVEGRKIEVNNA   86 (93)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESC--HHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHCCEEEECCCCCCCCCCCCEEEEEECC--HHHHHHHHHHCCCCEECCEEEEEEEC
T ss_conf             9999899979899899999999986344330001125666774023789889--99999999981999899988899865


Q ss_pred             CCHH
Q ss_conf             4013
Q 003717           89 KEHY   92 (800)
Q Consensus        89 kPk~   92 (800)
                      +++.
T Consensus        87 ~~r~   90 (93)
T d2cq3a1          87 TARV   90 (93)
T ss_dssp             CSSC
T ss_pred             CCCC
T ss_conf             7579

>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=99.71  E-value=2e-17  Score=120.55  Aligned_cols=82  Identities=21%  Similarity=0.458  Sum_probs=74.4

Q ss_pred             HCCCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC--CCCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEE
Q ss_conf             0057849999079988998899985303896249999656--99767999936899889999998459947679377997
Q 003717            9 EVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--KGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLE   86 (800)
Q Consensus         9 Ev~q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd--TGRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe   86 (800)
                      +....++|||||||+.+++++|+++|++||.|..|.++++  +++|||||+|.+  .++|..|+..|||..|.|+.|+|.
T Consensus         4 d~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~--~~~A~~A~~~l~~~~~~g~~i~v~   81 (90)
T d2cqia1           4 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYE--HRDAAAALAAMNGRKILGKEVKVN   81 (90)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESS--HHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHCCCCEEEEEECCCCCCCEEEEEEECC--HHHHHHHHHHCCCCEECCEEEEEE
T ss_conf             789999999989999798999999997639943664412667641002888889--999999999819998999988999


Q ss_pred             ECCCHH
Q ss_conf             424013
Q 003717           87 RAKEHY   92 (800)
Q Consensus        87 ~AkPk~   92 (800)
                      +|++..
T Consensus        82 ~a~~~~   87 (90)
T d2cqia1          82 WATTPS   87 (90)
T ss_dssp             ECCCTT
T ss_pred             ECCCCC
T ss_conf             768977

>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=99.71  E-value=2.2e-17  Score=120.34  Aligned_cols=82  Identities=26%  Similarity=0.498  Sum_probs=74.2

Q ss_pred             HCCCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC--CC--CCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEE
Q ss_conf             0057849999079988998899985303896249999656--99--7679999368998899999984599476793779
Q 003717            9 EVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--KG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLR   84 (800)
Q Consensus         9 Ev~q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd--TG--RGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLk   84 (800)
                      +....++|||||||+.+++++|+++|++||.|.++.++++  ++  ||||||+|.+  .++|.+|+..|||..|+||.|+
T Consensus         5 ~~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~--~~~A~~Ai~~l~g~~~~g~~l~   82 (93)
T d1x5ua1           5 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLS--EEDADYAIKIMDMIKLYGKPIR   82 (93)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESS--HHHHHHHHHHSSSCBCSSCBCE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCCCEEECCCCCCCCCCEEEEECC--HHHHHHHHHHCCCCEECCEEEE
T ss_conf             67999899990899858899999999984976542121012543566520799899--9999999998599989998879


Q ss_pred             EEECCCHH
Q ss_conf             97424013
Q 003717           85 LERAKEHY   92 (800)
Q Consensus        85 Ve~AkPk~   92 (800)
                      |.+|+++.
T Consensus        83 V~~A~~~~   90 (93)
T d1x5ua1          83 VNKASAHN   90 (93)
T ss_dssp             EEETTTTS
T ss_pred             EEECCCCC
T ss_conf             98728989

>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=99.70  E-value=7.7e-17  Score=117.04  Aligned_cols=78  Identities=15%  Similarity=0.227  Sum_probs=72.1

Q ss_pred             CCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC-CCCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEECCC
Q ss_conf             7849999079988998899985303896249999656-997679999368998899999984599476793779974240
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT-KGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKE   90 (800)
Q Consensus        12 q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd-TGRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~AkP   90 (800)
                      ..++|||||||+.+++++|+++|++||.|.+|++.++ ..+|||||+|.+  .++|..|+..|||..|+||.|+|.+|.+
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 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYED--IFDAKNACDHLSGFNVCNRYLVVLYYNA   83 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTEEEEEESS--HHHHHHHHHHHTTCEETTEECEEEECCH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHCCCEEEECCCCCCCCCCEEEEEECC--HHHHHHHHHHHCCCEECCEEEEEEECCC
T ss_conf             99999997999989899999998526986760123467767769999788--9999999998289988998889998478


Q ss_pred             H
Q ss_conf             1
Q 003717           91 H   91 (800)
Q Consensus        91 k   91 (800)
                      .
T Consensus        84 ~   84 (114)
T d2f9da1          84 N   84 (114)
T ss_dssp             H
T ss_pred             C
T ss_conf             7

>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=99.70  E-value=4.2e-17  Score=118.63  Aligned_cols=78  Identities=19%  Similarity=0.406  Sum_probs=70.8

Q ss_pred             CCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC--C--CCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEE
Q ss_conf             7849999079988998899985303896249999656--9--97679999368998899999984599476793779974
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--K--GRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLER   87 (800)
Q Consensus        12 q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd--T--GRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~   87 (800)
                      +.++|||||||+.+++++|+++|++||.|..+.++++  +  .+|||||+|.+  .++|.+|+. +++..|+||.|.|.+
T Consensus        19 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~--~~~a~~al~-~~~~~l~G~~i~V~~   95 (103)
T d1x4ba1          19 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSS--MAEVDAAMA-ARPHSIDGRVVEPKR   95 (103)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSS--HHHHHHHHT-SCSEEETTEEEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEECCCCCCCCCCCEEEEEECC--HHHHHHHHH-HCCCEECCEEEEEEE
T ss_conf             89889995999858899999999761866300001235677755769999787--999999998-498959997979887


Q ss_pred             CCCHH
Q ss_conf             24013
Q 003717           88 AKEHY   92 (800)
Q Consensus        88 AkPk~   92 (800)
                      |.++.
T Consensus        96 a~~ke  100 (103)
T d1x4ba1          96 AVARE  100 (103)
T ss_dssp             CSSCC
T ss_pred             CCCCC
T ss_conf             74068

>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=7.4e-17  Score=117.16  Aligned_cols=79  Identities=20%  Similarity=0.432  Sum_probs=72.8

Q ss_pred             CCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC--CC--CCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEE
Q ss_conf             7849999079988998899985303896249999656--99--7679999368998899999984599476793779974
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--KG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLER   87 (800)
Q Consensus        12 q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd--TG--RGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~   87 (800)
                      ...+|||+|||+.+++++|+++|++||.|..+.++++  ++  ||||||+|.+  .++|.+|+..|||..++|++|+|.+
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~~   84 (90)
T d2cq0a1           7 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHR--REDAARAIAGVSGFGYDHLILNVEW   84 (90)
T ss_dssp             SSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESS--HHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEEECC--HHHHHHHHHHHCCCEECCEEEEEEE
T ss_conf             99999997999879899999999875623321111135544666320589899--9999999998289989998989986


Q ss_pred             CCCHH
Q ss_conf             24013
Q 003717           88 AKEHY   92 (800)
Q Consensus        88 AkPk~   92 (800)
                      |+|+.
T Consensus        85 akp~~   89 (90)
T d2cq0a1          85 AKPST   89 (90)
T ss_dssp             SSCCC
T ss_pred             EECCC
T ss_conf             34889

>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=99.69  E-value=6.2e-17  Score=117.64  Aligned_cols=79  Identities=20%  Similarity=0.378  Sum_probs=72.4

Q ss_pred             CCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC--CC--CCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEE
Q ss_conf             7849999079988998899985303896249999656--99--7679999368998899999984599476793779974
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--KG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLER   87 (800)
Q Consensus        12 q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd--TG--RGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~   87 (800)
                      ..++|||+|||+.+++++|+++|++||.|.++.++++  ++  ||||||+|.+  .++|..|+..|||..|.|++|+|.+
T Consensus        17 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~--~~~A~~Ai~~lng~~~~g~~i~V~~   94 (102)
T d2cpza1          17 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDN--PVSAQAAIQSMNGFQIGMKRLKVQL   94 (102)
T ss_dssp             TTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSS--HHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHHCCCCCCCEEEECCCCCCCCCEEEEECC--HHHHHHHHHHHCCCEECCEEEEEEE
T ss_conf             99999995999999999999999763345432100001369876533887489--9999999998589988999889987


Q ss_pred             CCCHH
Q ss_conf             24013
Q 003717           88 AKEHY   92 (800)
Q Consensus        88 AkPk~   92 (800)
                      |+++.
T Consensus        95 a~~k~   99 (102)
T d2cpza1          95 KRSKN   99 (102)
T ss_dssp             CCCSC
T ss_pred             ECCCC
T ss_conf             07888

>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=99.69  E-value=8.2e-17  Score=116.88  Aligned_cols=76  Identities=25%  Similarity=0.484  Sum_probs=71.0

Q ss_pred             CCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC--CC--CCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEEC
Q ss_conf             849999079988998899985303896249999656--99--76799993689988999999845994767937799742
Q 003717           13 QTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--KG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERA   88 (800)
Q Consensus        13 ~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd--TG--RGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~A   88 (800)
                      .++|||+|||+.+++++|+++|++||.|..+.++++  ++  +|||||+|.+  .++|.+|+..|||..++|++|+|.+|
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~--~~~A~~ai~~lng~~~~g~~l~v~~a   79 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTS--EMDSQRAIKVLNGITVRNKRLKVSYA   79 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESS--HHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCCEEEECC--HHHHHHHHHHHCCCEECCEEEEEEEC
T ss_conf             9999996979979899999999985981466466320368864224379899--99999999986899899999899971


Q ss_pred             CC
Q ss_conf             40
Q 003717           89 KE   90 (800)
Q Consensus        89 kP   90 (800)
                      +|
T Consensus        80 ~p   81 (82)
T d1b7fa1          80 RP   81 (82)
T ss_dssp             CC
T ss_pred             CC
T ss_conf             89

>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=99.69  E-value=5.9e-17  Score=117.76  Aligned_cols=79  Identities=18%  Similarity=0.409  Sum_probs=72.9

Q ss_pred             CCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC--CCCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEECC
Q ss_conf             7849999079988998899985303896249999656--99767999936899889999998459947679377997424
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--KGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAK   89 (800)
Q Consensus        12 q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd--TGRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~Ak   89 (800)
                      ...+|||+|||+.+++++|+++|++||.|..+.++++  +++|||||+|.+  .++|.+|+..|||..|+|++|+|.+|+
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~kg~afV~f~~--~~~A~~Ai~~l~g~~~~g~~i~V~~a~   84 (89)
T d1cvja2           7 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFET--QEAAERAIEKMNGMLLNDRKVFVGRFK   84 (89)
T ss_dssp             TTTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTBCCSCEEEEESC--HHHHHHHTTSSSEEEETTEEEEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHCCCCEEEEEEEECCCCCCEEEEEECC--HHHHHHHHHHCCCCEECCEEEEEEECC
T ss_conf             998899928999999999999998639960799985047874033799899--999999999809999999988998898


Q ss_pred             CHH
Q ss_conf             013
Q 003717           90 EHY   92 (800)
Q Consensus        90 Pk~   92 (800)
                      ++.
T Consensus        85 ~~~   87 (89)
T d1cvja2          85 SRK   87 (89)
T ss_dssp             CTT
T ss_pred             CCC
T ss_conf             878

>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=99.69  E-value=9.7e-17  Score=116.44  Aligned_cols=79  Identities=19%  Similarity=0.371  Sum_probs=72.2

Q ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC--CC--CCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEE
Q ss_conf             57849999079988998899985303896249999656--99--767999936899889999998459947679377997
Q 003717           11 EEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--KG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLE   86 (800)
Q Consensus        11 ~q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd--TG--RGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe   86 (800)
                      ....+|||||||+.+++++|+++|++||+|.+|.++++  ++  +|||||+|.+  .++|..|+..|||..++||+|+|+
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~--~~~A~~Ai~~l~g~~~~gr~i~V~   82 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYS--RADAENAMRYINGTRLDDRIIRTD   82 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESS--HHHHHHHHHHTTTSEETTEECEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHHCCCCEECCCCCCCCCCCCCEEEEEECC--HHHHHHHHHHHCCCEECCEEEEEE
T ss_conf             799999995999979899999999987886200102465532224157999889--999999999808998999888999


Q ss_pred             ECCCH
Q ss_conf             42401
Q 003717           87 RAKEH   91 (800)
Q Consensus        87 ~AkPk   91 (800)
                      +|...
T Consensus        83 ~a~~~   87 (93)
T d1h2vz_          83 WDAGF   87 (93)
T ss_dssp             EESCC
T ss_pred             ECCCC
T ss_conf             84898

>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=99.69  E-value=3.8e-17  Score=118.91  Aligned_cols=79  Identities=22%  Similarity=0.500  Sum_probs=72.4

Q ss_pred             CCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC--CC--CCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEE
Q ss_conf             7849999079988998899985303896249999656--99--7679999368998899999984599476793779974
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--KG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLER   87 (800)
Q Consensus        12 q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd--TG--RGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~   87 (800)
                      ..++|||+|||+.+++++|+++|++||.|.+|.++++  ++  ||||||+|.+  .++|.+|+..|||..|.|+.|+|++
T Consensus         7 ~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~--~~~a~~ai~~l~~~~~~g~~i~V~~   84 (104)
T d1p1ta_           7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQD--QETALSAMRNLNGREFSGRALRVDN   84 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSC--HHHHHHHHHHSSSBSCSSSCBEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCEECCCCCEEEEECC--HHHHHHHHHHCCCCEECCEEEEEEE
T ss_conf             87889997999869899999766403322221101110001147846789899--9999999998099988999879988


Q ss_pred             CCCHH
Q ss_conf             24013
Q 003717           88 AKEHY   92 (800)
Q Consensus        88 AkPk~   92 (800)
                      |.++.
T Consensus        85 a~~~~   89 (104)
T d1p1ta_          85 AASEK   89 (104)
T ss_dssp             TTCTT
T ss_pred             CCCCC
T ss_conf             99988

>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=99.69  E-value=4.3e-17  Score=118.60  Aligned_cols=78  Identities=27%  Similarity=0.457  Sum_probs=72.0

Q ss_pred             CCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC--C--CCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEE
Q ss_conf             7849999079988998899985303896249999656--9--97679999368998899999984599476793779974
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--K--GRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLER   87 (800)
Q Consensus        12 q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd--T--GRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~   87 (800)
                      ..++|||||||+.+++++|+++|++||+|.+|.++++  +  .||||||+|.+  .++|.+|+..|||..++|++|+|.+
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~--~~~A~~ai~~l~~~~i~g~~l~v~~   81 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFEL--AEDAAAAIDNMNESELFGRTIRVNL   81 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSS--HHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHCCEEEECCCCCCCCCCCCCCEEEEEECC--HHHHHHHHHHCCCCEECCEEEEEEE
T ss_conf             98299996999868899999988647838861102455654556304999889--9999999998599999999989998


Q ss_pred             CCCH
Q ss_conf             2401
Q 003717           88 AKEH   91 (800)
Q Consensus        88 AkPk   91 (800)
                      |+|+
T Consensus        82 a~p~   85 (89)
T d2cqba1          82 AKPM   85 (89)
T ss_dssp             CCCC
T ss_pred             ECCC
T ss_conf             2798

>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=99.68  E-value=1.1e-16  Score=116.05  Aligned_cols=76  Identities=25%  Similarity=0.522  Sum_probs=70.7

Q ss_pred             CEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC--CC--CCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEECC
Q ss_conf             49999079988998899985303896249999656--99--767999936899889999998459947679377997424
Q 003717           14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--KG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAK   89 (800)
Q Consensus        14 rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd--TG--RGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~Ak   89 (800)
                      ++|||||||+.+++++|+++|++||.|..++++++  .+  +|||||+|.+  .++|..|+..|||..|+|++|+|.+|+
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~--~~~a~~a~~~l~g~~~~g~~l~v~~Ak   80 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYID--PKDAEKAINTLNGLRLQTKTIKVSYAR   80 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESS--HHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHHCCCCCCCCEEECCCCCCEEEEEEEECC--HHHHHHHHHHHCCCEECCEEEEEEEEE
T ss_conf             889998989879899999999996976410100002578730258999899--999999999828999999999999854


Q ss_pred             CH
Q ss_conf             01
Q 003717           90 EH   91 (800)
Q Consensus        90 Pk   91 (800)
                      |.
T Consensus        81 Ps   82 (82)
T d1fxla1          81 PS   82 (82)
T ss_dssp             CC
T ss_pred             CC
T ss_conf             86

>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=99.68  E-value=1.2e-16  Score=115.93  Aligned_cols=79  Identities=19%  Similarity=0.376  Sum_probs=72.6

Q ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC--CC--CCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEE
Q ss_conf             57849999079988998899985303896249999656--99--767999936899889999998459947679377997
Q 003717           11 EEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--KG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLE   86 (800)
Q Consensus        11 ~q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd--TG--RGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe   86 (800)
                      .+..+|||+|||+.+++++|+++|++||.|.+++++++  ++  ||||||+|.+  .++|.+|+..|||..|+||.|+|+
T Consensus         5 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~--~~~A~~A~~~lng~~l~g~~l~V~   82 (88)
T d1rk8a_           5 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYET--HKQALAAKEALNGAEIMGQTIQVD   82 (88)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESS--HHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCEEEEECC--HHHHHHHHHHCCCCEECCEEEEEE
T ss_conf             899899994899989899999999872986410001234322556411689899--999999999819998999989999


Q ss_pred             ECCCH
Q ss_conf             42401
Q 003717           87 RAKEH   91 (800)
Q Consensus        87 ~AkPk   91 (800)
                      +|.++
T Consensus        83 ~a~~k   87 (88)
T d1rk8a_          83 WCFVK   87 (88)
T ss_dssp             ESEEC
T ss_pred             EECCC
T ss_conf             85589

>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=99.68  E-value=1.2e-16  Score=115.88  Aligned_cols=78  Identities=22%  Similarity=0.424  Sum_probs=71.9

Q ss_pred             CCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC--CC--CCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEE
Q ss_conf             7849999079988998899985303896249999656--99--7679999368998899999984599476793779974
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--KG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLER   87 (800)
Q Consensus        12 q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd--TG--RGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~   87 (800)
                      ...+|||+|||+.+++++|+++|.+||.|..|.++++  ++  +|||||+|.+  .++|..|+..|||..|+||.|+|.+
T Consensus         7 ~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~--~~~a~~A~~~l~g~~~~gr~i~V~~   84 (99)
T d1whwa_           7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMF--PEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESS--HHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCEEEEECC--HHHHHHHHHHCCCCEECCEEEEEEE
T ss_conf             99889997999869899999999764975065310244434667504999889--9999999998299989999879998


Q ss_pred             CCCH
Q ss_conf             2401
Q 003717           88 AKEH   91 (800)
Q Consensus        88 AkPk   91 (800)
                      |+++
T Consensus        85 a~~~   88 (99)
T d1whwa_          85 STIK   88 (99)
T ss_dssp             CCCC
T ss_pred             CCCC
T ss_conf             8888

>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=99.68  E-value=6.8e-17  Score=117.37  Aligned_cols=77  Identities=19%  Similarity=0.412  Sum_probs=70.1

Q ss_pred             CCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC--C--CCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEE
Q ss_conf             7849999079988998899985303896249999656--9--97679999368998899999984599476793779974
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--K--GRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLER   87 (800)
Q Consensus        12 q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd--T--GRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~   87 (800)
                      ..++|||||||+.+++++|+++|+.||.|.+|+++++  +  +||||||+|.+  .++|.+|+. |||..|+|+.|+|.+
T Consensus        17 ~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~--~e~a~~A~~-l~g~~~~G~~l~V~~   93 (101)
T d2cq4a1          17 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCE--IQSVPLAIG-LTGQRLLGVPIIVQA   93 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESC--GGGHHHHHH-HTTEEETTEEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHCCCCEEEEEEEEECCCCCCCCCEEEEEECC--HHHHHHHHH-HCCCEECCEEEEEEE
T ss_conf             79899998999989999999997189749998865448876434148999899--999999998-799888999989997


Q ss_pred             CCCH
Q ss_conf             2401
Q 003717           88 AKEH   91 (800)
Q Consensus        88 AkPk   91 (800)
                      |+++
T Consensus        94 a~~~   97 (101)
T d2cq4a1          94 SQAE   97 (101)
T ss_dssp             HHHH
T ss_pred             CCCC
T ss_conf             8887

>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=99.67  E-value=8.8e-17  Score=116.71  Aligned_cols=79  Identities=29%  Similarity=0.561  Sum_probs=72.1

Q ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC---CC--CCEEEEEECCCCHHHHHHHHHHC-CCCEECCEEEE
Q ss_conf             57849999079988998899985303896249999656---99--76799993689988999999845-99476793779
Q 003717           11 EEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT---KG--RSFGYVDFFPSSHKSLSKLFSTY-NGCVWKGGRLR   84 (800)
Q Consensus        11 ~q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd---TG--RGFGFVeFaS~D~EDAeKAIeeL-NG~eLdGRkLk   84 (800)
                      ...++|||+|||+.+++++|+.+|++||.|..|.++++   +|  ||||||+|.+  .++|.+|+..| ||..|+||+|+
T Consensus         6 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~--~~~A~~Ai~~l~~~~~~~Gr~l~   83 (94)
T d2cpha1           6 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFIT--KQDAKKAFNALCHSTHLYGRRLV   83 (94)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESS--HHHHHHHHHHHHTCCBSSSCBCE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHHCCCEEEEEEECCCCCCCCCCEEEEEECC--HHHHHHHHHHCCCCCEECCEEEE
T ss_conf             8998999969999899999999999859964889885366679836689999899--99999999972399488999989


Q ss_pred             EEECCCH
Q ss_conf             9742401
Q 003717           85 LERAKEH   91 (800)
Q Consensus        85 Ve~AkPk   91 (800)
                      |++|.+.
T Consensus        84 V~~A~~~   90 (94)
T d2cpha1          84 LEWADSE   90 (94)
T ss_dssp             EEECCCC
T ss_pred             EEECCCC
T ss_conf             9982997

>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=99.67  E-value=2.2e-16  Score=114.25  Aligned_cols=74  Identities=27%  Similarity=0.431  Sum_probs=69.3

Q ss_pred             CEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC--CC--CCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEECC
Q ss_conf             49999079988998899985303896249999656--99--767999936899889999998459947679377997424
Q 003717           14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--KG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAK   89 (800)
Q Consensus        14 rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd--TG--RGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~Ak   89 (800)
                      +.|||||||+.+++++|+++|++||+|.+++++++  ++  +|||||+|.+  .++|..|+..|||..+.||+|+|.+|+
T Consensus         1 aslfV~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           1 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQ--PADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESS--HHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHHCCEEEEEEEECCCCCCCCCCEEEEECC--HHHHHHHHHHCCCCEECCEEEEEEEEC
T ss_conf             999994798848799999999976988599998404544778836999889--999999999819998999998999827

>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=99.66  E-value=3.2e-16  Score=113.34  Aligned_cols=77  Identities=23%  Similarity=0.426  Sum_probs=69.7

Q ss_pred             CCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC--C--CCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEE
Q ss_conf             7849999079988998899985303896249999656--9--97679999368998899999984599476793779974
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--K--GRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLER   87 (800)
Q Consensus        12 q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd--T--GRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~   87 (800)
                      ..++|||||||+.+++++|+++|++||.|.++.++++  +  ++|||||+|.+  .++|.+|++.+|+ .|+||+|+|++
T Consensus         9 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~--~~~A~~Ai~~~~~-~l~Gr~l~V~~   85 (103)
T d2cqda1           9 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMAD--RAAAERACKDPNP-IIDGRKANVNL   85 (103)
T ss_dssp             SSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESS--HHHHHHHHTCSSC-EETTEECEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHCCCCCCEECCCCCCCCCCCCEEEEEECC--HHHHHHHHHHCCC-CCCCEEEEEEE
T ss_conf             97689996999969599999877614432110002334445568769999789--9999999997899-19998979987


Q ss_pred             CCCH
Q ss_conf             2401
Q 003717           88 AKEH   91 (800)
Q Consensus        88 AkPk   91 (800)
                      |.++
T Consensus        86 a~~~   89 (103)
T d2cqda1          86 AYLG   89 (103)
T ss_dssp             STTT
T ss_pred             CCCC
T ss_conf             2788

>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=3.3e-16  Score=113.26  Aligned_cols=77  Identities=22%  Similarity=0.420  Sum_probs=69.0

Q ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC--CC--CCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEE
Q ss_conf             057849999079988998899985303896249999656--99--76799993689988999999845994767937799
Q 003717           10 VEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--KG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRL   85 (800)
Q Consensus        10 v~q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd--TG--RGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkV   85 (800)
                      ..+.++|||||||+.+++++|+++|++||.|..+.++++  ++  +|||||+|.+  .++|.+|+. ++++.|+||.|+|
T Consensus         3 pe~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~--~~~a~~ai~-~~~~~i~Gr~i~V   79 (84)
T d1l3ka1           3 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYAT--VEEVDAAMN-ARPHKVDGRVVEP   79 (84)
T ss_dssp             CGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESS--HHHHHHHHH-TCSCEETTEECEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEECCCCCCCCCCCEEEEEECC--HHHHHHHHH-HCCCEECCEEEEE
T ss_conf             8888679997999979899999999750645210001146679962289999868--999999998-4999799999899


Q ss_pred             EECC
Q ss_conf             7424
Q 003717           86 ERAK   89 (800)
Q Consensus        86 e~Ak   89 (800)
                      +.|.
T Consensus        80 ~~A~   83 (84)
T d1l3ka1          80 KRAV   83 (84)
T ss_dssp             EECC
T ss_pred             EEEE
T ss_conf             9514

>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=99.66  E-value=6.7e-17  Score=117.41  Aligned_cols=80  Identities=20%  Similarity=0.190  Sum_probs=71.9

Q ss_pred             HCCCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECCCCCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEEC
Q ss_conf             00578499990799889988999853038962499996569976799993689988999999845994767937799742
Q 003717            9 EVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERA   88 (800)
Q Consensus         9 Ev~q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRdTGRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~A   88 (800)
                      ..+..++|||+|||+.+++++|+++|++||.|..|.+.+  .||||||+|.+  .++|.+|+..|||..|.||+|.|++|
T Consensus         6 ~~r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~--~kg~afV~f~~--~~~A~~A~~~lng~~~~gr~l~v~~a   81 (111)
T d1whxa_           6 SGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE--GGITAIVEFLE--PLEARKAFRHLAYSKFHHVPLYLEWA   81 (111)
T ss_dssp             TSEEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS--SSSCEEEEESC--HHHHHHHHHHHTTCBSSSSBCEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHCCCCCCEEEEEC--CCCEEEEEECC--HHHHHHHHHHHCCCCCCCCEEEEEEC
T ss_conf             898899999979899888999976640268861899604--68638999847--78999999997698358975899978


Q ss_pred             CCHH
Q ss_conf             4013
Q 003717           89 KEHY   92 (800)
Q Consensus        89 kPk~   92 (800)
                      ....
T Consensus        82 ~~~~   85 (111)
T d1whxa_          82 PIGV   85 (111)
T ss_dssp             ETTT
T ss_pred             CCCC
T ss_conf             7776

>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=99.66  E-value=3e-16  Score=113.48  Aligned_cols=77  Identities=27%  Similarity=0.441  Sum_probs=69.1

Q ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC--CC--CCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEE
Q ss_conf             57849999079988998899985303896249999656--99--767999936899889999998459947679377997
Q 003717           11 EEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--KG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLE   86 (800)
Q Consensus        11 ~q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd--TG--RGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe   86 (800)
                      ...++|||+|||+++++++|+++|++||.|..|.++++  ++  ||||||+|.+  .++|.+|++.  ++.|+||.|.|+
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~--~~~a~~al~~--~~~l~Gr~i~v~   81 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTE--YETQVKVMSQ--RHMIDGRWCDCK   81 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESS--HHHHHHHHHS--CEEETTEEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHHCCCCEEEECCCCCCCCCCCEEEEEECC--HHHHHHHHHC--CCCCCCEEEEEE
T ss_conf             689869997999989999999999762633000002478876667779999799--9999999866--983499896998


Q ss_pred             ECCCH
Q ss_conf             42401
Q 003717           87 RAKEH   91 (800)
Q Consensus        87 ~AkPk   91 (800)
                      +|.++
T Consensus        82 ~a~~k   86 (90)
T d2cqga1          82 LPNSK   86 (90)
T ss_dssp             CCCTT
T ss_pred             ECCCC
T ss_conf             68997

>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=99.66  E-value=3.7e-16  Score=112.93  Aligned_cols=80  Identities=26%  Similarity=0.505  Sum_probs=72.7

Q ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC-CCCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEEC
Q ss_conf             057849999079988998899985303896249999656-9976799993689988999999845994767937799742
Q 003717           10 VEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT-KGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERA   88 (800)
Q Consensus        10 v~q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd-TGRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~A   88 (800)
                      .+...+|||+|||+.+++++|+++|.+||.|..+.+.+. .++|||||+|.+  .++|..|+..|||+.|+|++|+|.+|
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~~g~afV~f~~--~e~a~~Ai~~l~g~~~~g~~l~V~~a   88 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFED--PRDAEDAVYGRDGYDYDGYRLRVEFP   88 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESC--HHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEECCCCCCCCEEEEEECC--HHHHHHHHHHHCCCEECCEEEEEEEC
T ss_conf             9999899997989889899999988427866998841565546539999889--99999999981999899989799825


Q ss_pred             CCH
Q ss_conf             401
Q 003717           89 KEH   91 (800)
Q Consensus        89 kPk   91 (800)
                      ++.
T Consensus        89 ~~~   91 (95)
T d1x4aa1          89 RSG   91 (95)
T ss_dssp             CCC
T ss_pred             CCC
T ss_conf             697

>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=99.65  E-value=8.6e-17  Score=116.76  Aligned_cols=79  Identities=27%  Similarity=0.543  Sum_probs=71.9

Q ss_pred             CCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC--C--CCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEE
Q ss_conf             7849999079988998899985303896249999656--9--97679999368998899999984599476793779974
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--K--GRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLER   87 (800)
Q Consensus        12 q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd--T--GRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~   87 (800)
                      ..++|||||||+.+++++|+++|++||.|..+.+++.  +  .+|||||+|.+  .++|..|+..|||..|.|++|+|++
T Consensus         4 ~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~--~~~a~~Ai~~l~~~~~~g~~l~V~~   81 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFEN--IDDAKDAMMAMNGKSVDGRQIRVDQ   81 (90)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSS--HHHHHHHHHHHTTCCTTSCCCEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHCCCCCCCEEECCCCCCCCCCCEEEEEECC--HHHHHHHHHHCCCCEECCEEEEEEE
T ss_conf             99899997999868799998756402222110110000333346638999878--9999999998099899999989998


Q ss_pred             CCCHH
Q ss_conf             24013
Q 003717           88 AKEHY   92 (800)
Q Consensus        88 AkPk~   92 (800)
                      |.++.
T Consensus        82 a~~~~   86 (90)
T d1x5sa1          82 AGKSS   86 (90)
T ss_dssp             EECCC
T ss_pred             CCCCC
T ss_conf             18999

>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=99.65  E-value=3.7e-16  Score=112.94  Aligned_cols=76  Identities=22%  Similarity=0.491  Sum_probs=71.5

Q ss_pred             CCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECCCCCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEECCCH
Q ss_conf             78499990799889988999853038962499996569976799993689988999999845994767937799742401
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKEH   91 (800)
Q Consensus        12 q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRdTGRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~AkPk   91 (800)
                      ..++|||||||..+++++|+++|++||.|.+|.+++  .||||||+|.+  .++|.+|+..|||..++|+.|+|.||+++
T Consensus        17 ~~~~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          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFP--EKGYSFVRFST--HESAAHAIVSVNGTTIEGHVVKCYWGKES   92 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEET--TTTEEEEEESS--HHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHHHHCCCEEEEEEE--CCEEEEEEECC--HHHHHHHHHHHCCCEECCEEEEEEECCCC
T ss_conf             999999908999899999999999829966999970--13089999899--99999999981999999999899975789

>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=99.65  E-value=2.6e-16  Score=113.90  Aligned_cols=84  Identities=18%  Similarity=0.398  Sum_probs=73.4

Q ss_pred             HHHCCCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC--C--CCCEEEEEECCCCHHHHHHHHHHCC------CC
Q ss_conf             010057849999079988998899985303896249999656--9--9767999936899889999998459------94
Q 003717            7 EAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--K--GRSFGYVDFFPSSHKSLSKLFSTYN------GC   76 (800)
Q Consensus         7 ~~Ev~q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd--T--GRGFGFVeFaS~D~EDAeKAIeeLN------G~   76 (800)
                      +.+..+.++|||||||+.+++++|+++|++||.|..+.++++  +  .+|||||+|.+  .++|.+|+..||      |.
T Consensus         2 P~~~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~--~~~a~~ai~~l~~~~~~~g~   79 (98)
T d1x4ha1           2 PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMT--QEAAQKCLAAASLEAEGGGL   79 (98)
T ss_dssp             CCCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESS--HHHHHHHHHHHCTTTTTCCE
T ss_pred             CCCCCCCCEEEECCCCCCCCHHHHHHHHHCCCCCEEEEECCCCCCCCCCCEEEEEECC--HHHHHHHHHHCCCCCCCCCC
T ss_conf             4489899899991899968899999877512422033320366554566258999869--99999999873522346990


Q ss_pred             EECCEEEEEEECCCHH
Q ss_conf             7679377997424013
Q 003717           77 VWKGGRLRLERAKEHY   92 (800)
Q Consensus        77 eLdGRkLkVe~AkPk~   92 (800)
                      .+.||.|+|.+|.++.
T Consensus        80 ~~~gr~l~v~~a~~k~   95 (98)
T d1x4ha1          80 KLDGRQLKVDLAVTRD   95 (98)
T ss_dssp             ESSSCEEEEECCCCCC
T ss_pred             EECCEEEEEEECCCCC
T ss_conf             8899988999898878

>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=99.65  E-value=4.3e-16  Score=112.56  Aligned_cols=74  Identities=23%  Similarity=0.475  Sum_probs=68.1

Q ss_pred             EEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC--C-----CCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEEC
Q ss_conf             999079988998899985303896249999656--9-----976799993689988999999845994767937799742
Q 003717           16 IYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--K-----GRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERA   88 (800)
Q Consensus        16 LFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd--T-----GRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~A   88 (800)
                      |||+|||+++++++|+++|++||.|.++.++++  +     .||||||+|.+  .++|.+|+..|||..|+||.|+|++|
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~--~~~A~~A~~~~~~~~~~g~~i~V~~a   78 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKK--PEQAQKALKQLQGHTVDGHKLEVRIS   78 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESS--HHHHHHHHHHSTTCEETTEECEEECS
T ss_pred             CEECCCCCCCCHHHHHHHHHHHCCCCCCCEECCCCCCCCCCCCEEEEEEECC--HHHHHHHHHHHCCCEECCEEEEEEEC
T ss_conf             9883899979899999999983980322100023323545331378999899--99999999982998899999799988


Q ss_pred             CCH
Q ss_conf             401
Q 003717           89 KEH   91 (800)
Q Consensus        89 kPk   91 (800)
                      .+.
T Consensus        79 ~~~   81 (85)
T d2cpfa1          79 ERA   81 (85)
T ss_dssp             SCS
T ss_pred             CCC
T ss_conf             889

>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=2e-16  Score=114.49  Aligned_cols=76  Identities=21%  Similarity=0.528  Sum_probs=70.9

Q ss_pred             CEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC--CC--CCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEECC
Q ss_conf             49999079988998899985303896249999656--99--767999936899889999998459947679377997424
Q 003717           14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--KG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAK   89 (800)
Q Consensus        14 rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd--TG--RGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~Ak   89 (800)
                      .+|||||||+.+++++|+++|++||+|..+.++++  ++  ||||||+|.+  .++|..|+..|||..|+|++|+|.+|.
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~   79 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVD--INVTDQAIAGLNGMQLGDKKLLVQRAS   79 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESS--SHHHHHHHHTSSSCCCSSSCCEEEECC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHCCCCCEEEEECCCCCCCCCEEEEEEECC--HHHHHHHHHHHCCCEECCEEEEEEECC
T ss_conf             889998999989999999999745765247760245665654059999889--999999999719988999987999888


Q ss_pred             CH
Q ss_conf             01
Q 003717           90 EH   91 (800)
Q Consensus        90 Pk   91 (800)
                      +.
T Consensus        80 ~~   81 (85)
T d2u2fa_          80 VG   81 (85)
T ss_dssp             CC
T ss_pred             CC
T ss_conf             98

>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=99.64  E-value=5.3e-16  Score=112.00  Aligned_cols=74  Identities=24%  Similarity=0.450  Sum_probs=67.7

Q ss_pred             CCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC--CC--CCEEEEEECCCCHHHHHHHHHHCCCCEECC--EEEEEE
Q ss_conf             849999079988998899985303896249999656--99--767999936899889999998459947679--377997
Q 003717           13 QTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--KG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKG--GRLRLE   86 (800)
Q Consensus        13 ~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd--TG--RGFGFVeFaS~D~EDAeKAIeeLNG~eLdG--RkLkVe   86 (800)
                      .++|||||||+.+++++|+++|++||+|.++.++++  ++  +|||||+|.+  .++|.+|+..|||..+.|  ++|+|+
T Consensus         6 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~--~~~a~~Ai~~lng~~~~G~~~~i~V~   83 (85)
T d1fxla2           6 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDK--RIEAEEAIKGLNGQKPSGATEPITVK   83 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESS--HHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEECC--HHHHHHHHHHHCCCEECCCCEEEEEE
T ss_conf             9999995989989899999999984976310301245443578716999858--99999999983899958998789998


Q ss_pred             EC
Q ss_conf             42
Q 003717           87 RA   88 (800)
Q Consensus        87 ~A   88 (800)
                      +|
T Consensus        84 ~A   85 (85)
T d1fxla2          84 FA   85 (85)
T ss_dssp             EC
T ss_pred             EC
T ss_conf             49

>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=99.63  E-value=3.9e-16  Score=112.78  Aligned_cols=77  Identities=14%  Similarity=0.298  Sum_probs=68.2

Q ss_pred             CCCEEEEECCCCCCC-HHHHHHHHHCCCCEEEEEEECC---C--CCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEE
Q ss_conf             784999907998899-8899985303896249999656---9--976799993689988999999845994767937799
Q 003717           12 EQTRIYVGGLGEKVT-DDDLAKVFSSLGEVKAVDIVRT---K--GRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRL   85 (800)
Q Consensus        12 q~rtLFVGNLp~sVT-EEdLrelFskFGeV~sVrVIRd---T--GRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkV   85 (800)
                      +.++|||+|||++++ ++.|+++|++||.|..|.+++.   +  .+|||||+|.+  .++|.+|+. |||..|+||.|+|
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~--~~~a~~Al~-~n~~~~~gr~l~V   79 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFEN--KDSAERALQ-MNRSLLGNREISV   79 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESS--HHHHHHHGG-GTTEEETTEEEEE
T ss_pred             CCCEEEEECCCCCCCCHHHHHHHHHHHHHCCCEEEECCCCCCCCCCEEEEEEECC--HHHHHHHHH-CCCCEECCEEEEE
T ss_conf             8889999799977434999999977531211100000257765552265689889--999999996-2999899999899


Q ss_pred             EECCCH
Q ss_conf             742401
Q 003717           86 ERAKEH   91 (800)
Q Consensus        86 e~AkPk   91 (800)
                      .+|+++
T Consensus        80 ~~a~~k   85 (86)
T d2ghpa3          80 SLADKK   85 (86)
T ss_dssp             EECCCC
T ss_pred             EECCCC
T ss_conf             974789

>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=99.63  E-value=3.2e-16  Score=113.29  Aligned_cols=84  Identities=20%  Similarity=0.317  Sum_probs=72.7

Q ss_pred             CHHHCCCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECCCCCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEE
Q ss_conf             00100578499990799889988999853038962499996569976799993689988999999845994767937799
Q 003717            6 AEAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRL   85 (800)
Q Consensus         6 A~~Ev~q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRdTGRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkV   85 (800)
                      .....+..++|||+|||+.+++++|+++|.+||.|..+.. ....+|||||+|.+  .++|.+|+..|||..|+||+|+|
T Consensus         9 ~~~~~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~-~~~~~~~afV~f~~--~~~A~~A~~~l~~~~~~gr~i~V   85 (96)
T d1fjca_           9 TSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-DGKSKGIAYIEFKS--EADAEKNLEEKQGAEIDGRSVSL   85 (96)
T ss_dssp             TTSTTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE-TTEEEEEEEEEESS--HHHHHHHHHHTTEEEETTEEEEE
T ss_pred             CCCCCCCCCEEEEECCCCCCCHHHHHHHHHHCCCCEEEEE-CCCCCCEEEEEECC--HHHHHHHHHHCCCCEECCEEEEE
T ss_conf             6576778999999189987989999999975165605634-37506688898689--99999999982999999999799


Q ss_pred             EECCCHH
Q ss_conf             7424013
Q 003717           86 ERAKEHY   92 (800)
Q Consensus        86 e~AkPk~   92 (800)
                      .+|.++.
T Consensus        86 ~~a~~k~   92 (96)
T d1fjca_          86 YYTGEKG   92 (96)
T ss_dssp             EECSSSC
T ss_pred             EEECCCC
T ss_conf             9807899

>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=99.63  E-value=7.4e-16  Score=111.10  Aligned_cols=73  Identities=21%  Similarity=0.352  Sum_probs=68.5

Q ss_pred             EEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC-C--CCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEECC
Q ss_conf             9999079988998899985303896249999656-9--9767999936899889999998459947679377997424
Q 003717           15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT-K--GRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAK   89 (800)
Q Consensus        15 tLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd-T--GRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~Ak   89 (800)
                      +|||+|||+.+++++|+++|++||.|..+.++++ +  .+|||||+|.+  .++|..|+..|||..+.||+|+|++|.
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 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFER--KADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESC--HHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHHCCCEEEEEEEEECCCCCEEEEEEECC--HHHHHHHHHHHCCCEECCEEEEEEEEE
T ss_conf             9999889987989999999998599728999986012454368999989--999999999838999999999999931

>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=99.63  E-value=5.9e-16  Score=111.72  Aligned_cols=75  Identities=13%  Similarity=0.229  Sum_probs=69.3

Q ss_pred             CEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC----CCCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEECC
Q ss_conf             49999079988998899985303896249999656----99767999936899889999998459947679377997424
Q 003717           14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT----KGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAK   89 (800)
Q Consensus        14 rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd----TGRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~Ak   89 (800)
                      .+|||+|||+.+++++|+++|++||.|..+.++++    ..||||||+|.+  .++|.+|+..|||..++|++|+|++|+
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~--~e~A~~Ai~~l~g~~~~g~~i~V~~a~   79 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTS--KEDARYCVEKLNGLKIEGYTLVTKVSN   79 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSS--HHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHHCCEEEEEEECCCCCCCCCCEEEEEECC--HHHHHHHHHHHCCCEECCEEEEEEECC
T ss_conf             699997979869899999999982968764220001123455215899899--999999999869978899999999740


Q ss_pred             C
Q ss_conf             0
Q 003717           90 E   90 (800)
Q Consensus        90 P   90 (800)
                      |
T Consensus        80 P   80 (81)
T d2ghpa1          80 P   80 (81)
T ss_dssp             C
T ss_pred             C
T ss_conf             8

>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=99.63  E-value=2.1e-16  Score=114.41  Aligned_cols=78  Identities=18%  Similarity=0.358  Sum_probs=70.5

Q ss_pred             CCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC-CC--CCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEEC
Q ss_conf             7849999079988998899985303896249999656-99--76799993689988999999845994767937799742
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT-KG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERA   88 (800)
Q Consensus        12 q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd-TG--RGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~A   88 (800)
                      ..++|||||||+++++++|+.+|++||.|..+.++++ ++  +|||||+|.+  .++|.+|+..|||..|.||++.|.++
T Consensus        17 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~--~~~A~~Ai~~lng~~i~gr~~~v~~~   94 (101)
T d1x5oa1          17 DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMES--TEKCEAVIGHFNGKFIKTPPGVSAPT   94 (101)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESC--HHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHCCCCCCEEEECCCCCCCCCCEEEEECC--HHHHHHHHHHHCCCEECCCCCCCCCC
T ss_conf             9998999699998989999988861366421011001123566310477689--99999999984899889839866789


Q ss_pred             CCH
Q ss_conf             401
Q 003717           89 KEH   91 (800)
Q Consensus        89 kPk   91 (800)
                      +|-
T Consensus        95 ~Pl   97 (101)
T d1x5oa1          95 EPL   97 (101)
T ss_dssp             SCB
T ss_pred             CCC
T ss_conf             886

>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=99.63  E-value=8.7e-16  Score=110.68  Aligned_cols=76  Identities=26%  Similarity=0.479  Sum_probs=69.2

Q ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC--CC--CCEEEEEECCCCHHHHHHHHHHCCCCEECC--EEEE
Q ss_conf             57849999079988998899985303896249999656--99--767999936899889999998459947679--3779
Q 003717           11 EEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--KG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKG--GRLR   84 (800)
Q Consensus        11 ~q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd--TG--RGFGFVeFaS~D~EDAeKAIeeLNG~eLdG--RkLk   84 (800)
                      ...++|||+|||+.+++++|+++|++||.|..++++++  ++  ||||||+|.+  .++|.+|+..|||..+.|  ++|+
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~--~~~A~~Ai~~l~g~~~~g~~~~l~   81 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNK--REEAQEAISALNNVIPEGGSQPLS   81 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESS--HHHHHHHHHHHTTCCCTTCSSCCE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHHCCEEEEEEECCCCCCCCCEEEEEEECC--HHHHHHHHHHHCCCEECCCCEEEE
T ss_conf             889999994989979999999999965987464310123555676069999899--999999999978888579981799


Q ss_pred             EEEC
Q ss_conf             9742
Q 003717           85 LERA   88 (800)
Q Consensus        85 Ve~A   88 (800)
                      |++|
T Consensus        82 V~~A   85 (85)
T d1b7fa2          82 VRLA   85 (85)
T ss_dssp             EEEC
T ss_pred             EEEC
T ss_conf             9979

>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=99.62  E-value=7.9e-16  Score=110.94  Aligned_cols=81  Identities=28%  Similarity=0.457  Sum_probs=69.4

Q ss_pred             HCCCCCEEEEECCCCCCCHHHHHHHHHCCCCEEE--------EEEECC--CC--CCEEEEEECCCCHHHHHHHHHHCCCC
Q ss_conf             0057849999079988998899985303896249--------999656--99--76799993689988999999845994
Q 003717            9 EVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKA--------VDIVRT--KG--RSFGYVDFFPSSHKSLSKLFSTYNGC   76 (800)
Q Consensus         9 Ev~q~rtLFVGNLp~sVTEEdLrelFskFGeV~s--------VrVIRd--TG--RGFGFVeFaS~D~EDAeKAIeeLNG~   76 (800)
                      +....++|||+|||+.+++++|+++|.+||.|..        +.+.++  ++  +|||||+|.+  .++|.+|+..|||.
T Consensus         4 ~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~--~~~a~~Ai~~l~g~   81 (101)
T d2cpea1           4 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYED--PPTAKAAVEWFDGK   81 (101)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSS--HHHHHHHHHHHTTC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHCCEEEEEEECCCCEEEEEECCCCCCCCCEEEEEECC--HHHHHHHHHHHCCC
T ss_conf             8998999999799986889999987887743787563253036775426644434123587669--99999999983999


Q ss_pred             EECCEEEEEEECCCH
Q ss_conf             767937799742401
Q 003717           77 VWKGGRLRLERAKEH   91 (800)
Q Consensus        77 eLdGRkLkVe~AkPk   91 (800)
                      .|+||.|+|.+|+++
T Consensus        82 ~~~gr~i~V~~a~~~   96 (101)
T d2cpea1          82 DFQGSKLKVSLARKK   96 (101)
T ss_dssp             EETTEECEEECSSCC
T ss_pred             EECCEEEEEEECCCC
T ss_conf             899998799975789

>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=99.62  E-value=5.8e-16  Score=111.74  Aligned_cols=76  Identities=22%  Similarity=0.333  Sum_probs=69.9

Q ss_pred             CCEEEEECCCC-CCCHHHHHHHHHCCCCEEEEEEECCCCCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEECCCH
Q ss_conf             84999907998-89988999853038962499996569976799993689988999999845994767937799742401
Q 003717           13 QTRIYVGGLGE-KVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKEH   91 (800)
Q Consensus        13 ~rtLFVGNLp~-sVTEEdLrelFskFGeV~sVrVIRdTGRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~AkPk   91 (800)
                      ..+|||+||++ .+++++|+++|+.||.|..|.|+++ .+|||||+|.+  .++|.+|+..|||..|+|+.|+|.+|+..
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~~~   78 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-KKENALVQMAD--GNQAQLAMSHLNGHKLHGKPIRITLSKHQ   78 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCT-TSCCEEEEESC--HHHHHHHHHHHTTCBCSSSBCEEECCSCC
T ss_pred             CCEEEEECCCCCCCCHHHHHHHHHHCCCCCEEEEEEC-CCCEEEEEECC--HHHHHHHHHHHCCCEECCEEEEEEECCCC
T ss_conf             9999996799252999999998750356404999760-34258999778--79999999983997879988899988788

>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=99.62  E-value=1.4e-15  Score=109.39  Aligned_cols=77  Identities=18%  Similarity=0.282  Sum_probs=70.7

Q ss_pred             CCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECCCCCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEECCCH
Q ss_conf             78499990799889988999853038962499996569976799993689988999999845994767937799742401
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKEH   91 (800)
Q Consensus        12 q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRdTGRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~AkPk   91 (800)
                      +.++|||||||+.+++++|+++|++||.|..+.+.+  .||||||+|.+  .++|..|+..|||..|.|+.|+|.+|+|+
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~--~rg~afV~f~~--~~~A~~Ai~~l~~~~i~g~~i~V~~akP~   82 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK--IRDYAFVHFSN--REDAVEAMKALNGKVLDGSPIEVTLAKPV   82 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE--CSSEEEEEESS--HHHHHHHHHHHSSEEETTEEEEEECCCCC
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHCCCCEEEEEEECC--CCEEEEEEECC--HHHHHHHHHHCCCCEECCEEEEEEECCCC
T ss_conf             899999929899788999998620653265579755--42799998699--99999999980998999989899966078


Q ss_pred             H
Q ss_conf             3
Q 003717           92 Y   92 (800)
Q Consensus        92 ~   92 (800)
                      .
T Consensus        83 ~   83 (86)
T d2cpda1          83 D   83 (86)
T ss_dssp             C
T ss_pred             C
T ss_conf             9

>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=99.62  E-value=7.6e-16  Score=111.06  Aligned_cols=76  Identities=21%  Similarity=0.430  Sum_probs=71.0

Q ss_pred             CCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECCCCCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEECCCH
Q ss_conf             78499990799889988999853038962499996569976799993689988999999845994767937799742401
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKEH   91 (800)
Q Consensus        12 q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRdTGRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~AkPk   91 (800)
                      +..+|||+|||+.+++++|+++|++||.|.+|.+++  .||||||+|.+  .++|..|+..|||..|+|++|+|++|.+.
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~--~k~~afV~f~~--~~~A~~A~~~l~g~~i~g~~l~V~~A~~~   82 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK--DKGFGFIRLET--RTLAEIAKVELDNMPLRGKQLRVRFACHS   82 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEET--TTTEEEEECSS--SHHHHHHHHHHTTCCBTTBCCEEEESSCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHHCCCEEEEEEC--CCCEEEEEECC--HHHHHHHHHHHCCCEECCEEEEEEECCCC
T ss_conf             998999979998798999999999869860763421--35369999889--99999999981998899988899978985

>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=2.1e-15  Score=108.36  Aligned_cols=73  Identities=26%  Similarity=0.541  Sum_probs=66.1

Q ss_pred             CCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC--CC--CCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEEC
Q ss_conf             849999079988998899985303896249999656--99--76799993689988999999845994767937799742
Q 003717           13 QTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--KG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERA   88 (800)
Q Consensus        13 ~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd--TG--RGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~A   88 (800)
                      .++|||||||+.+++++|+++|++||.|..+.++.+  ++  +|||||+|.+  .+++.+|+. +||+.|+||.|+|+.|
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 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD--HDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESS--HHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEECC--HHHHHHHHH-HCCCEECCEEEEEEEC
T ss_conf             8789987989858799999999975513322103578875544189999938--999999999-6998799979899978

>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=99.62  E-value=7.8e-16  Score=110.96  Aligned_cols=74  Identities=20%  Similarity=0.451  Sum_probs=68.0

Q ss_pred             CCCEEEEECCC-CCCCHHHHHHHHHCCCCEEEEEEECCCCCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEECCC
Q ss_conf             78499990799-88998899985303896249999656997679999368998899999984599476793779974240
Q 003717           12 EQTRIYVGGLG-EKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKE   90 (800)
Q Consensus        12 q~rtLFVGNLp-~sVTEEdLrelFskFGeV~sVrVIRdTGRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~AkP   90 (800)
                      ...+|||+||+ +.+++++|+++|++||.|..+.+    .||||||+|.+  .++|.+|+..|||..|+|++|+|++|++
T Consensus        14 ~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i----~rg~aFV~f~~--~~~A~~Ai~~lng~~~~g~~l~V~~a~~   87 (98)
T d1wf2a_          14 MNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV----HKGFAFVQYVN--ERNARAAVAGEDGRMIAGQVLDINLAAE   87 (98)
T ss_dssp             CCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE----ETEEEEEEESS--HHHHHHHHHTTTTCEETTEECEEEETTS
T ss_pred             CCCEEEEECCCCCCCCHHHHHHHHHHCCCEEEEEE----ECCEEEEEECC--HHHHHHHHHHCCCCEECCEEEEEEECCC
T ss_conf             97589993889021999999999862698799997----08868999799--9999999998199989998879997789


Q ss_pred             H
Q ss_conf             1
Q 003717           91 H   91 (800)
Q Consensus        91 k   91 (800)
                      +
T Consensus        88 ~   88 (98)
T d1wf2a_          88 P   88 (98)
T ss_dssp             C
T ss_pred             C
T ss_conf             9

>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=99.61  E-value=1.6e-15  Score=109.15  Aligned_cols=72  Identities=31%  Similarity=0.392  Sum_probs=66.4

Q ss_pred             CCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC--CC--CCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEE
Q ss_conf             7849999079988998899985303896249999656--99--76799993689988999999845994767937799
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--KG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRL   85 (800)
Q Consensus        12 q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd--TG--RGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkV   85 (800)
                      ..++|||+|||+.+++++|+++|++||.|.+|.++++  ++  +|||||+|.+  .++|.+|+..|||..|+||+|+|
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 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN--VDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESS--HHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEEECC--HHHHHHHHHHCCCCEECCEEEEC
T ss_conf             99899993999989899999999985977300111366665555302899889--99999999980999989999379

>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=99.61  E-value=1.7e-15  Score=108.93  Aligned_cols=78  Identities=17%  Similarity=0.187  Sum_probs=71.6

Q ss_pred             CCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECCCCCCEEEEEECCCCHHHHHHHHHHCCCCEE-CCEEEEEEECCC
Q ss_conf             7849999079988998899985303896249999656997679999368998899999984599476-793779974240
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVW-KGGRLRLERAKE   90 (800)
Q Consensus        12 q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRdTGRGFGFVeFaS~D~EDAeKAIeeLNG~eL-dGRkLkVe~AkP   90 (800)
                      ..++|||+|||+.+++++|+++|++||.|..+.++...++|||||+|.+  .++|.+|+..|||..+ +||.|+|.+|++
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~afV~f~~--~~~A~~A~~~l~~~~i~~g~~l~v~~sk~   86 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGS--VEEAVQALIDLHNHDLGENHHLRVSFSKS   86 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESS--HHHHHHHHHHHTTCBSSSSCBCEEEECSS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEEEECCCCEEEEEECC--HHHHHHHHHHCCCCEECCCCEEEEEECCC
T ss_conf             9788999799988899999998533697888887530244006999899--99999999751697926998899993798


Q ss_pred             H
Q ss_conf             1
Q 003717           91 H   91 (800)
Q Consensus        91 k   91 (800)
                      +
T Consensus        87 ~   87 (88)
T d2adca2          87 T   87 (88)
T ss_dssp             C
T ss_pred             C
T ss_conf             8

>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=99.61  E-value=1.1e-15  Score=110.15  Aligned_cols=75  Identities=19%  Similarity=0.405  Sum_probs=67.6

Q ss_pred             EEEECCCCCCCHHHHHHHHHCCCCEEEE-EEECC--CC--CCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEECCC
Q ss_conf             9990799889988999853038962499-99656--99--7679999368998899999984599476793779974240
Q 003717           16 IYVGGLGEKVTDDDLAKVFSSLGEVKAV-DIVRT--KG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKE   90 (800)
Q Consensus        16 LFVGNLp~sVTEEdLrelFskFGeV~sV-rVIRd--TG--RGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~AkP   90 (800)
                      |||||||+++++++|+++|++||.|..+ .++++  ++  +|||||+|.+  .++|.+|+..|||..++||+|+|.+|.+
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~--~~~a~~Ai~~~~g~~~~gr~l~v~~a~~   78 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFAS--FDASDAAIEAMNGQYLCNRPITVSYAFK   78 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSS--HHHHHHHHHTTTTCEETTEECEEEESCC
T ss_pred             CEECCCCCCCCHHHHHHHHHHHCCEEEEEEEEEECCCCCCCCEEEEEECC--HHHHHHHHHHCCCCEECCEEEEEEEECC
T ss_conf             99938989486999999998729450467997611332447539999899--9999999985799298999999999658


Q ss_pred             HH
Q ss_conf             13
Q 003717           91 HY   92 (800)
Q Consensus        91 k~   92 (800)
                      +.
T Consensus        79 k~   80 (83)
T d1x5ta1          79 KD   80 (83)
T ss_dssp             CC
T ss_pred             CC
T ss_conf             79

>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=99.61  E-value=4e-16  Score=112.74  Aligned_cols=79  Identities=22%  Similarity=0.157  Sum_probs=72.4

Q ss_pred             CCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECCCCCCEEEEEECCCCHHHHHHHHHHCCCCEE--CCEEEEEEECC
Q ss_conf             7849999079988998899985303896249999656997679999368998899999984599476--79377997424
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVW--KGGRLRLERAK   89 (800)
Q Consensus        12 q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRdTGRGFGFVeFaS~D~EDAeKAIeeLNG~eL--dGRkLkVe~Ak   89 (800)
                      ...+|||+||++.+++++|+++|++||.|..+.+++++.+|||||+|.+  .++|..|+..|||..|  .|+.|+|.+++
T Consensus         6 ~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~~~g~aFV~f~~--~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~   83 (108)
T d2adba1           6 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYAD--PVSAQHAKLSLDGQNIYNACCTLRIDFSK   83 (108)
T ss_dssp             CEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEETTEEEEEEEESC--HHHHHHHHHHHHSCCSSTTCCCCEEEECS
T ss_pred             CEEEEEEECCCCCCCHHHHHHHHCCCCCEEEEEEEEECCCCEEEEEECC--HHHHHHHHHHHCCCEECCCCCEEEEEECC
T ss_conf             8089999392999989999888703975899799850899818999899--99999999997788704698089999457


Q ss_pred             CHH
Q ss_conf             013
Q 003717           90 EHY   92 (800)
Q Consensus        90 Pk~   92 (800)
                      ++.
T Consensus        84 ~~~   86 (108)
T d2adba1          84 LTS   86 (108)
T ss_dssp             SCS
T ss_pred             CCC
T ss_conf             765

>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=99.60  E-value=2.5e-16  Score=113.95  Aligned_cols=80  Identities=26%  Similarity=0.434  Sum_probs=70.6

Q ss_pred             HCCCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEEC---CCCCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEE
Q ss_conf             005784999907998899889998530389624999965---69976799993689988999999845994767937799
Q 003717            9 EVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVR---TKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRL   85 (800)
Q Consensus         9 Ev~q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIR---dTGRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkV   85 (800)
                      +.....+|||+|||+.+++++|+++|++||.|..+.++.   .++||||||+|.+  .++|.+|++ |||..++||+|+|
T Consensus         9 ~~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~--~e~a~~Al~-~~g~~~~g~~i~V   85 (91)
T d1fjeb1           9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFES--AEDLEKALE-LTGLKVFGNEIKL   85 (91)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESS--HHHHHHHHH-GGGEEETTEEEEE
T ss_pred             CCCCCCEEEEECCCCCCHHHHHHHHHHCCCCEEEEEEEECCCCCCCEEEEEEECC--HHHHHHHHH-CCCCEECCEEEEE
T ss_conf             8999838999576576128899999863784787541006899853776786389--999999982-3994889999899


Q ss_pred             EECCCH
Q ss_conf             742401
Q 003717           86 ERAKEH   91 (800)
Q Consensus        86 e~AkPk   91 (800)
                      .+|+.+
T Consensus        86 ~~ak~k   91 (91)
T d1fjeb1          86 EKPKGR   91 (91)
T ss_dssp             ECCCCS
T ss_pred             EECCCC
T ss_conf             855889

>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=99.60  E-value=1.4e-15  Score=109.50  Aligned_cols=71  Identities=31%  Similarity=0.533  Sum_probs=65.2

Q ss_pred             EEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC--CC--CCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEEC
Q ss_conf             9999079988998899985303896249999656--99--76799993689988999999845994767937799742
Q 003717           15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--KG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERA   88 (800)
Q Consensus        15 tLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd--TG--RGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~A   88 (800)
                      +|||||||+++++++|+++|++||+|..+.++++  ++  +|||||+|.+  .++|.+|+. ++++.|+||.|+|+.|
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 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKE--SESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESS--HHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEECC--HHHHHHHHH-CCCCEECCCEEEEEEC
T ss_conf             98991899859899999999754503333213588877767659999898--999999996-2989799979785679

>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=99.59  E-value=6.3e-16  Score=111.55  Aligned_cols=75  Identities=20%  Similarity=0.352  Sum_probs=68.5

Q ss_pred             CEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECCCCCCEEEEEECCCCHHHHHHHHHHCCCC-EECCEEEEEEECCCHH
Q ss_conf             499990799889988999853038962499996569976799993689988999999845994-7679377997424013
Q 003717           14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGC-VWKGGRLRLERAKEHY   92 (800)
Q Consensus        14 rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRdTGRGFGFVeFaS~D~EDAeKAIeeLNG~-eLdGRkLkVe~AkPk~   92 (800)
                      .+|||||||+++++++|+++|++||.|..+.+++  .||||||+|.+  .++|..|+..|||. .+.|++|+|++|.|+.
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~--~rg~aFV~f~~--~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k~   77 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL--KSGYAFVDYPD--QNWAIRAIETLSGKVELHGKIMEVDYSVSKK   77 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE--ETTEEEECCSC--HHHHHHHHHHHTTTCEETTEECEEEECCCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHHCCEEEEEEEC--CCCEEEEEECC--HHHHHHHHHHHCCCEEECCEEEEEEECCCCC
T ss_conf             8899979999899999999999809689737861--26649999888--7879999998179969999898999758857

>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=99.59  E-value=1.9e-15  Score=108.68  Aligned_cols=76  Identities=20%  Similarity=0.308  Sum_probs=69.8

Q ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECCCCCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEECCC
Q ss_conf             57849999079988998899985303896249999656997679999368998899999984599476793779974240
Q 003717           11 EEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKE   90 (800)
Q Consensus        11 ~q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRdTGRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~AkP   90 (800)
                      ++.++|||+||+  +++++|+++|++||.|.++.+.+  .+|||||+|.+  .++|..|+..|||..++|++|+|.+|++
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~--~~~~afV~f~~--~~~A~~Ai~~lng~~~~g~~l~V~~a~~   76 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDP--PRNCAFVTYEK--MESADQAVAELNGTQVESVQLKVNIARK   76 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEET--TTTEEEEECSS--HHHHHHHHHHHTTCBCSSCBCEEEECCS
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHHCCCCCCEEEECC--CCCEEEEEECC--CHHHHHHHHHHCCCEECCEEEEEEEECC
T ss_conf             899899997897--99999999985507564352026--89889999924--1899999998599999999989997058


Q ss_pred             HH
Q ss_conf             13
Q 003717           91 HY   92 (800)
Q Consensus        91 k~   92 (800)
                      ++
T Consensus        77 ~P   78 (79)
T d2bz2a1          77 QP   78 (79)
T ss_dssp             SC
T ss_pred             CC
T ss_conf             98

>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=99.58  E-value=1.1e-15  Score=110.18  Aligned_cols=71  Identities=25%  Similarity=0.529  Sum_probs=65.8

Q ss_pred             EEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC--C--CCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEEC
Q ss_conf             9999079988998899985303896249999656--9--976799993689988999999845994767937799742
Q 003717           15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--K--GRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERA   88 (800)
Q Consensus        15 tLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd--T--GRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~A   88 (800)
                      +|||||||+.+++++|+++|++||.|..+.++++  +  +||||||+|.+  .++|.+|+. +|++.++||.|+|+.|
T Consensus         2 klfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~--~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMD--QAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCC--TTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHHCCCCEEEEECCCCCCCCCCEEEEEECC--HHHHHHHHH-CCCCEECCEEEEEEEC
T ss_conf             99991899969899999999986986202441136788866639999889--999999997-1989899949899979

>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=99.58  E-value=1.6e-15  Score=109.10  Aligned_cols=76  Identities=25%  Similarity=0.410  Sum_probs=68.3

Q ss_pred             CCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECCCCCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEECCCH
Q ss_conf             78499990799889988999853038962499996569976799993689988999999845994767937799742401
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKEH   91 (800)
Q Consensus        12 q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRdTGRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~AkPk   91 (800)
                      ..++|||||||+.+++++|+++|++||.|..|.+++ ..+|||||+|.+  .++|.+|+.  +++.|+|+.|+|.+|.++
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~-~~~gfafV~f~~--~~~a~~a~~--~~~~i~g~~l~v~~a~~k   78 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-PFRAFAFVTFAD--DQIAQSLCG--EDLIIKGISVHISNAEPK   78 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS-SCCSCCEEECSC--HHHHHHTTT--CEEEETTEEEEEECCCCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHCCCCEEEEEEE-CCCCEEEEEECC--HHHHHHHHH--CCCEECCEEEEEEECCCC
T ss_conf             998999928998898999988899829844999942-137658999889--999999972--989899999699867788


Q ss_pred             H
Q ss_conf             3
Q 003717           92 Y   92 (800)
Q Consensus        92 ~   92 (800)
                      .
T Consensus        79 ~   79 (88)
T d1wf0a_          79 H   79 (88)
T ss_dssp             C
T ss_pred             C
T ss_conf             8

>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=99.58  E-value=3.1e-15  Score=107.40  Aligned_cols=79  Identities=25%  Similarity=0.439  Sum_probs=70.1

Q ss_pred             CCCEEEEECCCCCCCHHHHH----HHHHCCCCEEEEEEECC-CCCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEE
Q ss_conf             78499990799889988999----85303896249999656-99767999936899889999998459947679377997
Q 003717           12 EQTRIYVGGLGEKVTDDDLA----KVFSSLGEVKAVDIVRT-KGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLE   86 (800)
Q Consensus        12 q~rtLFVGNLp~sVTEEdLr----elFskFGeV~sVrVIRd-TGRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe   86 (800)
                      ..++|||||||+.+++++|+    .+|++||+|..|.+.+. ..+|||||+|.+  .++|.+|+..|||..++|+.|+|.
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 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKE--VSSATNALRSMQGFPFYDKPMRIQ   79 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESS--HHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEEECCCCCCEEEEECC--HHHHHHHHHHHCCCEECCEEEEEE
T ss_conf             899999959999999999999999870312325532885430689815788899--999999999849988999888999


Q ss_pred             ECCCHH
Q ss_conf             424013
Q 003717           87 RAKEHY   92 (800)
Q Consensus        87 ~AkPk~   92 (800)
                      +|+++.
T Consensus        80 ~ak~~~   85 (91)
T d1nu4a_          80 YAKTDS   85 (91)
T ss_dssp             ECSSCC
T ss_pred             EECCCC
T ss_conf             807975

>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=99.57  E-value=5.6e-15  Score=105.79  Aligned_cols=76  Identities=16%  Similarity=0.259  Sum_probs=69.5

Q ss_pred             CCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECCCCCCEEEEEECCCCHHHHHHHHHHCCCCEE-CCEEEEEEECCC
Q ss_conf             7849999079988998899985303896249999656997679999368998899999984599476-793779974240
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVW-KGGRLRLERAKE   90 (800)
Q Consensus        12 q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRdTGRGFGFVeFaS~D~EDAeKAIeeLNG~eL-dGRkLkVe~AkP   90 (800)
                      ..++|||+|||+.+++++|+.+|++||.|..++++++ .+|||||+|.+  .++|..|+..|+|..+ +|++|+|.||+.
T Consensus         7 P~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~-~~g~afV~f~~--~~~A~~A~~~l~g~~~~~~~~i~v~~akk   83 (83)
T d2b0ga1           7 PNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN-RHDIAFVEFTT--ELQSNAAKEALQGFKITPTHAMKITFAKK   83 (83)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT-TCSCEEEEESS--HHHHHHHHHHHTTCBSSTTCBCEEEECCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHCCCCCEEEEEEECC-CCEEEEEECCC--HHHHHHHHHHHCCCEECCCCEEEEEEECC
T ss_conf             9889999889987779999754235764787431011-21148995199--99999999983994968992899998419

>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=99.57  E-value=6.3e-15  Score=105.51  Aligned_cols=76  Identities=25%  Similarity=0.441  Sum_probs=65.7

Q ss_pred             CCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC---CC--CCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEE
Q ss_conf             7849999079988998899985303896249999656---99--767999936899889999998459947679377997
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT---KG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLE   86 (800)
Q Consensus        12 q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd---TG--RGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe   86 (800)
                      ...+|||+|||+.+++++|+++|+.|| +..+.++++   ++  +|||||+|.+  .++|.+|+ .||+..|+||.|+|+
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~--~e~a~~~~-~~~~~~~~gr~l~V~   89 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFED--LDSLLSAL-SLNEESLGNKRIRVD   89 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESS--HHHHHHHH-GGGTCEETTEECEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHHC-CCCCEEEEEECCCCCCCEEEEEEECC--HHHHHHHH-HCCCCEECCEEEEEE
T ss_conf             997899809998698999999999832-15310234311478861354578779--99999999-809998999988999


Q ss_pred             ECCCH
Q ss_conf             42401
Q 003717           87 RAKEH   91 (800)
Q Consensus        87 ~AkPk   91 (800)
                      +|.++
T Consensus        90 ~a~~~   94 (104)
T d1wi8a_          90 VADQA   94 (104)
T ss_dssp             ECCCC
T ss_pred             ECCCC
T ss_conf             78998

>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=1.1e-15  Score=110.19  Aligned_cols=79  Identities=23%  Similarity=0.303  Sum_probs=71.6

Q ss_pred             CCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC----CCCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEE
Q ss_conf             7849999079988998899985303896249999656----997679999368998899999984599476793779974
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT----KGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLER   87 (800)
Q Consensus        12 q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd----TGRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~   87 (800)
                      ..++|||+|||+.+++++|+++|++||.|..+.++.+    ..+|||||+|.+  .++|..|+..|||..|.|++|+|.+
T Consensus        17 ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~--~~~A~~Ai~~l~g~~~~g~~l~V~~   94 (102)
T d2cpxa1          17 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPN--KEIAWQALHLVNGYKLYGKILVIEF   94 (102)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSS--HHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEECCCCCCCCCCCCEEEECC--HHHHHHHHHHHCCCEECCEEEEEEE
T ss_conf             99899996999989899999978534542467753046655555321477433--7899999998589988999889996


Q ss_pred             CCCHH
Q ss_conf             24013
Q 003717           88 AKEHY   92 (800)
Q Consensus        88 AkPk~   92 (800)
                      |+++.
T Consensus        95 ak~k~   99 (102)
T d2cpxa1          95 GKNKK   99 (102)
T ss_dssp             CCCCS
T ss_pred             CCCCC
T ss_conf             77803

>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=99.56  E-value=5.4e-15  Score=105.92  Aligned_cols=80  Identities=14%  Similarity=0.236  Sum_probs=71.9

Q ss_pred             HHHCCCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECCCCCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEE
Q ss_conf             01005784999907998899889998530389624999965699767999936899889999998459947679377997
Q 003717            7 EAEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLE   86 (800)
Q Consensus         7 ~~Ev~q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRdTGRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe   86 (800)
                      +...+...+|||+|||+.+++++|+++|.+||.|..|.+.+   +|||||+|.+  .++|.+|++.|||..|.|+.|+|.
T Consensus         9 p~~~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~---~g~afV~f~~--~~~a~~Ai~~lng~~~~g~~i~v~   83 (98)
T d1wg4a_           9 PPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK---DGMGMVEYLR--KEDMEYALRKLDDTKFRSHEGETS   83 (98)
T ss_dssp             CCCCSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET---TTEEEEEESS--HHHHHHHHHHHSSEEEECTTSCEE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCC---CCEEEEEECC--HHHHHHHHHHHCCCEECCEEEEEE
T ss_conf             77999888899977999998999999997522343200133---4469999789--999999999968899689088999


Q ss_pred             ECCCH
Q ss_conf             42401
Q 003717           87 RAKEH   91 (800)
Q Consensus        87 ~AkPk   91 (800)
                      +++++
T Consensus        84 ~~~~~   88 (98)
T d1wg4a_          84 YIRVY   88 (98)
T ss_dssp             EEEEE
T ss_pred             EEECC
T ss_conf             97137

>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=99.56  E-value=1.3e-15  Score=109.58  Aligned_cols=72  Identities=18%  Similarity=0.270  Sum_probs=67.4

Q ss_pred             EEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECCCCCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEECCCH
Q ss_conf             99990799889988999853038962499996569976799993689988999999845994767937799742401
Q 003717           15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKEH   91 (800)
Q Consensus        15 tLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRdTGRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~AkPk   91 (800)
                      +|||||||+.+++++|+++|++||.|..+.+++   .|||||+|.+  .++|.+|+..|||..|.|+.|+|.+++++
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~---~g~afV~f~~--~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~   73 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR---DGTGVVEFVR--KEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECT---TSEEEEEESS--HHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             EEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCC---CCEEEEEECC--HHHHHHHHHHHCCCEECCCEEEEEEEECC
T ss_conf             699979998588999999875221232110022---3213577488--89999999996879979967587577617

>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=99.56  E-value=3e-14  Score=101.44  Aligned_cols=81  Identities=23%  Similarity=0.456  Sum_probs=72.0

Q ss_pred             HCCCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC--CC--CCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEE
Q ss_conf             0057849999079988998899985303896249999656--99--7679999368998899999984599476793779
Q 003717            9 EVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--KG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLR   84 (800)
Q Consensus         9 Ev~q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd--TG--RGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLk   84 (800)
                      .....++|||+|||+.+++++|+++|+.||.|..+.++++  ++  +|||||+|.+  .++|.+|+. +++..+.|++|+
T Consensus        93 ~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~--~e~A~~Al~-~~~~~~~G~~i~  169 (183)
T d1u1qa_          93 AHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD--HDSVDKIVI-QKYHTVNGHNCE  169 (183)
T ss_dssp             TTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESC--HHHHHHHHT-SSCEEETTEEEE
T ss_pred             CCCCCCEEEECCCCCCCCHHHHHHHHCCCCCEEEEEEECCCCCCCCCEEEEEEECC--HHHHHHHHH-HCCCEECCEEEE
T ss_conf             34564235881677767899996543158865322330026668501059999789--999999998-599909997979


Q ss_pred             EEECCCHH
Q ss_conf             97424013
Q 003717           85 LERAKEHY   92 (800)
Q Consensus        85 Ve~AkPk~   92 (800)
                      |.+|.++.
T Consensus       170 V~~A~~k~  177 (183)
T d1u1qa_         170 VRKALSKQ  177 (183)
T ss_dssp             EEECCCHH
T ss_pred             EEECCCCC
T ss_conf             99668844

>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=99.56  E-value=3.9e-15  Score=106.78  Aligned_cols=71  Identities=24%  Similarity=0.429  Sum_probs=65.1

Q ss_pred             EEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC--CC--CCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEEC
Q ss_conf             9999079988998899985303896249999656--99--76799993689988999999845994767937799742
Q 003717           15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--KG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERA   88 (800)
Q Consensus        15 tLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd--TG--RGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~A   88 (800)
                      +|||||||+++++++|+++|++||.|..+.++++  ++  +|||||+|.+  .++|.+|++ +||+.|+||+|+|++|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~--~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFES--EDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSC--HHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEECCCCCCCHHHHHHHHHHHCCCCEEEEEEECCCCCCCCEEEEEECC--HHHHHHHHH-CCCCEECCEEEEEEEC
T ss_conf             98990899988899999999986874022332103433567336999989--999999995-2999899949899889

>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=99.55  E-value=5.2e-15  Score=106.02  Aligned_cols=74  Identities=19%  Similarity=0.410  Sum_probs=66.1

Q ss_pred             CCCCEEEEECCCCCCCHHHH---HHHHHCCCCEEEEEEECCC--C-----CCEEEEEECCCCHHHHHHHHHHCCCCEECC
Q ss_conf             57849999079988998899---9853038962499996569--9-----767999936899889999998459947679
Q 003717           11 EEQTRIYVGGLGEKVTDDDL---AKVFSSLGEVKAVDIVRTK--G-----RSFGYVDFFPSSHKSLSKLFSTYNGCVWKG   80 (800)
Q Consensus        11 ~q~rtLFVGNLp~sVTEEdL---relFskFGeV~sVrVIRdT--G-----RGFGFVeFaS~D~EDAeKAIeeLNG~eLdG   80 (800)
                      -+..+|||+|||+.+++++|   +++|++||.|..|.++++.  +     +|||||+|.+  .++|.+|+..|||..|+|
T Consensus         6 iq~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~--~~~A~~Ai~~lng~~~~g   83 (89)
T d2cpia1           6 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIR--SEDALRAIQCVNNVVVDG   83 (89)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESS--HHHHHHHHHHHTTEEETT
T ss_pred             EECCEEEEECCCCCCCHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCCEEEEEECCC--CHHHHHHHHHHCCCEECC
T ss_conf             826889997989763878999889876355882587772026768777765379985154--122999999858999999


Q ss_pred             EEEEEE
Q ss_conf             377997
Q 003717           81 GRLRLE   86 (800)
Q Consensus        81 RkLkVe   86 (800)
                      |.|+|.
T Consensus        84 r~lkvS   89 (89)
T d2cpia1          84 RTLKAS   89 (89)
T ss_dssp             EEEEEE
T ss_pred             EEEEEC
T ss_conf             788879

>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=1.8e-14  Score=102.68  Aligned_cols=75  Identities=21%  Similarity=0.292  Sum_probs=67.7

Q ss_pred             CCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC-CC--CCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEEC
Q ss_conf             7849999079988998899985303896249999656-99--76799993689988999999845994767937799742
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT-KG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERA   88 (800)
Q Consensus        12 q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd-TG--RGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~A   88 (800)
                      ..++|||+|||+.+++++|+++|+.||.|..|.++++ ++  ||||||+|.+  .++|.+|++ ++|..+.||.|.|.++
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~--~e~a~~al~-~~~~~~~g~~l~v~~~   81 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDS--IESAKKFVE-TPGQKYKETDLLILFK   81 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESC--HHHHHHHHT-CCCCEETTEECEEEEG
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHHCCCCCCEEEEECCCCCCEEEEEEECC--HHHHHHHHH-HCCCEECCEEEEEEEC
T ss_conf             8678999797987979999998987552423003210258863578999848--999999999-7899799989899973


Q ss_pred             C
Q ss_conf             4
Q 003717           89 K   89 (800)
Q Consensus        89 k   89 (800)
                      .
T Consensus        82 ~   82 (85)
T d1zh5a2          82 D   82 (85)
T ss_dssp             G
T ss_pred             C
T ss_conf             7

>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=99.55  E-value=3e-15  Score=107.49  Aligned_cols=71  Identities=20%  Similarity=0.441  Sum_probs=64.5

Q ss_pred             EEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC--C--CCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEEC
Q ss_conf             9999079988998899985303896249999656--9--976799993689988999999845994767937799742
Q 003717           15 RIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--K--GRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERA   88 (800)
Q Consensus        15 tLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd--T--GRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~A   88 (800)
                      +|||||||+++++++|+++|++||.|..|.++++  +  +||||||+|.+  .++|.+|++ ++++.++|+.|.|+.|
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 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKE--EEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESS--SHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             CEEECCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEECC--HHHHHHHHH-HCCCEECCEEEEEEEC
T ss_conf             98991899989899999999985876521224465545665289999788--999999983-0998799978599889

>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=99.55  E-value=8.9e-15  Score=104.58  Aligned_cols=77  Identities=31%  Similarity=0.582  Sum_probs=70.2

Q ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECCCCCCEEEEEECCCCHHHHHHHHHHCCCCEECC--EEEEEEEC
Q ss_conf             5784999907998899889998530389624999965699767999936899889999998459947679--37799742
Q 003717           11 EEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKG--GRLRLERA   88 (800)
Q Consensus        11 ~q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRdTGRGFGFVeFaS~D~EDAeKAIeeLNG~eLdG--RkLkVe~A   88 (800)
                      ...++|||+|||+++++++|+++|++||.|..+.+++  +++||||+|.+  .++|..|+..||+..|.|  ++|+|++|
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~--~~~~afV~f~~--~~~A~~A~~~l~~~~i~g~~~~l~v~~a   90 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVK--GDSFAYIQYES--LDAAQAACAKMRGFPLGGPDRRLRVDFA   90 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECS--SSCCEEEEESS--HHHHHHHHHHHTTCBCSSSSCBCEEEEC
T ss_pred             CCCCEEEECCCCCCCCHHHHHHHHHHHCCCCEEEEEC--CCCEEEECCCC--HHHHHHHHHHHCCCEECCCCEEEEEEEC
T ss_conf             9999999848999898999999997534562476402--22178761499--9999999998588896999658999868


Q ss_pred             CCH
Q ss_conf             401
Q 003717           89 KEH   91 (800)
Q Consensus        89 kPk   91 (800)
                      ++.
T Consensus        91 k~~   93 (97)
T d1whya_          91 KSG   93 (97)
T ss_dssp             CCC
T ss_pred             CCC
T ss_conf             898

>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=99.55  E-value=7.5e-15  Score=105.05  Aligned_cols=77  Identities=17%  Similarity=0.350  Sum_probs=68.0

Q ss_pred             CEEEEECCCCCCCHHHHHHHHHCCCC-EEEEEEECC---C--CCCEEEEEECCCCHHHHHHHHHHCCC--CEECCEEEEE
Q ss_conf             49999079988998899985303896-249999656---9--97679999368998899999984599--4767937799
Q 003717           14 TRIYVGGLGEKVTDDDLAKVFSSLGE-VKAVDIVRT---K--GRSFGYVDFFPSSHKSLSKLFSTYNG--CVWKGGRLRL   85 (800)
Q Consensus        14 rtLFVGNLp~sVTEEdLrelFskFGe-V~sVrVIRd---T--GRGFGFVeFaS~D~EDAeKAIeeLNG--~eLdGRkLkV   85 (800)
                      .+|||||||+.+++++|+++|++||+ |..+.++++   +  +||||||+|.+  .++|..|+..|++  ..++|+.|+|
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~--~~~A~~Ai~~l~~~~~~~~g~~i~V   79 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYES--HRAAAMARRKLMPGRIQLWGHQIAV   79 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESS--HHHHHHHHTTTTTCCSCBTTBCCEE
T ss_pred             CEEEECCCCCCCCHHHHHHHHHHHCCCCEEEEEEEECCCCCCCCCEEEEEECC--HHHHHHHHHHHCCCCEEECCEEEEE
T ss_conf             79999498986889999999998697505899864112323678759999839--9999999999768982789988899


Q ss_pred             EECCCHH
Q ss_conf             7424013
Q 003717           86 ERAKEHY   92 (800)
Q Consensus        86 e~AkPk~   92 (800)
                      +||+|+.
T Consensus        80 ~~A~p~~   86 (96)
T d2disa1          80 DWAEPEI   86 (96)
T ss_dssp             EESCSSC
T ss_pred             EECCCCC
T ss_conf             9718988

>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=99.55  E-value=8.1e-15  Score=104.83  Aligned_cols=75  Identities=9%  Similarity=0.202  Sum_probs=65.4

Q ss_pred             CCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECCCCCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEECCCH
Q ss_conf             78499990799889988999853038962499996569976799993689988999999845994767937799742401
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKEH   91 (800)
Q Consensus        12 q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRdTGRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~AkPk   91 (800)
                      ..++|||+|||+.+++++|+++|.+||. ..+.+.  ..+|||||+|.+  .++|.+|+..||+..++||+|+|.+|+.+
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G~-~~~~~~--~~kg~afV~f~~--~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~   78 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYDL-KYCYVD--RNKRTAFVTLLN--GEQAQNAIQMFHQYSFRGKDLIVQLQPTD   78 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSCC-CCEEEE--GGGTEEEECCSC--HHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHCCC-EEEEEE--CCCCCEEEEECC--HHHHHHHHHHHCCCEECCEEEEEEECCCC
T ss_conf             9989999699986375788777886096-035301--157714899889--99999999985899899989899983899

>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=99.54  E-value=1.9e-14  Score=102.65  Aligned_cols=73  Identities=18%  Similarity=0.226  Sum_probs=66.2

Q ss_pred             CEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC--CCCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEECC
Q ss_conf             49999079988998899985303896249999656--99767999936899889999998459947679377997424
Q 003717           14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--KGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAK   89 (800)
Q Consensus        14 rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd--TGRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~Ak   89 (800)
                      ++|||+|||+.+++++|+++|..||.|..++++++  .+++||||+|.+  .++|.+|+ .||+..|+|++|.|..+.
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~~~~afV~F~~--~~~a~~Al-~~~~~~i~g~~i~V~~~T   75 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFAR--YDGALAAI-TKTHKVVGQNEIIVSHLT   75 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESS--HHHHHHHH-TTTTCEETTEECEEEECC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEEEECCCCCEEEEEEECC--HHHHHHHH-HHCCCEECCEEEEEEECC
T ss_conf             9999989999998899999871288169999975023331699999832--67768888-736969999999999898

>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=99.52  E-value=3.2e-14  Score=101.27  Aligned_cols=81  Identities=11%  Similarity=0.140  Sum_probs=69.1

Q ss_pred             HHCCCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC--C--CCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEE
Q ss_conf             10057849999079988998899985303896249999656--9--9767999936899889999998459947679377
Q 003717            8 AEVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--K--GRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRL   83 (800)
Q Consensus         8 ~Ev~q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd--T--GRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkL   83 (800)
                      ++......|||+||||++++++|+++|..+|.+..+.++..  +  .+|||||+|.+  .++|.+|++ +|+..|+||.|
T Consensus        10 ~~~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~--~e~a~~a~~-~~~~~i~gR~i   86 (104)
T d1wg5a_          10 PDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFAS--QEIAEKALK-KHKERIGHRYI   86 (104)
T ss_dssp             SSCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESS--HHHHHHHHT-TTTCCSSSSCC
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHHCCCCEEEEEEEECCCCCCCEEEEEEECC--HHHHHHHHH-HCCCEECCEEE
T ss_conf             988998589985899989899999988753872478897768999723688997489--999999874-48988933599


Q ss_pred             EEEECCCH
Q ss_conf             99742401
Q 003717           84 RLERAKEH   91 (800)
Q Consensus        84 kVe~AkPk   91 (800)
                      +|.++.++
T Consensus        87 ~V~~~~~~   94 (104)
T d1wg5a_          87 EIFKSSRA   94 (104)
T ss_dssp             EEEEECTT
T ss_pred             EEEECCHH
T ss_conf             99988977

>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=99.51  E-value=8.8e-14  Score=98.59  Aligned_cols=77  Identities=9%  Similarity=0.233  Sum_probs=69.5

Q ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECCCCCCEEEEEECCCCHHHHHHHHHHC--CCCEECCEEEEEEEC
Q ss_conf             578499990799889988999853038962499996569976799993689988999999845--994767937799742
Q 003717           11 EEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTY--NGCVWKGGRLRLERA   88 (800)
Q Consensus        11 ~q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRdTGRGFGFVeFaS~D~EDAeKAIeeL--NG~eLdGRkLkVe~A   88 (800)
                      ...++|||||||+.+++++|+++|++||.|..+.+++  .+|||||+|.+  .++|..|+..|  ++..+.||+|+|.+|
T Consensus         6 ~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~--~~~~afV~f~~--~e~A~~a~~~~~~~~~~~~g~~l~v~~s   81 (88)
T d2cq1a1           6 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLK--GKNQAFLELAT--EEAAITMVNYYSAVTPHLRNQPIYIQYS   81 (88)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEET--TTTEEEEEESS--HHHHHHHHHHHHHSCCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCC--CCEEEEEEECC--HHHHHHHHHHHCCCCCCCCCCEEEEEEC
T ss_conf             9999999967998888999998875024222200023--44179998489--9999999999805997459977999978


Q ss_pred             CCH
Q ss_conf             401
Q 003717           89 KEH   91 (800)
Q Consensus        89 kPk   91 (800)
                      +.+
T Consensus        82 k~~   84 (88)
T d2cq1a1          82 NHK   84 (88)
T ss_dssp             SCS
T ss_pred             CCC
T ss_conf             887

>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=99.50  E-value=7.4e-14  Score=99.04  Aligned_cols=71  Identities=15%  Similarity=0.259  Sum_probs=64.0

Q ss_pred             EEEECCCCCCCHHHHHHHHHCCCCEEEEEEECCCCCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEECCCH
Q ss_conf             9990799889988999853038962499996569976799993689988999999845994767937799742401
Q 003717           16 IYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKEH   91 (800)
Q Consensus        16 LFVGNLp~sVTEEdLrelFskFGeV~sVrVIRdTGRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~AkPk   91 (800)
                      |||+|||+++++++|+++|++|| +..+.+.  ..+|||||+|.+  .++|.+|+..|||..+.||+|+|.+|+..
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--KYKGTAFVTLLN--GEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEE--TTTTEEEEEESS--HHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEECCCCCCCHHHHHHHHHCCC-CCCEEEC--CCCEEEEEEECC--HHHHHHHHHHHCCCCCCCCEEEEEEECCC
T ss_conf             99969999678999999874325-2211554--632169999877--78888888985796679989999996798

>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=2.6e-14  Score=101.74  Aligned_cols=77  Identities=9%  Similarity=0.089  Sum_probs=69.0

Q ss_pred             CCCEEEEECCCCCC-CH----HHHHHHHHCCCCEEEEEEECCCCCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEE
Q ss_conf             78499990799889-98----89998530389624999965699767999936899889999998459947679377997
Q 003717           12 EQTRIYVGGLGEKV-TD----DDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLE   86 (800)
Q Consensus        12 q~rtLFVGNLp~sV-TE----EdLrelFskFGeV~sVrVIRdTGRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe   86 (800)
                      ...+|||+||+..+ ++    +.|+.+|++||.|.++.+++  ++|||||+|.+  .++|.+|+..|||..|+|++|+|.
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k--~~~~afV~f~~--~~~A~~Ai~~lng~~~~g~~l~v~   79 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK--SFKRVRINFSN--PLSAADARLRLHKTEFLGKEMKLY   79 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET--TTTEEEEECSS--TTHHHHHHHTSTTSEETTEECEEE
T ss_pred             CCCEEEEEECCCHHCCCHHHHHHHHHHHCCCCCCEEEEEEC--CCCEEEEEECC--HHHHHHHHHHHCCCCCCCCEEEEE
T ss_conf             87608999589011371888999998720355526899966--88789999899--999999999855013389876885


Q ss_pred             ECCCHH
Q ss_conf             424013
Q 003717           87 RAKEHY   92 (800)
Q Consensus        87 ~AkPk~   92 (800)
                      +|+++.
T Consensus        80 ~a~~~~   85 (104)
T d1weya_          80 FAQTLH   85 (104)
T ss_dssp             CCCCSS
T ss_pred             ECCCCC
T ss_conf             344689

>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=99.50  E-value=3.8e-14  Score=100.76  Aligned_cols=78  Identities=13%  Similarity=0.223  Sum_probs=69.7

Q ss_pred             CCCCCEEEEECCCCC-CCHHHHHHHHHCCCCEEEEEEECCCCCCEEEEEECCCCHHHHHHHHH--HCCCCEECCEEEEEE
Q ss_conf             057849999079988-99889998530389624999965699767999936899889999998--459947679377997
Q 003717           10 VEEQTRIYVGGLGEK-VTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFS--TYNGCVWKGGRLRLE   86 (800)
Q Consensus        10 v~q~rtLFVGNLp~s-VTEEdLrelFskFGeV~sVrVIRdTGRGFGFVeFaS~D~EDAeKAIe--eLNG~eLdGRkLkVe   86 (800)
                      ....++|||+|||+. +++++|+++|++||.|..+.+++  .+|||||+|.+  .++|..|+.  .+++..++||+|+|.
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~--~k~~afV~f~~--~~~A~~Ai~~~~~~~~~~~gr~l~V~   90 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR--MKSQAFIEMET--REDAMAMVDHCLKKALWFQGRCVKVD   90 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET--TTTEEEEECSS--HHHHHHHHHHHHHSCCCSSSSCCEEE
T ss_pred             CCCCCEEEEECCCCCCCCHHHHHHHHCCCCCEEEEEEEE--CCCCEEEEECC--HHHHHHHHHHHHCCCCEECCEEEEEE
T ss_conf             788878999378677538999986653445304898760--47727999635--68999999997368964899788999


Q ss_pred             ECCCH
Q ss_conf             42401
Q 003717           87 RAKEH   91 (800)
Q Consensus        87 ~AkPk   91 (800)
                      +|+.+
T Consensus        91 ~s~~~   95 (99)
T d1x4fa1          91 LSEKY   95 (99)
T ss_dssp             EECSC
T ss_pred             ECCCC
T ss_conf             82870

>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=99.49  E-value=5.9e-14  Score=99.64  Aligned_cols=76  Identities=11%  Similarity=0.028  Sum_probs=66.2

Q ss_pred             CCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEE-C-CC--CCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEEC
Q ss_conf             8499990799889988999853038962499996-5-69--976799993689988999999845994767937799742
Q 003717           13 QTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV-R-TK--GRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERA   88 (800)
Q Consensus        13 ~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVI-R-dT--GRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~A   88 (800)
                      ...|||+|||+.+++++|+++|..||.+..+.++ . .+  .+|||||+|.+  .++|.+|+. +|+..|+||.|.|.++
T Consensus         8 ~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s--~~~a~~Al~-~n~~~i~gr~i~V~~~   84 (103)
T d2cpya1           8 KVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKN--EDDARKSER-LHRKKLNGREAFVHVV   84 (103)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSS--HHHHHHHGG-GCSEEETTEEEEEEEE
T ss_pred             CEEEEEECCCCCCCHHHHHHHHCCCCEEEEEEEEEECCCCCCCCCEEEEECC--HHHHHHHHH-CCCCEECCCEEEEEEC
T ss_conf             2089995989888889986421022237778888768989857637899889--999999996-3987499918999989


Q ss_pred             CCH
Q ss_conf             401
Q 003717           89 KEH   91 (800)
Q Consensus        89 kPk   91 (800)
                      .+.
T Consensus        85 ~~~   87 (103)
T d2cpya1          85 TLE   87 (103)
T ss_dssp             CHH
T ss_pred             CHH
T ss_conf             988

>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=99.49  E-value=2.9e-14  Score=101.45  Aligned_cols=82  Identities=13%  Similarity=0.193  Sum_probs=69.4

Q ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEE--CCCC--CCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEE
Q ss_conf             0578499990799889988999853038962499996--5699--76799993689988999999845994767937799
Q 003717           10 VEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIV--RTKG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRL   85 (800)
Q Consensus        10 v~q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVI--RdTG--RGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkV   85 (800)
                      .....+|||+||||.+++++|+++|+.||.+..+.++  ...|  +|||||+|.+  .++|.+|+. |||..|+||.|.|
T Consensus        15 ~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~--~e~a~~al~-~~~~~i~gR~i~V   91 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRN--EADYKAALC-RHKQYMGNRFIQV   91 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSS--SHHHHHHHT-SCSBCSTTSCBEE
T ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHCCCCCCCEEEECCCCCCEEEEEEEEECC--HHHHHHHHH-CCCCCCCCEEEEE
T ss_conf             8897699994699757599996677533444321022107654300478999889--999999997-1898479989899


Q ss_pred             EECCCHHHH
Q ss_conf             742401368
Q 003717           86 ERAKEHYLA   94 (800)
Q Consensus        86 e~AkPk~l~   94 (800)
                      ..+.++...
T Consensus        92 ~~~~~~~~~  100 (112)
T d1wela1          92 HPITKKGML  100 (112)
T ss_dssp             EEECHHHHH
T ss_pred             EECCHHHHH
T ss_conf             986957899

>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=99.48  E-value=5.2e-14  Score=99.99  Aligned_cols=79  Identities=18%  Similarity=0.197  Sum_probs=67.2

Q ss_pred             HCCCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC-CC--CCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEE
Q ss_conf             0057849999079988998899985303896249999656-99--76799993689988999999845994767937799
Q 003717            9 EVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT-KG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRL   85 (800)
Q Consensus         9 Ev~q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd-TG--RGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkV   85 (800)
                      +......|||+||||++|+++|+++|..||. ..+.++++ .+  +|||||+|.+  .++|.+|+. ||+..|+||.|+|
T Consensus        11 ~~~~~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~~~g~~~G~afVeF~~--~~~a~~Al~-~~~~~i~gR~I~V   86 (102)
T d1weza_          11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGPDGRVTGEADVEFAT--HEDAVAAMA-KDKANMQHRYVEL   86 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESSSSCEEEEEEEECSS--SHHHHHHHT-TSSCCSSSSCCEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHCCCC-CEEEEEEECCCCCEEEEEEEECC--HHHHHHHHH-CCCCEECCEEEEE
T ss_conf             6899988998089986889999878742475-22466772478604777899879--999999997-2999899999999


Q ss_pred             EECCCH
Q ss_conf             742401
Q 003717           86 ERAKEH   91 (800)
Q Consensus        86 e~AkPk   91 (800)
                      .++.++
T Consensus        87 ~~s~~~   92 (102)
T d1weza_          87 FLNSTA   92 (102)
T ss_dssp             EEECCC
T ss_pred             EECCCC
T ss_conf             975889

>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=99.48  E-value=1.3e-13  Score=97.61  Aligned_cols=79  Identities=18%  Similarity=0.186  Sum_probs=70.2

Q ss_pred             HCCCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECCCCCCEEEEEECCCCHHHHHHHHHHC--CCCEECCEEEEEE
Q ss_conf             00578499990799889988999853038962499996569976799993689988999999845--9947679377997
Q 003717            9 EVEEQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTY--NGCVWKGGRLRLE   86 (800)
Q Consensus         9 Ev~q~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRdTGRGFGFVeFaS~D~EDAeKAIeeL--NG~eLdGRkLkVe   86 (800)
                      .....+.|||+|||+.+++++|+.+|.+||.|..+.+.+  .+|||||+|.+  .++|..|+..|  ++..+.|++|+|.
T Consensus        11 ~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~--~k~~AfV~f~~--~e~A~~ai~~~~~~~~~~~g~~l~v~   86 (104)
T d1wexa_          11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP--FKRQALVEFEN--IDSAKECVTFAADVPVYIAGQQAFFN   86 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEET--TTTEEEEEESS--HHHHHHHHHHHHHSCCBSSSSBCEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHCCCCEEEEEEE--CCEEEEEEECC--HHHHHHHHHHHCCCCCEEEEEEEEEE
T ss_conf             699998999918999997999997660256534999973--11037998689--99999999987479948703788999


Q ss_pred             ECCCH
Q ss_conf             42401
Q 003717           87 RAKEH   91 (800)
Q Consensus        87 ~AkPk   91 (800)
                      +++.+
T Consensus        87 ~s~~~   91 (104)
T d1wexa_          87 YSTSK   91 (104)
T ss_dssp             ECSSS
T ss_pred             ECCCC
T ss_conf             74788

>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=99.48  E-value=5e-14  Score=100.08  Aligned_cols=75  Identities=16%  Similarity=0.135  Sum_probs=65.7

Q ss_pred             CCCEEEEECCCCCCCHHHHHHHHHCCCCEEEE-EEE-CCCC--CCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEE
Q ss_conf             78499990799889988999853038962499-996-5699--7679999368998899999984599476793779974
Q 003717           12 EQTRIYVGGLGEKVTDDDLAKVFSSLGEVKAV-DIV-RTKG--RSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLER   87 (800)
Q Consensus        12 q~rtLFVGNLp~sVTEEdLrelFskFGeV~sV-rVI-RdTG--RGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~   87 (800)
                      ....|||+|||+.+++++|+++|..||.+..+ .+. ..++  +|||||+|.+  .++|.+|+..||+..+.||+|+|.+
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~--~e~a~~Ai~~l~~~~l~gr~i~v~l   85 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFES--RDEATAAVIDLNDRPIGSRKVKLVL   85 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESC--HHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHCCCCEEEEEEEECCCCCCCEEEEEEECC--CHHHHHHHHHCCCCEECCEEEEEEE
T ss_conf             99889997989989899999877512464269999768999966089999828--5799999998089999999999997


Q ss_pred             C
Q ss_conf             2
Q 003717           88 A   88 (800)
Q Consensus        88 A   88 (800)
                      |
T Consensus        86 ~   86 (86)
T d2cqpa1          86 G   86 (86)
T ss_dssp             S
T ss_pred             C
T ss_conf             9

>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=99.44  E-value=2.8e-13  Score=95.53  Aligned_cols=78  Identities=10%  Similarity=0.154  Sum_probs=69.2

Q ss_pred             CCCCCEEEEECCCCC-CCHHHHHHHHHCCCCEEEEEEECCCCCCEEEEEECCCCHHHHHHHHHHC--CCCEECCEEEEEE
Q ss_conf             057849999079988-9988999853038962499996569976799993689988999999845--9947679377997
Q 003717           10 VEEQTRIYVGGLGEK-VTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTY--NGCVWKGGRLRLE   86 (800)
Q Consensus        10 v~q~rtLFVGNLp~s-VTEEdLrelFskFGeV~sVrVIRdTGRGFGFVeFaS~D~EDAeKAIeeL--NG~eLdGRkLkVe   86 (800)
                      .+..+.|||+|||.. +++++|+++|+.||.|..+.+++  .++||||.|.+  .++|..|+..|  ++..+.||+|+|.
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~--~k~~afV~f~~--~~~A~~A~~~l~~~~~~~~gr~l~V~   80 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILN--KINEAFIEMAT--TEDAQAAVDYYTTTPALVFGKPVRVH   80 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECS--SSSCEEEEESS--HHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCCCEEEEECCCCCCCCHHHHHHHHHHHCCEEEEEEEC--CCEEEEEEECC--HHHHHHHHHHHHHCCCCCCCCEEEEE
T ss_conf             899968999789987678999999998638727887604--42289999746--05579999987508886699248999


Q ss_pred             ECCCH
Q ss_conf             42401
Q 003717           87 RAKEH   91 (800)
Q Consensus        87 ~AkPk   91 (800)
                      +|+..
T Consensus        81 ~s~~~   85 (89)
T d1x4da1          81 LSQKY   85 (89)
T ss_dssp             EECCC
T ss_pred             ECCCC
T ss_conf             78885

>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=99.43  E-value=5.1e-14  Score=99.99  Aligned_cols=67  Identities=21%  Similarity=0.409  Sum_probs=62.0

Q ss_pred             EEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC--C--CCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEE
Q ss_conf             999079988998899985303896249999656--9--97679999368998899999984599476793779
Q 003717           16 IYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--K--GRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLR   84 (800)
Q Consensus        16 LFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd--T--GRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLk   84 (800)
                      |||+|||+.+++++|+++|++||.|..+.++++  +  .+|||||+|.+  .++|.+|+..|||..+.||.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~--~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDS--PSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESC--HHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEECCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEECC--HHHHHHHHHHHCCCEECCEECC
T ss_conf             9994799858899999988632333221110002332234115999889--9999999998389987888886

>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=99.43  E-value=3.3e-13  Score=95.08  Aligned_cols=76  Identities=22%  Similarity=0.225  Sum_probs=66.2

Q ss_pred             CCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECCCCCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEECCCH
Q ss_conf             8499990799889988999853038962499996569976799993689988999999845994767937799742401
Q 003717           13 QTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAKEH   91 (800)
Q Consensus        13 ~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRdTGRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~AkPk   91 (800)
                      ...+||||||+.+|+++|+.+|++||+|.+|.+++  ++|||||.|.+ ..++|..|+..||+..+.++.+.|.++...
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~--~kg~gfV~F~~-~~~~A~~a~~~~~~~~l~~~~~~v~~~~~~   86 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVR--GAKEGIILFKE-KAKEALGKAKDANNGNLQLRNKEVTWEVLE   86 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCT--TCSEEEEEESS-CHHHHHHHHHHTTTSCBCTTSSSEEEEECC
T ss_pred             CEEEEECCCCCCCCHHHHHHHHHHCCCHHEEEEEC--CCCEEEEEECC-CHHHHHHHHHHHCCCCEECCCEEEEEEECC
T ss_conf             76999879998787999999998357741488745--88668999668-278999999983488331574289876345

>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=99.36  E-value=9.5e-15  Score=104.42  Aligned_cols=73  Identities=16%  Similarity=0.503  Sum_probs=63.1

Q ss_pred             CEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEEC-------C--CCCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEE
Q ss_conf             4999907998899889998530389624999965-------6--997679999368998899999984599476793779
Q 003717           14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVR-------T--KGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLR   84 (800)
Q Consensus        14 rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIR-------d--TGRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLk   84 (800)
                      ++|||||||+.+++++|+++|++||.+..+.++.       .  ..+|||||+|.+  .++|.+|+. |||..++||+|+
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~--~e~a~~a~~-l~g~~~~Gr~l~   78 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRS--VDETTQAMA-FDGIIFQGQSLK   78 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESS--CTTTTTGGG-GSSCCSSSSCCC
T ss_pred             CEEEECCCCCCCCHHHHHHHHHHHCCEEEEEEECCCEEEECCCCCCCEEEEEEECC--HHHHHHHHH-HCCCEECCEEEE
T ss_conf             99999699976245898888986085779999425605664469976289998389--999999986-199588998889


Q ss_pred             EEECC
Q ss_conf             97424
Q 003717           85 LERAK   89 (800)
Q Consensus        85 Ve~Ak   89 (800)
                      |..++
T Consensus        79 V~r~k   83 (90)
T d1u2fa_          79 IRRPH   83 (90)
T ss_dssp             CBCTT
T ss_pred             ECCCC
T ss_conf             78888

>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=5.7e-12  Score=87.64  Aligned_cols=83  Identities=11%  Similarity=0.195  Sum_probs=71.3

Q ss_pred             HHHCCCCCEEEEECC--CCCCC---------HHHHHHHHHCCCCEEEEEEECCCCCCEEEEEECCCCHHHHHHHHHHCCC
Q ss_conf             010057849999079--98899---------8899985303896249999656997679999368998899999984599
Q 003717            7 EAEVEEQTRIYVGGL--GEKVT---------DDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNG   75 (800)
Q Consensus         7 ~~Ev~q~rtLFVGNL--p~sVT---------EEdLrelFskFGeV~sVrVIRdTGRGFGFVeFaS~D~EDAeKAIeeLNG   75 (800)
                      ++.....+.|+|.||  +..+.         .++|+..|++||.|..+.+.++..+||+||.|.+  .++|.+|+..|||
T Consensus         2 p~~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~~~G~~fV~f~~--~e~A~~A~~~lng   79 (99)
T d2dita1           2 PSRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRD--PEEADYCIQTLDG   79 (99)
T ss_dssp             CCCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSC--HHHHHHHHHHSTT
T ss_pred             CCCCCCCCEEEECCCCCHHHHHCCHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCEEEEEECC--HHHHHHHHHHHCC
T ss_conf             98877761999956999788434467789999999987267660799963477886479999898--9999999998689


Q ss_pred             CEECCEEEEEEECCCH
Q ss_conf             4767937799742401
Q 003717           76 CVWKGGRLRLERAKEH   91 (800)
Q Consensus        76 ~eLdGRkLkVe~AkPk   91 (800)
                      ..++||+|+|.++.++
T Consensus        80 ~~~~gr~i~v~~~~g~   95 (99)
T d2dita1          80 RWFGGRQITAQAWDGT   95 (99)
T ss_dssp             CEETTEECEEEECCSC
T ss_pred             CEECCEEEEEEEECCC
T ss_conf             6989979999983796

>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=99.27  E-value=6.9e-12  Score=87.13  Aligned_cols=71  Identities=18%  Similarity=0.315  Sum_probs=60.4

Q ss_pred             CCCCEEEEE--CCCCCCCHHHHHHHHHCCCCEEEEEEECCCCCCEEEEEECCCCHHHHHHHHHHCCCCEE-CCEEEEE
Q ss_conf             578499990--79988998899985303896249999656997679999368998899999984599476-7937799
Q 003717           11 EEQTRIYVG--GLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVW-KGGRLRL   85 (800)
Q Consensus        11 ~q~rtLFVG--NLp~sVTEEdLrelFskFGeV~sVrVIRdTGRGFGFVeFaS~D~EDAeKAIeeLNG~eL-dGRkLkV   85 (800)
                      ...++|||+  ||++.+++++|+++|++||.|..+.+++  ++|||||+|.+  .++|..|+..|||..+ +++.+++
T Consensus        16 ~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~--~k~~aFV~f~~--~e~A~~A~~~lng~~i~~~~~~~i   89 (101)
T d2cq2a1          16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP--NKPYSFARYRT--TEESKRAYVTLNGKEVVDDLGQKI   89 (101)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT--TCSCEEEEESS--HHHHHHHHHHTTTCEEECTTSCEE
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHHHCCCCEEEECC--CCCEEEEEECC--HHHHHHHHHHHCCCCCCCCCCCEE
T ss_conf             997659997778999878999999997527661786326--75089999899--899999999838989779999478

>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=9.1e-13  Score=92.45  Aligned_cols=73  Identities=14%  Similarity=0.189  Sum_probs=66.2

Q ss_pred             CEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC---CCCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEEC
Q ss_conf             49999079988998899985303896249999656---9976799993689988999999845994767937799742
Q 003717           14 TRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT---KGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERA   88 (800)
Q Consensus        14 rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd---TGRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~A   88 (800)
                      ..++|+++...+++++|+++|++||.|.+|.|+++   ..||||||+|.+  .++|.+|+..|||..++||+|+|++.
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 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRR--EEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESC--HHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             CHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCCEEEEEEEEEEC--HHHHHHHHHHHCCCEECCEEEEEEEC
T ss_conf             56886630166569999998505787899996218999884179999954--03799999997898899999999977

>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=99.17  E-value=5.8e-11  Score=81.55  Aligned_cols=73  Identities=12%  Similarity=0.164  Sum_probs=62.6

Q ss_pred             CCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECCCCCCEEEEEECCCCHHHHHHHHHHCCCCEECCEE-EEEEECCCH
Q ss_conf             8499990799889988999853038962499996569976799993689988999999845994767937-799742401
Q 003717           13 QTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGR-LRLERAKEH   91 (800)
Q Consensus        13 ~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRdTGRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRk-LkVe~AkPk   91 (800)
                      ...|||+++|+.++++.| ++|++||+|.++++.+  .+|||||+|.+  .++|.+|+. +||..+.||. |.|..+..+
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~--~~~~~fV~f~~--~~~A~~Al~-~nG~~~~g~~~vgV~~~~~k   77 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSN--TGNWMHIRYQS--KLQARKALS-KDGRIFGESIMIGVKPCIDK   77 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECS--SSSEEEEEESS--HHHHHHHHT-TTTCEETTTEECEEEECCCH
T ss_pred             CCEEEEECCCHHHHHHHH-HHHHHHHHHHEEEECC--CCCEEEEEECC--CHHHHHHHH-CCCCEECCCEEEEEEECCCH
T ss_conf             409999898857779999-9997420110689548--99889999763--279999986-07875799579999968874

>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=98.91  E-value=9e-10  Score=74.34  Aligned_cols=78  Identities=17%  Similarity=0.198  Sum_probs=65.3

Q ss_pred             CCCEEEEECC--CCCCC--------HHHHHHHHHCCCCEEEEEEECCC------CCCEEEEEECCCCHHHHHHHHHHCCC
Q ss_conf             7849999079--98899--------88999853038962499996569------97679999368998899999984599
Q 003717           12 EQTRIYVGGL--GEKVT--------DDDLAKVFSSLGEVKAVDIVRTK------GRSFGYVDFFPSSHKSLSKLFSTYNG   75 (800)
Q Consensus        12 q~rtLFVGNL--p~sVT--------EEdLrelFskFGeV~sVrVIRdT------GRGFGFVeFaS~D~EDAeKAIeeLNG   75 (800)
                      .++.|.+.|+  +..+.        .++|++.|++||.|.+|.|++..      .+|++||.|.+  .++|.+|+..|||
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~--~e~A~~A~~~l~G   80 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTS--VFDCQKAMQGLTG   80 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESC--HHHHHHHHHHHSS
T ss_pred             CCCEEEEECCCCHHHCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCEEEEEEECC--HHHHHHHHHHHCC
T ss_conf             87599996889877737831488899999999616682577897523777765773289999899--9999999999789


Q ss_pred             CEECCEEEEEEECCCH
Q ss_conf             4767937799742401
Q 003717           76 CVWKGGRLRLERAKEH   91 (800)
Q Consensus        76 ~eLdGRkLkVe~AkPk   91 (800)
                      ..++||.|.+.++.+.
T Consensus        81 r~f~gR~v~v~f~~~~   96 (104)
T d1o0pa_          81 RKFANRVVVTKYCDPD   96 (104)
T ss_dssp             CCSSSSCCEEEEECHH
T ss_pred             CEECCEEEEEEECCHH
T ss_conf             9989918999985878

>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=97.82  E-value=1.6e-06  Score=54.79  Aligned_cols=69  Identities=16%  Similarity=0.146  Sum_probs=52.1

Q ss_pred             CCCCCCCCCCCCCHHHCCCCCCCCCEEE---ECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCC
Q ss_conf             3479988888852000011467642366---0158999721-11133368999964344102123546414681026899
Q 003717          124 TRLDTPKKLLDKDKKLNIFFPRLRKVKT---LPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPAA  199 (800)
Q Consensus       124 ~is~~Lk~svsesd~LreyFskyGKVKs---Vp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n~  199 (800)
                      ++ ++|+.++++ ++|+.+|++||.|..   ++++.+|+++ |||         |.|.+.+++..|++.    .-|.+++
T Consensus         3 fV-gnLp~~~te-~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~F---------V~f~~~~~a~~al~~----~~~~i~g   67 (75)
T d1x0fa1           3 FV-GGLSPDTPE-EKIREYFGGFGEVESIELPMDNKTNKRRGFCF---------ITFKEEEPVKKIMEK----KYHNVGL   67 (75)
T ss_dssp             EE-ESCCSSCCH-HHHHHHHHHHSCEEEEECCCCTTTCCTTCCEE---------EEESSSHHHHHHTTC----SSCCBTT
T ss_pred             EE-CCCCCCCCH-HHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEE---------EEECCHHHHHHHHHH----CCCEECC
T ss_conf             99-189998989-99999999858765212244655456652899---------997889999999830----9987999


Q ss_pred             CCCCCCHH
Q ss_conf             86321021
Q 003717          200 GQEEIHDM  207 (800)
Q Consensus       200 ~q~~i~~~  207 (800)
                      ++++|++|
T Consensus        68 ~~i~vk~A   75 (75)
T d1x0fa1          68 SKCEIKVA   75 (75)
T ss_dssp             BCCEEECC
T ss_pred             EEEEEEEC
T ss_conf             78599889

>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=97.80  E-value=6.8e-06  Score=50.93  Aligned_cols=69  Identities=10%  Similarity=0.054  Sum_probs=52.7

Q ss_pred             CCCCCCCCCCCCCCHHHCCCCCCCCCE---EEECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCC
Q ss_conf             334799888888520000114676423---660158999721-1113336899996434410212354641468102689
Q 003717          123 ATRLDTPKKLLDKDKKLNIFFPRLRKV---KTLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPA  198 (800)
Q Consensus       123 l~is~~Lk~svsesd~LreyFskyGKV---KsVp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n  198 (800)
                      ++++ +|+.++++ ++|+.+|++||.|   ++++++.+|+++ |||         |.|.+-+++..|+. +|+..+   +
T Consensus         3 lfV~-nLp~~~te-~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aF---------V~f~~~~~a~~al~-~~~~~i---~   67 (77)
T d1uawa_           3 MFIG-GLSWQTTQ-EGLREYFGQFGEVKECLVMRDPLTKRSRGFGF---------VTFMDQAGVDKVLA-QSRHEL---D   67 (77)
T ss_dssp             EEEE-SCCSSCCS-HHHHHHHTTTSCCCCEEEECCCCSSSCSSEEE---------ECCCCTTHHHHHHH-TTTCCC---S
T ss_pred             EEEE-CCCCCCCH-HHHHHHHHHHCCCCEEEEECCCCCCCCCCEEE---------EEECCHHHHHHHHH-CCCCEE---C
T ss_conf             9991-89996989-99999999869862024411367888666399---------99889999999997-198989---9


Q ss_pred             CCCCCCCH
Q ss_conf             98632102
Q 003717          199 AGQEEIHD  206 (800)
Q Consensus       199 ~~q~~i~~  206 (800)
                      |....|+.
T Consensus        68 Gr~i~V~~   75 (77)
T d1uawa_          68 SKTIDPKV   75 (77)
T ss_dssp             SCCCEEEE
T ss_pred             CEEEEEEE
T ss_conf             94989997

>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=97.75  E-value=7.3e-06  Score=50.74  Aligned_cols=76  Identities=14%  Similarity=0.092  Sum_probs=60.7

Q ss_pred             CCCCCCCCCCCCCCCHHHCCCCCCCCCEEEE---CCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCC
Q ss_conf             7334799888888520000114676423660---158999721-111333689999643441021235464146810268
Q 003717          122 DATRLDTPKKLLDKDKKLNIFFPRLRKVKTL---PFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHP  197 (800)
Q Consensus       122 kl~is~~Lk~svsesd~LreyFskyGKVKsV---p~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~  197 (800)
                      .+++++ |+..+++ ++|+.+|++||.|..+   +++.+|+++ |||         |.|.+.+++..|+.+|||..+.  
T Consensus        11 tlfV~n-Lp~~~t~-~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~af---------V~f~~~~~A~~Ai~~l~g~~~~--   77 (93)
T d1x5ua1          11 TVYVGG-LDEKVSE-PLLWELFLQAGPVVNTHMPKDRVTGQHQGYGF---------VEFLSEEDADYAIKIMDMIKLY--   77 (93)
T ss_dssp             EEEEEC-CCTTCCH-HHHHHHHHTTSCEEEEECCBCSSSCSBCSCEE---------EEESSHHHHHHHHHHSSSCBCS--
T ss_pred             EEEEEC-CCCCCCH-HHHHHHHHHHCCCCCCCEEECCCCCCCCCCEE---------EEECCHHHHHHHHHHCCCCEEC--
T ss_conf             999908-9985889-99999999849765421210125435665207---------9989999999999985999899--


Q ss_pred             CCCCCCCCHHHHCC
Q ss_conf             99863210211027
Q 003717          198 AAGQEEIHDMEELG  211 (800)
Q Consensus       198 n~~q~~i~~~ee~~  211 (800)
                       +....|..+.+..
T Consensus        78 -g~~l~V~~A~~~~   90 (93)
T d1x5ua1          78 -GKPIRVNKASAHN   90 (93)
T ss_dssp             -SCBCEEEETTTTS
T ss_pred             -CEEEEEEECCCCC
T ss_conf             -9887998728989

>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=97.69  E-value=5.5e-06  Score=51.49  Aligned_cols=78  Identities=14%  Similarity=0.086  Sum_probs=59.1

Q ss_pred             CCCCCCCCCCCCCCCHHHCCCCCCCCCEEE---ECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCC
Q ss_conf             733479988888852000011467642366---0158999721-111333689999643441021235464146810268
Q 003717          122 DATRLDTPKKLLDKDKKLNIFFPRLRKVKT---LPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHP  197 (800)
Q Consensus       122 kl~is~~Lk~svsesd~LreyFskyGKVKs---Vp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~  197 (800)
                      .+++++ |+..+++ ++|+.+|.+||.|..   ++++.+++++ |||         |.|.+.+++..|+. ++|..+   
T Consensus        22 ~lfVgn-Lp~~~te-~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aF---------V~f~~~~~a~~al~-~~~~~l---   86 (103)
T d1x4ba1          22 KLFIGG-LSFETTE-ESLRNYYEQWGKLTDCVVMRDPASKRSRGFGF---------VTFSSMAEVDAAMA-ARPHSI---   86 (103)
T ss_dssp             EEEEEC-CTTCCCH-HHHHHHHTSSCCCSEEEEECCTTTSSCCSEEE---------EECSSHHHHHHHHT-SCSEEE---
T ss_pred             EEEEEC-CCCCCCH-HHHHHHHHHHCCCCCEEECCCCCCCCCCCEEE---------EEECCHHHHHHHHH-HCCCEE---
T ss_conf             899959-9985889-99999997618663000012356777557699---------99787999999998-498959---


Q ss_pred             CCCCCCCCHHHHCCCCC
Q ss_conf             99863210211027553
Q 003717          198 AAGQEEIHDMEELGASV  214 (800)
Q Consensus       198 n~~q~~i~~~ee~~gsg  214 (800)
                      +|..+.|+.+-+++-+|
T Consensus        87 ~G~~i~V~~a~~ke~~g  103 (103)
T d1x4ba1          87 DGRVVEPKRAVAREESG  103 (103)
T ss_dssp             TTEEEEEECCSSCCCCC
T ss_pred             CCEEEEEEECCCCCCCC
T ss_conf             99797988774068896

>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=97.67  E-value=6.1e-06  Score=51.22  Aligned_cols=69  Identities=7%  Similarity=0.055  Sum_probs=56.8

Q ss_pred             CCCCCCCCCCCCCCHHHCCCCCCCCCEEEECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCC
Q ss_conf             334799888888520000114676423660158999721-1113336899996434410212354641468102689986
Q 003717          123 ATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPAAGQ  201 (800)
Q Consensus       123 l~is~~Lk~svsesd~LreyFskyGKVKsVp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n~~q  201 (800)
                      +++. .|+..+++ ++|..+|++||.|..++++.+++++ |||         |.|.+.++|..|++.|||..+.   |..
T Consensus        10 l~V~-nLp~~~te-~~l~~~F~~~G~v~~i~~~~~~~~kG~af---------V~f~~~~~A~~Ai~~l~g~~~~---gr~   75 (114)
T d2f9da1          10 LYIR-NLPYKITA-EEMYDIFGKYGPIRQIRVGNTPETRGTAY---------VVYEDIFDAKNACDHLSGFNVC---NRY   75 (114)
T ss_dssp             EEEE-SCCTTCCH-HHHHHHHHTTSCEEEEEEECSTTTTTEEE---------EEESSHHHHHHHHHHHTTCEET---TEE
T ss_pred             EEEE-CCCCCCCH-HHHHHHHHHCCCEEEECCCCCCCCCCEEE---------EEECCHHHHHHHHHHHCCCEEC---CEE
T ss_conf             9997-99998989-99999985269867601234677677699---------9978899999999982899889---988


Q ss_pred             CCCC
Q ss_conf             3210
Q 003717          202 EEIH  205 (800)
Q Consensus       202 ~~i~  205 (800)
                      ..|.
T Consensus        76 l~V~   79 (114)
T d2f9da1          76 LVVL   79 (114)
T ss_dssp             CEEE
T ss_pred             EEEE
T ss_conf             8999

>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=97.66  E-value=8.2e-06  Score=50.44  Aligned_cols=70  Identities=14%  Similarity=0.095  Sum_probs=52.2

Q ss_pred             CCCCCCCCCCCCCCHHHCCCCCCCCCEEE---ECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCC
Q ss_conf             33479988888852000011467642366---0158999721-1113336899996434410212354641468102689
Q 003717          123 ATRLDTPKKLLDKDKKLNIFFPRLRKVKT---LPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPA  198 (800)
Q Consensus       123 l~is~~Lk~svsesd~LreyFskyGKVKs---Vp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n  198 (800)
                      ++++ .|+..+++ ++|+.+|++||.|..   ++++.+|+++ |||         |.|.+-+++..|+. +++.+   ++
T Consensus         2 lfV~-nl~~~~te-~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~af---------V~f~~~~~a~~Al~-~~~~~---l~   66 (75)
T d1hd0a_           2 MFIG-GLSWDTTK-KDLKDYFSKFGEVVDCTLKLDPITGRSRGFGF---------VLFKESESVDKVMD-QKEHK---LN   66 (75)
T ss_dssp             EEEE-CCCTTCCH-HHHHHHHHTTSCEEEEECCCBTTTTBCCSEEE---------EEESSHHHHHHHHH-TCCCC---BT
T ss_pred             EEEE-CCCCCCCH-HHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEE---------EEECCHHHHHHHHH-CCCCE---EC
T ss_conf             8991-89985989-99999997545033332135888777676599---------99898999999996-29897---99


Q ss_pred             CCCCCCCHH
Q ss_conf             986321021
Q 003717          199 AGQEEIHDM  207 (800)
Q Consensus       199 ~~q~~i~~~  207 (800)
                      |...+|++|
T Consensus        67 Gr~i~V~rA   75 (75)
T d1hd0a_          67 GKVIDPKRA   75 (75)
T ss_dssp             TBCCEECCC
T ss_pred             CCEEEEEEC
T ss_conf             979785679

>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=97.65  E-value=6.2e-06  Score=51.15  Aligned_cols=75  Identities=16%  Similarity=0.137  Sum_probs=58.0

Q ss_pred             CCCCCCCCCCCCCCCCHHHCCCCCCCCCEE---EECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCC
Q ss_conf             873347998888885200001146764236---60158999721-11133368999964344102123546414681026
Q 003717          121 KDATRLDTPKKLLDKDKKLNIFFPRLRKVK---TLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHH  196 (800)
Q Consensus       121 pkl~is~~Lk~svsesd~LreyFskyGKVK---sVp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n  196 (800)
                      ..+++.+ |+.++++ ++|+.+|+.||.|.   +++++.+|+++ |||         |.|.+.+++..|++.+     +.
T Consensus         9 ~~lfV~n-Lp~~~te-~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aF---------V~f~~~~~a~~al~~~-----~~   72 (90)
T d2cqga1           9 SDLIVLG-LPWKTTE-QDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGF---------VRFTEYETQVKVMSQR-----HM   72 (90)
T ss_dssp             CCEEEES-CCSSCCH-HHHHHHHGGGSCEEEEEEEECSSSCSEEEEEE---------EEESSHHHHHHHHHSC-----EE
T ss_pred             CEEEEEC-CCCCCCH-HHHHHHHHHHCCCCEEEECCCCCCCCCCCEEE---------EEECCHHHHHHHHHCC-----CC
T ss_conf             8699979-9998999-99999997626330000024788766677799---------9979999999998669-----83


Q ss_pred             CCCCCCCCCHHHHCC
Q ss_conf             899863210211027
Q 003717          197 PAAGQEEIHDMEELG  211 (800)
Q Consensus       197 ~n~~q~~i~~~ee~~  211 (800)
                      ++|..+.|+.+.++.
T Consensus        73 l~Gr~i~v~~a~~k~   87 (90)
T d2cqga1          73 IDGRWCDCKLPNSKQ   87 (90)
T ss_dssp             ETTEEEEEECCCTTC
T ss_pred             CCCEEEEEEECCCCC
T ss_conf             499896998689977

>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=97.63  E-value=1.4e-05  Score=49.02  Aligned_cols=66  Identities=15%  Similarity=0.182  Sum_probs=53.5

Q ss_pred             CCCCCCCCCCCCCCCCCCHHHCCCCCCCCCEE---EECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCC
Q ss_conf             99873347998888885200001146764236---60158999721-111333689999643441021235464146810
Q 003717          119 DNKDATRLDTPKKLLDKDKKLNIFFPRLRKVK---TLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQI  194 (800)
Q Consensus       119 q~pkl~is~~Lk~svsesd~LreyFskyGKVK---sVp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i  194 (800)
                      ...++++.+ |+..+++ ++|+.+|.+||.|.   .++++.+|+++ |||         |.|.+.+++..|+..+||..+
T Consensus         5 ~~t~lfV~n-lp~~~te-~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~af---------V~f~~~~~A~~Ai~~l~g~~~   73 (85)
T d1b7fa2           5 KDTNLYVTN-LPRTITD-DQLDTIFGKYGSIVQKNILRDKLTGRPRGVAF---------VRYNKREEAQEAISALNNVIP   73 (85)
T ss_dssp             TTCEEEEES-CCTTCCH-HHHHHHHTSSSCEEEEEEEECTTTCCEEEEEE---------EEESSHHHHHHHHHHHTTCCC
T ss_pred             CCCEEEEEC-CCCCCCH-HHHHHHHHHHCCEEEEEEECCCCCCCCCEEEE---------EEECCHHHHHHHHHHHCCCEE
T ss_conf             899999949-8997999-99999999659874643101235556760699---------998999999999999788885


Q ss_pred             C
Q ss_conf             2
Q 003717          195 H  195 (800)
Q Consensus       195 ~  195 (800)
                      .
T Consensus        74 ~   74 (85)
T d1b7fa2          74 E   74 (85)
T ss_dssp             T
T ss_pred             C
T ss_conf             7

>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=97.62  E-value=1.1e-05  Score=49.66  Aligned_cols=75  Identities=16%  Similarity=0.129  Sum_probs=57.1

Q ss_pred             CCCCCCCCCCCCCCCHHHCCCCCCCCCEE---EECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCC
Q ss_conf             73347998888885200001146764236---60158999721-111333689999643441021235464146810268
Q 003717          122 DATRLDTPKKLLDKDKKLNIFFPRLRKVK---TLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHP  197 (800)
Q Consensus       122 kl~is~~Lk~svsesd~LreyFskyGKVK---sVp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~  197 (800)
                      .+++++ |+..+++ ++|+.+|++||.|.   +++++.+|+++ |||         |.|.+.+++..|+.++||..+   
T Consensus         7 tlfV~n-Lp~~~te-~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~af---------V~f~~~~~A~~ai~~l~~~~i---   72 (89)
T d2cqba1           7 VLYVGG-LAEEVDD-KVLHAAFIPFGDITDIQIPLDYETEKHRGFAF---------VEFELAEDAAAAIDNMNESEL---   72 (89)
T ss_dssp             CEEEES-CCSSCCH-HHHHHHHTTTSCCCCEECCCCSSSCCCSSEEE---------ECCSSHHHHHHHHHHHTTEEE---
T ss_pred             EEEEEC-CCCCCCH-HHHHHHHHHCCEEEECCCCCCCCCCCCCCEEE---------EEECCHHHHHHHHHHCCCCEE---
T ss_conf             999969-9986889-99999886478388611024556545563049---------998899999999998599999---


Q ss_pred             CCCCCCCCHHHHC
Q ss_conf             9986321021102
Q 003717          198 AAGQEEIHDMEEL  210 (800)
Q Consensus       198 n~~q~~i~~~ee~  210 (800)
                      .|..+.|..+.++
T Consensus        73 ~g~~l~v~~a~p~   85 (89)
T d2cqba1          73 FGRTIRVNLAKPM   85 (89)
T ss_dssp             TTEEEEEEECCCC
T ss_pred             CCEEEEEEEECCC
T ss_conf             9999899982798

>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=97.59  E-value=2.2e-05  Score=47.84  Aligned_cols=66  Identities=17%  Similarity=0.218  Sum_probs=52.6

Q ss_pred             CCCCCCCCCCCCCCCCHHHCCCCCCCCCEEEECC--CCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCC
Q ss_conf             8733479988888852000011467642366015--8999721-111333689999643441021235464146810268
Q 003717          121 KDATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPF--CGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHP  197 (800)
Q Consensus       121 pkl~is~~Lk~svsesd~LreyFskyGKVKsVp~--kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~  197 (800)
                      .++++.+ |+.++++ ++|+.+|++||.|..+..  ..+++++ |+|         |.|.+.+++..|+..|||..+...
T Consensus        19 ~~lfV~n-Lp~~~te-~~L~~~F~~~G~i~~~~~~~~~~~~~~g~af---------V~f~~~~~A~~Ai~~lng~~i~gr   87 (101)
T d1x5oa1          19 TNLYISN-LPLSMDE-QELENMLKPFGQVISTRILRDSSGTSRGVGF---------ARMESTEKCEAVIGHFNGKFIKTP   87 (101)
T ss_dssp             TEEEEES-CCTTCCH-HHHHHTTTTTSCEEEEEEEECSSSCEEEEEE---------EEESCHHHHHHHHHHHBTCCCCCC
T ss_pred             CEEEEEC-CCCCCCH-HHHHHHHHHCCCCCCEEEECCCCCCCCCCEE---------EEECCHHHHHHHHHHHCCCEECCC
T ss_conf             9899969-9998989-9999888613664210110011235663104---------776899999999998489988983

>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=97.58  E-value=9.5e-06  Score=50.05  Aligned_cols=73  Identities=15%  Similarity=0.135  Sum_probs=57.8

Q ss_pred             CCCCCCCCCCCCCCCHHHCCCCCCCCCEE---EECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCC
Q ss_conf             73347998888885200001146764236---60158999721-111333689999643441021235464146810268
Q 003717          122 DATRLDTPKKLLDKDKKLNIFFPRLRKVK---TLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHP  197 (800)
Q Consensus       122 kl~is~~Lk~svsesd~LreyFskyGKVK---sVp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~  197 (800)
                      .+++++ |+.++++ ++|+.+|.+||.|.   +++++.+|+++ |+|         |.|.+.+++..|++.+||.++.  
T Consensus        44 ~l~V~n-Lp~~~te-~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~af---------V~f~~~~~A~~Ai~~lng~~~~--  110 (139)
T d1u6fa1          44 NLMVNY-IPTTVDE-VQLRQLFERYGPIESVKIVCDRETRQSRGYGF---------VKFQSGSSAQQAIAGLNGFNIL--  110 (139)
T ss_dssp             EEEEES-CSTTCCH-HHHHHHHHHHSCEEEEEEEEETTTTEEEEEEE---------EEESSHHHHHHHHHHTTTEECS--
T ss_pred             EEEEEC-CCCCCCH-HHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEE---------EEECCHHHHHHHHHHHCCCEEC--
T ss_conf             899969-7988999-99999997650032211112211111222036---------8979999999999984898889--


Q ss_pred             CCCCCCCCHHH
Q ss_conf             99863210211
Q 003717          198 AAGQEEIHDME  208 (800)
Q Consensus       198 n~~q~~i~~~e  208 (800)
                       +....|..+.
T Consensus       111 -gr~l~V~~a~  120 (139)
T d1u6fa1         111 -NKRLKVALAA  120 (139)
T ss_dssp             -SCEEEEEESS
T ss_pred             -CEEEEEEECC
T ss_conf             -9888998768

>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=97.58  E-value=1.1e-05  Score=49.60  Aligned_cols=64  Identities=19%  Similarity=0.190  Sum_probs=53.0

Q ss_pred             CCCCCCCCCCCCCCCCHHHCCCCCCCCCEE---EECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCC
Q ss_conf             873347998888885200001146764236---60158999721-1113336899996434410212354641468102
Q 003717          121 KDATRLDTPKKLLDKDKKLNIFFPRLRKVK---TLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIH  195 (800)
Q Consensus       121 pkl~is~~Lk~svsesd~LreyFskyGKVK---sVp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~  195 (800)
                      .++++++ |+..+++ ++|+.+|++||.|.   +++++.+|+++ |||         |.|.+.+++..|+..|||..+.
T Consensus         7 ~~lfV~n-Lp~~~te-~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~af---------V~f~~~~~a~~Ai~~lng~~~~   74 (85)
T d1fxla2           7 ANLYVSG-LPKTMTQ-KELEQLFSQYGRIITSRILVDQVTGVSRGVGF---------IRFDKRIEAEEAIKGLNGQKPS   74 (85)
T ss_dssp             CEEEEES-CCTTCCH-HHHHHHHGGGSCEEEEEEEECTTTCCEEEEEE---------EEESSHHHHHHHHHHHTTCCCT
T ss_pred             CEEEEEC-CCCCCCH-HHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEE---------EEECCHHHHHHHHHHHCCCEEC
T ss_conf             9999959-8998989-99999999849763103012454435787169---------9985899999999983899958

>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=97.56  E-value=2.8e-05  Score=47.18  Aligned_cols=75  Identities=16%  Similarity=0.118  Sum_probs=57.7

Q ss_pred             CCCCCCCCCCCCCCCCHHHCCCCCCCCCE---EEECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCC
Q ss_conf             87334799888888520000114676423---660158999721-11133368999964344102123546414681026
Q 003717          121 KDATRLDTPKKLLDKDKKLNIFFPRLRKV---KTLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHH  196 (800)
Q Consensus       121 pkl~is~~Lk~svsesd~LreyFskyGKV---KsVp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n  196 (800)
                      .++++.+ |+..+++ ++|+.+|..||.+   +.+.++.+|+++ |+|         |.|.+.+++..|+++|||..+..
T Consensus        19 ~~l~V~n-Lp~~~te-~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~af---------V~f~~~~~A~~Ai~~lng~~~~g   87 (102)
T d2cpza1          19 ANLFIYH-LPQEFGD-QDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGF---------VSYDNPVSAQAAIQSMNGFQIGM   87 (102)
T ss_dssp             CCEEEES-CCSSCCH-HHHHHHHGGGSCCSEEEEEECSSSCSEEEEEE---------EECSSHHHHHHHHHHHTTCEETT
T ss_pred             CEEEEEC-CCCCCCH-HHHHHHHHHHCCCCCCCEEEECCCCCCCCCEE---------EEECCHHHHHHHHHHHCCCEECC
T ss_conf             9999959-9999999-99999997633454321000013698765338---------87489999999999858998899


Q ss_pred             CCCCCCCCCHHHH
Q ss_conf             8998632102110
Q 003717          197 PAAGQEEIHDMEE  209 (800)
Q Consensus       197 ~n~~q~~i~~~ee  209 (800)
                         ....|.-+.+
T Consensus        88 ---~~i~V~~a~~   97 (102)
T d2cpza1          88 ---KRLKVQLKRS   97 (102)
T ss_dssp             ---EECEEECCCC
T ss_pred             ---EEEEEEEECC
T ss_conf             ---9889987078

>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=97.52  E-value=1.5e-05  Score=48.86  Aligned_cols=71  Identities=21%  Similarity=0.239  Sum_probs=55.8

Q ss_pred             CCCCCCCCCHHHCCCCCCCCCE----EEECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCC
Q ss_conf             9888888520000114676423----660158999721-11133368999964344102123546414681026899863
Q 003717          128 TPKKLLDKDKKLNIFFPRLRKV----KTLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPAAGQE  202 (800)
Q Consensus       128 ~Lk~svsesd~LreyFskyGKV----KsVp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n~~q~  202 (800)
                      .|+..+++ ++|+.+|++||.|    ++++++.+|+++ |||         |.|.+.+++..|++.|+|..+.   +...
T Consensus         5 nLp~~~te-~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~af---------V~f~~~~~a~~Ai~~~~g~~~~---gr~l   71 (83)
T d1x5ta1           5 NLDPEIDE-KLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAF---------INFASFDASDAAIEAMNGQYLC---NRPI   71 (83)
T ss_dssp             CCCTTCCH-HHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEE---------EEBSSHHHHHHHHHTTTTCEET---TEEC
T ss_pred             CCCCCCCH-HHHHHHHHHHCCEEEEEEEEEECCCCCCCCEEE---------EEECCHHHHHHHHHHCCCCEEC---CEEE
T ss_conf             89894869-999999987294504679976113324475399---------9989999999999857992989---9999


Q ss_pred             CCCHHHHCC
Q ss_conf             210211027
Q 003717          203 EIHDMEELG  211 (800)
Q Consensus       203 ~i~~~ee~~  211 (800)
                      .|.-+.+++
T Consensus        72 ~v~~a~~k~   80 (83)
T d1x5ta1          72 TVSYAFKKD   80 (83)
T ss_dssp             EEEESCCCC
T ss_pred             EEEEECCCC
T ss_conf             999965879

>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=97.50  E-value=2.6e-05  Score=47.36  Aligned_cols=73  Identities=15%  Similarity=0.175  Sum_probs=57.2

Q ss_pred             CCCCCCCCCCCCCCHHHCCCCCCCCCEE---EECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCC
Q ss_conf             3347998888885200001146764236---60158999721-1113336899996434410212354641468102689
Q 003717          123 ATRLDTPKKLLDKDKKLNIFFPRLRKVK---TLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPA  198 (800)
Q Consensus       123 l~is~~Lk~svsesd~LreyFskyGKVK---sVp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n  198 (800)
                      +++++ |+..+++ ++|+.+|++||.|.   +++++.+|+++ |||         |.|.+.+++..|+..+||..+.   
T Consensus         4 lfV~n-lp~~~te-~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aF---------V~f~~~~~A~~a~~~l~~~~l~---   69 (85)
T d2u2fa_           4 LFIGG-LPNYLND-DQVKELLTSFGPLKAFNLVKDSATGLSKGYAF---------CEYVDINVTDQAIAGLNGMQLG---   69 (85)
T ss_dssp             EEEET-CCSSCCS-HHHHHHHTSSSCEEEEEEECCCSSSCCCCEEE---------EEESSSHHHHHHHHTSSSCCCS---
T ss_pred             EEEEC-CCCCCCH-HHHHHHHHHCCCCCEEEEECCCCCCCCCEEEE---------EEECCHHHHHHHHHHHCCCEEC---
T ss_conf             99989-9998999-99999997457652477602456656540599---------9988999999999971998899---


Q ss_pred             CCCCCCCHHHH
Q ss_conf             98632102110
Q 003717          199 AGQEEIHDMEE  209 (800)
Q Consensus       199 ~~q~~i~~~ee  209 (800)
                      +.+..|..+..
T Consensus        70 g~~l~V~~A~~   80 (85)
T d2u2fa_          70 DKKLLVQRASV   80 (85)
T ss_dssp             SSCCEEEECCC
T ss_pred             CEEEEEEECCC
T ss_conf             99879998889

>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=97.46  E-value=2.5e-05  Score=47.56  Aligned_cols=74  Identities=12%  Similarity=0.101  Sum_probs=55.8

Q ss_pred             CCCCCCCCCCCCCCCCCCHHHCCCCCCCCCEE---EECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCC
Q ss_conf             99873347998888885200001146764236---60158999721-111333689999643441021235464146810
Q 003717          119 DNKDATRLDTPKKLLDKDKKLNIFFPRLRKVK---TLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQI  194 (800)
Q Consensus       119 q~pkl~is~~Lk~svsesd~LreyFskyGKVK---sVp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i  194 (800)
                      ...++++++ |+..+++ ++|+.+|++||.|.   +++++.+|+++ |||         |.|.+-+++..|++.+|+ . 
T Consensus         9 ~~~~lfV~n-Lp~~~te-~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~af---------V~f~~~~~A~~Ai~~~~~-~-   75 (103)
T d2cqda1           9 TFTKIFVGG-LPYHTTD-ASLRKYFEGFGDIEEAVVITDRQTGKSRGYGF---------VTMADRAAAERACKDPNP-I-   75 (103)
T ss_dssp             SSSEEEEEC-CCSSCCH-HHHHHHHHTTSCEEEEEESCCSSSCCCCSEEE---------EEESSHHHHHHHHTCSSC-E-
T ss_pred             CCCEEEEEC-CCCCCCH-HHHHHHHHHCCCCCCEECCCCCCCCCCCCEEE---------EEECCHHHHHHHHHHCCC-C-
T ss_conf             976899969-9996959-99998776144321100023344455687699---------997899999999997899-1-


Q ss_pred             CCCCCCCCCCCHH
Q ss_conf             2689986321021
Q 003717          195 HHPAAGQEEIHDM  207 (800)
Q Consensus       195 ~n~n~~q~~i~~~  207 (800)
                        ++|....|..+
T Consensus        76 --l~Gr~l~V~~a   86 (103)
T d2cqda1          76 --IDGRKANVNLA   86 (103)
T ss_dssp             --ETTEECEEEES
T ss_pred             --CCCEEEEEEEC
T ss_conf             --99989799872

>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=97.43  E-value=3.1e-05  Score=46.90  Aligned_cols=74  Identities=16%  Similarity=0.286  Sum_probs=55.7

Q ss_pred             CCCCCCCCCCCCCCCHHHCCCCCCCCCEEEECCC----CCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHH-CCCCCC
Q ss_conf             7334799888888520000114676423660158----999721-1113336899996434410212354641-468102
Q 003717          122 DATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPFC----GTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAA-EGKQIH  195 (800)
Q Consensus       122 kl~is~~Lk~svsesd~LreyFskyGKVKsVp~k----gTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAm-NG~~i~  195 (800)
                      .+++.+ |+..+++ ++|+.+|.+||.|..++.+    .+|+++ |||         |.|.+.+++..|+..| ||..++
T Consensus        10 ~l~V~n-Lp~~~~e-~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~af---------V~f~~~~~A~~Ai~~l~~~~~~~   78 (94)
T d2cpha1          10 KILVRN-IPFQANQ-REIRELFSTFGELKTVRLPKKMTGTGAHRGFGF---------VDFITKQDAKKAFNALCHSTHLY   78 (94)
T ss_dssp             CEEEES-CCTTCCH-HHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEE---------EEESSHHHHHHHHHHHHTCCBSS
T ss_pred             EEEEEC-CCCCCCH-HHHHHHHHHHCCCEEEEEEECCCCCCCCCCEEE---------EEECCHHHHHHHHHHCCCCCEEC
T ss_conf             999969-9998999-999999998599648898853666798366899---------99899999999999723994889


Q ss_pred             CCCCCCCCCCHHHH
Q ss_conf             68998632102110
Q 003717          196 HPAAGQEEIHDMEE  209 (800)
Q Consensus       196 n~n~~q~~i~~~ee  209 (800)
                         |....|.-+.+
T Consensus        79 ---Gr~l~V~~A~~   89 (94)
T d2cpha1          79 ---GRRLVLEWADS   89 (94)
T ss_dssp             ---SCBCEEEECCC
T ss_pred             ---CEEEEEEECCC
T ss_conf             ---99989998299

>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=97.42  E-value=1.7e-05  Score=48.54  Aligned_cols=63  Identities=16%  Similarity=0.210  Sum_probs=52.2

Q ss_pred             CCCCCCCCCCCCCCCHHHCCCCCCCCCEEE---ECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCC
Q ss_conf             733479988888852000011467642366---0158999721-1113336899996434410212354641468102
Q 003717          122 DATRLDTPKKLLDKDKKLNIFFPRLRKVKT---LPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIH  195 (800)
Q Consensus       122 kl~is~~Lk~svsesd~LreyFskyGKVKs---Vp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~  195 (800)
                      ++++.+ |+..+++ ++|+.+|++||.|+.   ++++.+|+++ |+|         |.|.+.+++..|+..|||..+.
T Consensus         4 ~l~V~n-Lp~~~t~-~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~af---------V~f~~~~~A~~ai~~lng~~~~   70 (82)
T d1b7fa1           4 NLIVNY-LPQDMTD-RELYALFRAIGPINTCRIMRDYKTGYSYGYAF---------VDFTSEMDSQRAIKVLNGITVR   70 (82)
T ss_dssp             EEEEEC-CCTTCCH-HHHHHHHHTTSCEEEEECCEETTTTEECSEEE---------EEESSHHHHHHHHHHHTTCEET
T ss_pred             EEEEEC-CCCCCCH-HHHHHHHHHHCCCCEEEEEEECCCCCCCCCCE---------EEECCHHHHHHHHHHHCCCEEC
T ss_conf             999969-7997989-99999999859814664663203688642243---------7989999999999986899899

>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=97.41  E-value=2.6e-05  Score=47.38  Aligned_cols=70  Identities=14%  Similarity=0.256  Sum_probs=53.9

Q ss_pred             CCCCCCCCCCCCCCHHHCCCCCCCCCEE---EECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCC
Q ss_conf             3347998888885200001146764236---60158999721-1113336899996434410212354641468102689
Q 003717          123 ATRLDTPKKLLDKDKKLNIFFPRLRKVK---TLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPA  198 (800)
Q Consensus       123 l~is~~Lk~svsesd~LreyFskyGKVK---sVp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n  198 (800)
                      ++++ .|+..+++ ++|+.+|..||.|.   +++++.+|+++ |||         |.|.+.+++..|+ +|||..+.   
T Consensus        21 ifV~-nL~~~~te-~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~af---------V~F~~~e~a~~A~-~l~g~~~~---   85 (101)
T d2cq4a1          21 VFCM-QLAARIRP-RDLEDFFSAVGKVRDVRIISDRNSRRSKGIAY---------VEFCEIQSVPLAI-GLTGQRLL---   85 (101)
T ss_dssp             EEEE-SCCTTCCH-HHHHHHHTTTSCEEEEEECCSCCSSSCCCCEE---------EEESCGGGHHHHH-HHTTEEET---
T ss_pred             EEEE-CCCCCCCH-HHHHHHHCCCCEEEEEEEEECCCCCCCCCEEE---------EEECCHHHHHHHH-HHCCCEEC---
T ss_conf             9998-99998999-99999971897499988654488764341489---------9989999999999-87998889---


Q ss_pred             CCCCCCCHH
Q ss_conf             986321021
Q 003717          199 AGQEEIHDM  207 (800)
Q Consensus       199 ~~q~~i~~~  207 (800)
                      |..+.|+.+
T Consensus        86 G~~l~V~~a   94 (101)
T d2cq4a1          86 GVPIIVQAS   94 (101)
T ss_dssp             TEEEEEEEH
T ss_pred             CEEEEEEEC
T ss_conf             999899978

>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=97.41  E-value=2.4e-05  Score=47.59  Aligned_cols=63  Identities=13%  Similarity=-0.006  Sum_probs=51.7

Q ss_pred             CCCCCCCCCCCCCCHHHCCCCCCCCCEE---EECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCC
Q ss_conf             3347998888885200001146764236---60158999721-11133368999964344102123546414681026
Q 003717          123 ATRLDTPKKLLDKDKKLNIFFPRLRKVK---TLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHH  196 (800)
Q Consensus       123 l~is~~Lk~svsesd~LreyFskyGKVK---sVp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n  196 (800)
                      +++++ |+..+++ ++|+.+|.+||.|.   +++++.+|+++ |+|         |.|.+.+++..|++.+||..+..
T Consensus         3 lfV~n-L~~~~te-~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aF---------V~f~~~~~a~~ai~~l~g~~~~g   69 (80)
T d1cvja1           3 LYVGD-LHPDVTE-AMLYEKFSPAGPILSIRVCRDMITRRSLGYAY---------VNFQQPADAERALDTMNFDVIKG   69 (80)
T ss_dssp             EEEES-CCTTCCH-HHHHHHHGGGSCEEEEEEEECTTTCCEEEEEE---------EEESSHHHHHHHHTTSTTCEETT
T ss_pred             EEEEC-CCCCCCH-HHHHHHHHHHCCEEEEEEEECCCCCCCCCCEE---------EEECCHHHHHHHHHHCCCCEECC
T ss_conf             99947-9884879-99999999769885999984045447788369---------99889999999999819998999

>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=97.39  E-value=2.8e-05  Score=47.23  Aligned_cols=70  Identities=13%  Similarity=0.053  Sum_probs=52.5

Q ss_pred             CCCCCCCCCCCCCCHHHCCCCCCCCCEEEE---CCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCC
Q ss_conf             334799888888520000114676423660---158999721-1113336899996434410212354641468102689
Q 003717          123 ATRLDTPKKLLDKDKKLNIFFPRLRKVKTL---PFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPA  198 (800)
Q Consensus       123 l~is~~Lk~svsesd~LreyFskyGKVKsV---p~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n  198 (800)
                      ++++ .|+.++++ ++|+.+|++||.+..+   +.+.+|+++ |+|         |.|.+.+++..|++ +||..+   +
T Consensus         2 lfV~-nLp~~~te-~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~af---------V~F~~~~~a~~al~-~~~~~l---~   66 (75)
T d2msta_           2 IFVG-GLSVNTTV-EDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGF---------VTFESEDIVEKVCE-IHFHEI---N   66 (75)
T ss_dssp             EEEE-CCCSSCCH-HHHHHHHHTTSCCSEECCBCCTTCTTSCCEEE---------EECSCHHHHHHHHH-CSSCCB---T
T ss_pred             EEEE-CCCCCCCH-HHHHHHHHHHCCCCEEEEEEECCCCCCCCEEE---------EEECCHHHHHHHHH-CCCCEE---C
T ss_conf             8990-89998889-99999999868740223321034335673369---------99989999999995-299989---9


Q ss_pred             CCCCCCCHH
Q ss_conf             986321021
Q 003717          199 AGQEEIHDM  207 (800)
Q Consensus       199 ~~q~~i~~~  207 (800)
                      |..++|++|
T Consensus        67 gr~i~V~~A   75 (75)
T d2msta_          67 NKMVECKKA   75 (75)
T ss_dssp             TBCCEEEEC
T ss_pred             CEEEEEEEC
T ss_conf             949899889

>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=97.39  E-value=2e-05  Score=48.10  Aligned_cols=70  Identities=14%  Similarity=0.114  Sum_probs=54.2

Q ss_pred             CCCCCCCCCCCCCCHHHCCCCCCCCCEE---EECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCC
Q ss_conf             3347998888885200001146764236---60158999721-1113336899996434410212354641468102689
Q 003717          123 ATRLDTPKKLLDKDKKLNIFFPRLRKVK---TLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPA  198 (800)
Q Consensus       123 l~is~~Lk~svsesd~LreyFskyGKVK---sVp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n  198 (800)
                      ++++ .|+..+++ ++|+.+|.+||.|.   ++.++.+|+++ |||         |.|.+-+++..|++. ++..+   +
T Consensus         9 lfV~-nlp~~~te-~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~af---------V~f~~~~~a~~ai~~-~~~~i---~   73 (84)
T d1l3ka1           9 LFIG-GLSFETTD-ESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGF---------VTYATVEEVDAAMNA-RPHKV---D   73 (84)
T ss_dssp             EEEE-SCCTTCCH-HHHHHHHGGGSCEEEEEEEECTTTCCEEEEEE---------EEESSHHHHHHHHHT-CSCEE---T
T ss_pred             EEEE-CCCCCCCH-HHHHHHHHHHCCCCCEEECCCCCCCCCCCEEE---------EEECCHHHHHHHHHH-CCCEE---C
T ss_conf             9997-99997989-99999997506452100011466799622899---------998689999999984-99979---9


Q ss_pred             CCCCCCCHH
Q ss_conf             986321021
Q 003717          199 AGQEEIHDM  207 (800)
Q Consensus       199 ~~q~~i~~~  207 (800)
                      |...+|++|
T Consensus        74 Gr~i~V~~A   82 (84)
T d1l3ka1          74 GRVVEPKRA   82 (84)
T ss_dssp             TEECEEEEC
T ss_pred             CEEEEEEEE
T ss_conf             999899951

>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=97.39  E-value=2.2e-05  Score=47.87  Aligned_cols=63  Identities=17%  Similarity=0.089  Sum_probs=51.7

Q ss_pred             CCCCCCCCCCCCCCHHHCCCCCCCCCEE---EECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCC
Q ss_conf             3347998888885200001146764236---60158999721-11133368999964344102123546414681026
Q 003717          123 ATRLDTPKKLLDKDKKLNIFFPRLRKVK---TLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHH  196 (800)
Q Consensus       123 l~is~~Lk~svsesd~LreyFskyGKVK---sVp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n  196 (800)
                      +++. .|+..+++ ++|+.+|++||.|.   .++++.+|+++ |+|         |.|.+.+++..|+..|||..+..
T Consensus        10 l~V~-nL~~~~t~-~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~af---------V~f~~~~~A~~A~~~lng~~l~g   76 (88)
T d1rk8a_          10 LFVT-SIHEEAQE-DEIQEKFCDYGEIKNIHLNLDRRTGFSKGYAL---------VEYETHKQALAAKEALNGAEIMG   76 (88)
T ss_dssp             EEEE-SCCTTCCH-HHHHHHHGGGSCEEEEEEEECTTTSSEEEEEE---------EEESSHHHHHHHHHHHTTCEETT
T ss_pred             EEEE-CCCCCCCH-HHHHHHHHHCCCCCCCCCCCCCCCCCCCCCEE---------EEECCHHHHHHHHHHCCCCEECC
T ss_conf             9994-89998989-99999998729864100012343225564116---------89899999999999819998999

>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=97.37  E-value=2.7e-05  Score=47.34  Aligned_cols=75  Identities=15%  Similarity=0.085  Sum_probs=56.3

Q ss_pred             CCCCCCCCCCCCCCCCHHHCCCCCCCCCEEEE---CCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCC
Q ss_conf             87334799888888520000114676423660---158999721-11133368999964344102123546414681026
Q 003717          121 KDATRLDTPKKLLDKDKKLNIFFPRLRKVKTL---PFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHH  196 (800)
Q Consensus       121 pkl~is~~Lk~svsesd~LreyFskyGKVKsV---p~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n  196 (800)
                      ..+++.+ |+..+++ ++|+.+|.+||.|..+   +++.+|+++ |+|         |.|.+.+++..|++.|||..+..
T Consensus         9 ~~lfV~n-L~~~~t~-~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~af---------V~f~~~~~a~~A~~~l~g~~~~g   77 (99)
T d1whwa_           9 GRLFVRN-LSYTSSE-EDLEKLFSAYGPLSELHYPIDSLTKKPKGFAF---------VTFMFPEHAVKAYAEVDGQVFQG   77 (99)
T ss_dssp             EEEEEEC-CCTTCCH-HHHHHHHHTTSCEEEEECCCCTTTCCCCSEEE---------EEESSHHHHHHHHHHTTTEESSS
T ss_pred             CEEEEEC-CCCCCCH-HHHHHHHHHCCCCEEEEECCCCCCCCCCCCEE---------EEECCHHHHHHHHHHCCCCEECC
T ss_conf             8899979-9986989-99999997649750653102444346675049---------99889999999999829998999


Q ss_pred             CCCCCCCCCHHHH
Q ss_conf             8998632102110
Q 003717          197 PAAGQEEIHDMEE  209 (800)
Q Consensus       197 ~n~~q~~i~~~ee  209 (800)
                         ....|..+.+
T Consensus        78 ---r~i~V~~a~~   87 (99)
T d1whwa_          78 ---RMLHVLPSTI   87 (99)
T ss_dssp             ---CEEEEEECCC
T ss_pred             ---EEEEEEECCC
T ss_conf             ---9879998888

>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=97.37  E-value=2.5e-05  Score=47.50  Aligned_cols=73  Identities=18%  Similarity=0.198  Sum_probs=56.6

Q ss_pred             CCCCCCCCCCCCCCHHHCCCCCCCCCE---EEECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCC
Q ss_conf             334799888888520000114676423---660158999721-1113336899996434410212354641468102689
Q 003717          123 ATRLDTPKKLLDKDKKLNIFFPRLRKV---KTLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPA  198 (800)
Q Consensus       123 l~is~~Lk~svsesd~LreyFskyGKV---KsVp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n  198 (800)
                      +++++ |+..+++ ++|+.+|++||+|   ++++++.+|+++ |+|         |.|.+.+++..|+..+||..+.   
T Consensus        11 l~V~n-Lp~~~te-~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~af---------V~f~~~~~a~~ai~~l~~~~~~---   76 (104)
T d1p1ta_          11 VFVGN-IPYEATE-EQLKDIFSEVGPVVSFRLVYDRETGKPKGYGF---------CEYQDQETALSAMRNLNGREFS---   76 (104)
T ss_dssp             EEEES-CCTTSCH-HHHHHHHHTTSCCSEEEEEEETTTTEEEEEEE---------EECSCHHHHHHHHHHSSSBSCS---
T ss_pred             EEEEC-CCCCCCH-HHHHHHHHCCCCCCCCCCCCCCCEECCCCCEE---------EEECCHHHHHHHHHHCCCCEEC---
T ss_conf             99979-9986989-99997664033222211011100011478467---------8989999999999980999889---


Q ss_pred             CCCCCCCHHHH
Q ss_conf             98632102110
Q 003717          199 AGQEEIHDMEE  209 (800)
Q Consensus       199 ~~q~~i~~~ee  209 (800)
                      +....|..+.+
T Consensus        77 g~~i~V~~a~~   87 (104)
T d1p1ta_          77 GRALRVDNAAS   87 (104)
T ss_dssp             SSCBEEEETTC
T ss_pred             CEEEEEEECCC
T ss_conf             99879988999

>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=97.31  E-value=3.5e-05  Score=46.62  Aligned_cols=77  Identities=9%  Similarity=0.056  Sum_probs=59.5

Q ss_pred             CCCCCCCCCCCCCCCHHHCCCCCCCCCEEEECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCC
Q ss_conf             7334799888888520000114676423660158999721-111333689999643441021235464146810268998
Q 003717          122 DATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPAAG  200 (800)
Q Consensus       122 kl~is~~Lk~svsesd~LreyFskyGKVKsVp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n~~  200 (800)
                      .+++.+ |+..+++ ++|+.+|.+||.|..+..+..+..+ |+|         |.|.+.+++..|+..|||..+.   +.
T Consensus        16 ~l~V~n-Lp~~~t~-~~l~~~F~~~G~v~~~~~~~~~~~~g~af---------V~f~~~e~a~~Ai~~l~g~~~~---g~   81 (95)
T d1x4aa1          16 RIYVGN-LPPDIRT-KDIEDVFYKYGAIRDIDLKNRRGGPPFAF---------VEFEDPRDAEDAVYGRDGYDYD---GY   81 (95)
T ss_dssp             EEEEES-CCTTCCH-HHHHHHHGGGSCEEEEEECCSSSSSCCEE---------EEESCHHHHHHHHHHHTTCEET---TE
T ss_pred             EEEEEC-CCCCCCH-HHHHHHHHCCCCEEEEEECCCCCCCCEEE---------EEECCHHHHHHHHHHHCCCEEC---CE
T ss_conf             999979-8988989-99999884278669988415655465399---------9988999999999981999899---98


Q ss_pred             CCCCCHHHHCCC
Q ss_conf             632102110275
Q 003717          201 QEEIHDMEELGA  212 (800)
Q Consensus       201 q~~i~~~ee~~g  212 (800)
                      ...|..+-+..+
T Consensus        82 ~l~V~~a~~~r~   93 (95)
T d1x4aa1          82 RLRVEFPRSGRG   93 (95)
T ss_dssp             ECEEECCCCCCC
T ss_pred             EEEEEECCCCCC
T ss_conf             979982569797

>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=97.30  E-value=3.9e-05  Score=46.34  Aligned_cols=63  Identities=13%  Similarity=0.241  Sum_probs=51.5

Q ss_pred             CCCCCCCCCCCCCCHHHCCCCCCCCCEE---EECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCC
Q ss_conf             3347998888885200001146764236---60158999721-11133368999964344102123546414681026
Q 003717          123 ATRLDTPKKLLDKDKKLNIFFPRLRKVK---TLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHH  196 (800)
Q Consensus       123 l~is~~Lk~svsesd~LreyFskyGKVK---sVp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n  196 (800)
                      +++. .|+..+++ ++|+.+|++||.|.   +++++.+|+++ |+|         |.|.+.+++..|+.+|+|..+..
T Consensus        12 l~V~-nL~~~~te-~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~af---------V~f~~~~~A~~Ai~~l~g~~~~g   78 (83)
T d2cqca1          12 LGVF-GLSLYTTE-RDLREVFSKYGPIADVSIVYDQQSRRSRGFAF---------VYFENVDDAKEAKERANGMELDG   78 (83)
T ss_dssp             EEEE-SCCSSCCH-HHHHHHHHTTSCEEEEEEEECSSSSSEEEEEE---------EEESSHHHHHHHHHHHTTEEETT
T ss_pred             EEEE-CCCCCCCH-HHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEE---------EEECCHHHHHHHHHHCCCCEECC
T ss_conf             9993-99998989-99999999859773001113666655553028---------99889999999999809999899

>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=97.29  E-value=6.9e-05  Score=44.83  Aligned_cols=64  Identities=8%  Similarity=0.050  Sum_probs=52.3

Q ss_pred             CCCCCCCCCCCCCCCHHHCCCCCCCCCEEE---ECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCC
Q ss_conf             733479988888852000011467642366---0158999721-11133368999964344102123546414681026
Q 003717          122 DATRLDTPKKLLDKDKKLNIFFPRLRKVKT---LPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHH  196 (800)
Q Consensus       122 kl~is~~Lk~svsesd~LreyFskyGKVKs---Vp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n  196 (800)
                      .+++++ |+..+++ ++|+.+|++||.|..   ++++.+|+++ |||         |.|.+.+++..|+..|||..+..
T Consensus         9 tlfV~n-lp~~~te-~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~af---------V~f~~~~~A~~Ai~~l~g~~~~g   76 (93)
T d1h2vz_           9 TLYVGN-LSFYTTE-EQIYELFSKSGDIKKIIMGLDKMKKTACGFCF---------VEYYSRADAENAMRYINGTRLDD   76 (93)
T ss_dssp             EEEEES-CCTTCCH-HHHHHHHGGGSCEEEEEEEECTTTCCEEEEEE---------EEESSHHHHHHHHHHTTTSEETT
T ss_pred             EEEEEC-CCCCCCH-HHHHHHHHHHCCCCEECCCCCCCCCCCCCEEE---------EEECCHHHHHHHHHHHCCCEECC
T ss_conf             999959-9997989-99999999878862001024655322241579---------99889999999999808998999

>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=97.25  E-value=5.6e-05  Score=45.41  Aligned_cols=70  Identities=16%  Similarity=0.227  Sum_probs=52.2

Q ss_pred             CCCCCCCCCCCCCCHHHCCCCCCCCCEE---EECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCC
Q ss_conf             3347998888885200001146764236---60158999721-1113336899996434410212354641468102689
Q 003717          123 ATRLDTPKKLLDKDKKLNIFFPRLRKVK---TLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPA  198 (800)
Q Consensus       123 l~is~~Lk~svsesd~LreyFskyGKVK---sVp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n  198 (800)
                      ++++ .|+.++++ ++|+.+|.+||.+.   .++++.+++++ |||         |.|.+.|++.+|+. ++|..+   +
T Consensus         5 lfV~-nLp~~~te-~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~af---------V~f~~~e~~~~al~-~~~~~l---~   69 (79)
T d1l3ka2           5 IFVG-GIKEDTEE-HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAF---------VTFDDHDSVDKIVI-QKYHTV---N   69 (79)
T ss_dssp             EEEE-CCTTTCCH-HHHHHHHTTTSCEEEEEEEECTTTCCEEEEEE---------EEESSHHHHHHHHH-CSCCEE---T
T ss_pred             EEEC-CCCCCCCH-HHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEE---------EEECCHHHHHHHHH-HCCCEE---C
T ss_conf             9987-98985879-99999999755133221035788755441899---------99938999999999-699879---9


Q ss_pred             CCCCCCCHH
Q ss_conf             986321021
Q 003717          199 AGQEEIHDM  207 (800)
Q Consensus       199 ~~q~~i~~~  207 (800)
                      |..++|++|
T Consensus        70 Gr~i~V~~A   78 (79)
T d1l3ka2          70 GHNCEVRKA   78 (79)
T ss_dssp             TEECEEEEC
T ss_pred             CEEEEEEEC
T ss_conf             979899978

>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=97.20  E-value=7.7e-05  Score=44.55  Aligned_cols=64  Identities=17%  Similarity=0.208  Sum_probs=52.0

Q ss_pred             CCCCCCCCCCCCCCCHHHCCCCCCCCCEEE---ECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCC
Q ss_conf             733479988888852000011467642366---0158999721-11133368999964344102123546414681026
Q 003717          122 DATRLDTPKKLLDKDKKLNIFFPRLRKVKT---LPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHH  196 (800)
Q Consensus       122 kl~is~~Lk~svsesd~LreyFskyGKVKs---Vp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n  196 (800)
                      .+++.+ |+..+++ ++|+.+|.+||.|..   ++++.+|+++ |+|         |.|.+.+++..|++.+||..+..
T Consensus        10 ~i~V~n-Lp~~~t~-~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~af---------V~f~~~~~A~~Ai~~l~g~~~~g   77 (90)
T d2cq0a1          10 TIRVTN-LSEDTRE-TDLQELFRPFGSISRIYLAKDKTTGQSKGFAF---------ISFHRREDAARAIAGVSGFGYDH   77 (90)
T ss_dssp             EEEEES-CCTTCCH-HHHHTTSTTTCCEEEEEEEECSSSCSEEEEEE---------EEESSHHHHHHHHHHTTTCEETT
T ss_pred             EEEEEC-CCCCCCH-HHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEE---------EEECCHHHHHHHHHHHCCCEECC
T ss_conf             999979-9987989-99999998756233211111355446663205---------89899999999999828998999

>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=97.17  E-value=6.3e-05  Score=45.10  Aligned_cols=76  Identities=13%  Similarity=0.175  Sum_probs=57.9

Q ss_pred             CCCCCCCCCCCCCCCCHHHCCCCCCCCCEEE---ECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCC
Q ss_conf             8733479988888852000011467642366---0158999721-11133368999964344102123546414681026
Q 003717          121 KDATRLDTPKKLLDKDKKLNIFFPRLRKVKT---LPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHH  196 (800)
Q Consensus       121 pkl~is~~Lk~svsesd~LreyFskyGKVKs---Vp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n  196 (800)
                      ..+++++ |+..+++ ++|..+|.+||.|..   ++.+.+|+++ |||         |.|.+.+++..|+..|+|..+  
T Consensus         6 ~kifV~n-Lp~~~t~-~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~af---------V~f~~~~~a~~Ai~~l~~~~~--   72 (90)
T d1x5sa1           6 GKLFVGG-LSFDTNE-QSLEQVFSKYGQISEVVVVKDRETQRSRGFGF---------VTFENIDDAKDAMMAMNGKSV--   72 (90)
T ss_dssp             SEEEEES-CCTTCCH-HHHHHHHHHHSCCCEEEECCCSSSCSCCSEEE---------EECSSHHHHHHHHHHHTTCCT--
T ss_pred             CEEEEEC-CCCCCCH-HHHHHHHHCCCCCCCEEECCCCCCCCCCCEEE---------EEECCHHHHHHHHHHCCCCEE--
T ss_conf             8999979-9986879-99987564022221101100003333466389---------998789999999998099899--


Q ss_pred             CCCCCCCCCHHHHC
Q ss_conf             89986321021102
Q 003717          197 PAAGQEEIHDMEEL  210 (800)
Q Consensus       197 ~n~~q~~i~~~ee~  210 (800)
                       .|....|..+.+.
T Consensus        73 -~g~~l~V~~a~~~   85 (90)
T d1x5sa1          73 -DGRQIRVDQAGKS   85 (90)
T ss_dssp             -TSCCCEEEEEECC
T ss_pred             -CCEEEEEEECCCC
T ss_conf             -9999899981899

>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=97.16  E-value=7.4e-05  Score=44.66  Aligned_cols=64  Identities=13%  Similarity=0.231  Sum_probs=51.7

Q ss_pred             CCCCCCCCCCCCCCCHHHCCCCCCCCCEEE---ECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCC
Q ss_conf             733479988888852000011467642366---0158999721-11133368999964344102123546414681026
Q 003717          122 DATRLDTPKKLLDKDKKLNIFFPRLRKVKT---LPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHH  196 (800)
Q Consensus       122 kl~is~~Lk~svsesd~LreyFskyGKVKs---Vp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n  196 (800)
                      ++++++ |+..+++ ++|+.+|++||.|..   ++++.+|+++ |||         +.|.+.+++..|+..|||..+..
T Consensus         4 ~l~V~n-Lp~~~te-~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~af---------v~f~~~~~a~~a~~~l~g~~~~g   71 (82)
T d1fxla1           4 NLIVNY-LPQNMTQ-EEFRSLFGSIGEIESCKLVRDKITGQSLGYGF---------VNYIDPKDAEKAINTLNGLRLQT   71 (82)
T ss_dssp             EEEEES-CCTTCCH-HHHHHHHHTTSCEEEEEEEECTTTCCEEEEEE---------EEESSHHHHHHHHHHHTTCEETT
T ss_pred             EEEEEC-CCCCCCH-HHHHHHHHHHCCCCCCCCEEECCCCCCEEEEE---------EEECCHHHHHHHHHHHCCCEECC
T ss_conf             899989-8987989-99999999969764101000025787302589---------99899999999999828999999

>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=97.11  E-value=0.00014  Score=43.08  Aligned_cols=77  Identities=19%  Similarity=0.100  Sum_probs=57.7

Q ss_pred             CCCCCCCCCCCCCCCCCHHHCCCCCCCCCEE-----------EECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHH
Q ss_conf             9873347998888885200001146764236-----------60158999721-11133368999964344102123546
Q 003717          120 NKDATRLDTPKKLLDKDKKLNIFFPRLRKVK-----------TLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFH  187 (800)
Q Consensus       120 ~pkl~is~~Lk~svsesd~LreyFskyGKVK-----------sVp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~e  187 (800)
                      ...+++++ |+..+++ ++|+.+|..||.|+           ...++.+|+++ |+|         |.|.+.+++..|+.
T Consensus         8 ~~~i~V~n-Lp~~~te-~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~af---------V~f~~~~~a~~Ai~   76 (101)
T d2cpea1           8 NSAIYVQG-LNDSVTL-DDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDAT---------VSYEDPPTAKAAVE   76 (101)
T ss_dssp             CCEEEEEC-CCTTCCH-HHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEE---------EEBSSHHHHHHHHH
T ss_pred             CCEEEEEC-CCCCCCH-HHHHHHHHHCCEEEEEEECCCCEEEEEECCCCCCCCCEEE---------EEECCHHHHHHHHH
T ss_conf             99999979-9986889-9999878877437875632530367754266444341235---------87669999999999


Q ss_pred             HHCCCCCCCCCCCCCCCCHHHHC
Q ss_conf             41468102689986321021102
Q 003717          188 AAEGKQIHHPAAGQEEIHDMEEL  210 (800)
Q Consensus       188 AmNG~~i~n~n~~q~~i~~~ee~  210 (800)
                      .++|..+   ++....|..+.++
T Consensus        77 ~l~g~~~---~gr~i~V~~a~~~   96 (101)
T d2cpea1          77 WFDGKDF---QGSKLKVSLARKK   96 (101)
T ss_dssp             HHTTCEE---TTEECEEECSSCC
T ss_pred             HHCCCEE---CCEEEEEEECCCC
T ss_conf             8399989---9998799975789

>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=97.10  E-value=5.6e-05  Score=45.40  Aligned_cols=63  Identities=10%  Similarity=0.065  Sum_probs=49.7

Q ss_pred             CCCCCCCCCCCCCCHHHCCCCCCCCCEEEECCC--CCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCC
Q ss_conf             334799888888520000114676423660158--999721-11133368999964344102123546414681026
Q 003717          123 ATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPFC--GTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHH  196 (800)
Q Consensus       123 l~is~~Lk~svsesd~LreyFskyGKVKsVp~k--gTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n  196 (800)
                      +++.+ |+..+++ ++|+.+|.+||.|..+...  .+|+++ |+|         |.|.+.+++..|+..+||..+..
T Consensus         3 l~V~n-Lp~~~~~-~~l~~~F~~~G~v~~~~i~~~~~g~~~g~af---------V~f~~~~~A~~Ai~~l~g~~l~g   68 (78)
T d1no8a_           3 LLVSN-LDFGVSD-ADIQELFAEFGTLKKAAVHYDRSGRSLGTAD---------VHFERKADALKAMKQYNGVPLDG   68 (78)
T ss_dssp             EEEES-CCTTCCH-HHHHHHHHHHSCEEEEEESCSSCCCSCCEEE---------EEESCHHHHHHHHHHHTTCEETT
T ss_pred             EEEEC-CCCCCCH-HHHHHHHHHHCCCEEEEEEEEECCCCCEEEE---------EEECCHHHHHHHHHHHCCCEECC
T ss_conf             99988-9987989-9999999985997289999860124543689---------99989999999999838999999

>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=97.03  E-value=6.4e-05  Score=45.04  Aligned_cols=75  Identities=13%  Similarity=0.170  Sum_probs=57.7

Q ss_pred             CCCCCCCCCCCCCCCHHHCCCCCCCCCEEEECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCC
Q ss_conf             7334799888888520000114676423660158999721-111333689999643441021235464146810268998
Q 003717          122 DATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPAAG  200 (800)
Q Consensus       122 kl~is~~Lk~svsesd~LreyFskyGKVKsVp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n~~  200 (800)
                      .++++ .|+..+++ ++|+.+|.+||.|..++.  +|+.+ |+|         |.|.+.+++..|+..+||..+   ++.
T Consensus        18 ~l~V~-nL~~~~te-~~l~~~F~~~g~v~~~~~--~~~~~~~af---------V~f~~~~~A~~A~~~l~~~~~---~gr   81 (96)
T d1fjca_          18 TLLAK-NLSFNITE-DELKEVFEDALEIRLVSQ--DGKSKGIAY---------IEFKSEADAEKNLEEKQGAEI---DGR   81 (96)
T ss_dssp             EEEEE-SCCSSCCH-HHHHHHHCSEEEECCEEE--TTEEEEEEE---------EEESSHHHHHHHHHHTTEEEE---TTE
T ss_pred             EEEEE-CCCCCCCH-HHHHHHHHHCCCCEEEEE--CCCCCCEEE---------EEECCHHHHHHHHHHCCCCEE---CCE
T ss_conf             99991-89987989-999999975165605634--375066888---------986899999999998299999---999


Q ss_pred             CCCCCHHHHCCC
Q ss_conf             632102110275
Q 003717          201 QEEIHDMEELGA  212 (800)
Q Consensus       201 q~~i~~~ee~~g  212 (800)
                      ...|.-+.++++
T Consensus        82 ~i~V~~a~~k~~   93 (96)
T d1fjca_          82 SVSLYYTGEKGG   93 (96)
T ss_dssp             EEEEEECSSSCC
T ss_pred             EEEEEEECCCCC
T ss_conf             979998078999

>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=97.02  E-value=0.00017  Score=42.46  Aligned_cols=76  Identities=13%  Similarity=0.174  Sum_probs=54.1

Q ss_pred             CCCCCCCCCCCCCCCCHHHCCCCCCCCCEEEECCC-CCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCC
Q ss_conf             87334799888888520000114676423660158-999721-1113336899996434410212354641468102689
Q 003717          121 KDATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPFC-GTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPA  198 (800)
Q Consensus       121 pkl~is~~Lk~svsesd~LreyFskyGKVKsVp~k-gTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n  198 (800)
                      ..++++ .|+..+++ ++|+.+|.+||.|..+... +.+.++ |||         |.|.+-+++..|+..|||..+.   
T Consensus        12 ~~l~v~-nLp~~~t~-~~L~~~F~~~G~v~~v~~~~~~~~~kg~af---------V~f~~~~~a~~Ai~~l~~~~~~---   77 (93)
T d2cq3a1          12 KRLHVS-NIPFRFRD-PDLRQMFGQFGKILDVEIIFNERGSKGFGF---------VTFENSADADRAREKLHGTVVE---   77 (93)
T ss_dssp             CEEEEE-SCCTTCCH-HHHHHHGGGTSCEEEEEEECCTTTTCCEEE---------EEESCHHHHHHHHHHHTTCEET---
T ss_pred             CEEEEE-CCCCCCCH-HHHHHHHHHCCEEEECCCCCCCCCCCCEEE---------EEECCHHHHHHHHHHCCCCEEC---
T ss_conf             989997-98998999-999999863443300011256667740237---------8988999999999981999899---


Q ss_pred             CCCCCCCHHHHC
Q ss_conf             986321021102
Q 003717          199 AGQEEIHDMEEL  210 (800)
Q Consensus       199 ~~q~~i~~~ee~  210 (800)
                      +....|..+.++
T Consensus        78 g~~l~V~~A~~r   89 (93)
T d2cq3a1          78 GRKIEVNNATAR   89 (93)
T ss_dssp             TEECEEEECCSS
T ss_pred             CEEEEEEECCCC
T ss_conf             988899865757

>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=96.98  E-value=7.1e-05  Score=44.77  Aligned_cols=72  Identities=17%  Similarity=0.183  Sum_probs=52.0

Q ss_pred             CCCCCCCCCCCCCCCHHHCCCCCCCCCEEEECCC-CCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCC
Q ss_conf             7334799888888520000114676423660158-999721-11133368999964344102123546414681026899
Q 003717          122 DATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPFC-GTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPAA  199 (800)
Q Consensus       122 kl~is~~Lk~svsesd~LreyFskyGKVKsVp~k-gTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n~  199 (800)
                      ++++.+ |+..+++ ++|+.+|.+||.|..+... +.+.++ |||         |.|.+.+++..|++.|||..+.   +
T Consensus        10 ~l~V~n-Lp~~~t~-~~l~~~F~~~G~v~~~~i~~~~~~~kg~af---------V~f~~~~~A~~Ai~~l~g~~~~---g   75 (89)
T d1cvja2          10 NIFIKN-LDKSIDN-KALYDTFSAFGNILSCKVVCDENGSKGYGF---------VHFETQEAAERAIEKMNGMLLN---D   75 (89)
T ss_dssp             EEEEES-CCSSCCH-HHHHHHHHTTSCEEEEEECCBTTBCCSCEE---------EEESCHHHHHHHTTSSSEEEET---T
T ss_pred             EEEEEC-CCCCCCH-HHHHHHHHHCCCCEEEEEEEECCCCCCEEE---------EEECCHHHHHHHHHHCCCCEEC---C
T ss_conf             899928-9999999-999999986399607999850478740337---------9989999999999980999999---9


Q ss_pred             CCCCCCHH
Q ss_conf             86321021
Q 003717          200 GQEEIHDM  207 (800)
Q Consensus       200 ~q~~i~~~  207 (800)
                      ....|..+
T Consensus        76 ~~i~V~~a   83 (89)
T d1cvja2          76 RKVFVGRF   83 (89)
T ss_dssp             EEEEEEEC
T ss_pred             EEEEEEEC
T ss_conf             98899889

>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=96.98  E-value=0.00019  Score=42.20  Aligned_cols=79  Identities=14%  Similarity=0.034  Sum_probs=56.2

Q ss_pred             CCCCCCCCCCCCCCCCHHHCCCCCCCCCEEE---ECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCC-
Q ss_conf             8733479988888852000011467642366---0158999721-1113336899996434410212354641468102-
Q 003717          121 KDATRLDTPKKLLDKDKKLNIFFPRLRKVKT---LPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIH-  195 (800)
Q Consensus       121 pkl~is~~Lk~svsesd~LreyFskyGKVKs---Vp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~-  195 (800)
                      ..+++++ |+..+++ ++|+.+|.+||.+..   +..+.+++++ |||         |.|.+.+++..|+.++|+.... 
T Consensus         9 ~tlfV~n-Lp~~~te-~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~af---------V~F~~~~~a~~ai~~l~~~~~~~   77 (98)
T d1x4ha1           9 KTVFIRN-LSFDSEE-EALGEVLQQFGDLKYVRVVLHPDTEHSKGCAF---------AQFMTQEAAQKCLAAASLEAEGG   77 (98)
T ss_dssp             CCEEEES-CCTTCCH-HHHHHHHHTTSCEEEEECCBCSSSCCBCSEEE---------EEESSHHHHHHHHHHHCTTTTTC
T ss_pred             CEEEECC-CCCCCCH-HHHHHHHHCCCCCEEEEECCCCCCCCCCCEEE---------EEECCHHHHHHHHHHCCCCCCCC
T ss_conf             8999918-9996889-99998775124220333203665545662589---------99869999999998735223469


Q ss_pred             --CCCCCCCCCCHHHHC
Q ss_conf             --689986321021102
Q 003717          196 --HPAAGQEEIHDMEEL  210 (800)
Q Consensus       196 --n~n~~q~~i~~~ee~  210 (800)
                        .++|..+.|..+.++
T Consensus        78 g~~~~gr~l~v~~a~~k   94 (98)
T d1x4ha1          78 GLKLDGRQLKVDLAVTR   94 (98)
T ss_dssp             CEESSSCEEEEECCCCC
T ss_pred             CCEECCEEEEEEECCCC
T ss_conf             90889998899989887

>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=96.96  E-value=0.00012  Score=43.48  Aligned_cols=59  Identities=17%  Similarity=0.099  Sum_probs=49.5

Q ss_pred             CCCCCCCCCHHHCCCCCCCCCEE---EECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCC
Q ss_conf             98888885200001146764236---60158999721-11133368999964344102123546414681026
Q 003717          128 TPKKLLDKDKKLNIFFPRLRKVK---TLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHH  196 (800)
Q Consensus       128 ~Lk~svsesd~LreyFskyGKVK---sVp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n  196 (800)
                      .|+.++++ +.|+.+|.+||.|.   .++.+.+++++ |+|         |.|.+.+++..|+..|||..+..
T Consensus         5 nLp~~~te-~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~af---------V~f~~~~~A~~Ai~~lng~~~~G   67 (72)
T d1x4ea1           5 GLQPGTTD-QDLVKLCQPYGKIVSTKAILDKTTNKCKGYGF---------VDFDSPSAAQKAVTALKASGVQA   67 (72)
T ss_dssp             SCCTTCCH-HHHHTTSTTTSCEEEEEEECCSSSCSCCSEEE---------EEESCHHHHHHHHHHHHHHTCCE
T ss_pred             CCCCCCCH-HHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEE---------EEECCHHHHHHHHHHHCCCEECC
T ss_conf             79985889-99999886323332211100023322341159---------99889999999999838998788

>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=96.81  E-value=0.00019  Score=42.13  Aligned_cols=62  Identities=13%  Similarity=0.047  Sum_probs=49.3

Q ss_pred             CCCCCCCCCCCCCCCHHHCCCCCCCCCEEEECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCC
Q ss_conf             7334799888888520000114676423660158999721-111333689999643441021235464146810268
Q 003717          122 DATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHP  197 (800)
Q Consensus       122 kl~is~~Lk~svsesd~LreyFskyGKVKsVp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~  197 (800)
                      .+++.+ |+..+++ ++|+.+|.+||+|..+.++   +.+ |+|         |.|.+.+++..|++.|||..+...
T Consensus        12 ~l~V~n-Lp~~~t~-~~L~~~F~~fG~I~~v~l~---~~kg~af---------V~f~~~~~A~~A~~~lng~~~~gr   74 (111)
T d1whxa_          12 VILAKN-LPAGTLA-AEIQETFSRFGSLGRVLLP---EGGITAI---------VEFLEPLEARKAFRHLAYSKFHHV   74 (111)
T ss_dssp             EEEEES-CCTTCCH-HHHHHHHHTTSCEEEEECC---SSSSCEE---------EEESCHHHHHHHHHHHTTCBSSSS
T ss_pred             EEEEEC-CCCCCCH-HHHHHHHHCCCCCCEEEEE---CCCCEEE---------EEECCHHHHHHHHHHHCCCCCCCC
T ss_conf             999979-8998889-9997664026886189960---4686389---------998477899999999769835897

>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=96.78  E-value=0.00036  Score=40.53  Aligned_cols=69  Identities=13%  Similarity=0.194  Sum_probs=49.6

Q ss_pred             CCCCCCCCCC-CCCCCCHHHCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCC
Q ss_conf             8733479988-888852000011467642366015899972111133368999964344102123546414681026899
Q 003717          121 KDATRLDTPK-KLLDKDKKLNIFFPRLRKVKTLPFCGTGKHKYSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPAA  199 (800)
Q Consensus       121 pkl~is~~Lk-~svsesd~LreyFskyGKVKsVp~kgTGK~KYGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n~  199 (800)
                      ..+++.+ |. ..+++ .+|+.+|.+||.|..+..+    ..|+|         |.|.+-+++..|+..|||..+..   
T Consensus        16 ~~lfV~n-L~~~~~~~-~~L~~~F~~~G~i~~~~i~----rg~aF---------V~f~~~~~A~~Ai~~lng~~~~g---   77 (98)
T d1wf2a_          16 SRVFIGN-LNTLVVKK-SDVEAIFSKYGKIVGCSVH----KGFAF---------VQYVNERNARAAVAGEDGRMIAG---   77 (98)
T ss_dssp             CCEEEEE-ECTTTCCH-HHHHHSSTTSSCEEEEEEE----TEEEE---------EEESSHHHHHHHHHTTTTCEETT---
T ss_pred             CEEEEEC-CCCCCCCH-HHHHHHHHHCCCEEEEEEE----CCEEE---------EEECCHHHHHHHHHHCCCCEECC---
T ss_conf             5899938-89021999-9999998626987999970----88689---------99799999999999819998999---


Q ss_pred             CCCCCCHH
Q ss_conf             86321021
Q 003717          200 GQEEIHDM  207 (800)
Q Consensus       200 ~q~~i~~~  207 (800)
                      ..+.|.-+
T Consensus        78 ~~l~V~~a   85 (98)
T d1wf2a_          78 QVLDINLA   85 (98)
T ss_dssp             EECEEEET
T ss_pred             EEEEEEEC
T ss_conf             88799977

>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=96.74  E-value=0.00072  Score=38.69  Aligned_cols=73  Identities=25%  Similarity=0.234  Sum_probs=52.4

Q ss_pred             CCCCCCCCCCCCCCHHHCCCCCCCCCEE---EECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCC
Q ss_conf             3347998888885200001146764236---60158999721-1113336899996434410212354641468102689
Q 003717          123 ATRLDTPKKLLDKDKKLNIFFPRLRKVK---TLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPA  198 (800)
Q Consensus       123 l~is~~Lk~svsesd~LreyFskyGKVK---sVp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n  198 (800)
                      .+..+.|+.++++ ++|+.||..++.+.   .+....+++++ |+|         |.|.+-+++.+|++ +++.++   .
T Consensus        17 ~v~v~nLP~~~te-~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~af---------V~F~~~e~a~~a~~-~~~~~i---~   82 (104)
T d1wg5a_          17 FVRLRGLPFGCSK-EEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAF---------VQFASQEIAEKALK-KHKERI---G   82 (104)
T ss_dssp             EEEEESCCTTCCH-HHHHHHTTTCCEEEEEEECCBCSSSCBCSEEE---------EEESSHHHHHHHHT-TTTCCS---S
T ss_pred             EEEEECCCCCCCH-HHHHHHHHHCCCCEEEEEEEECCCCCCCEEEE---------EEECCHHHHHHHHH-HCCCEE---C
T ss_conf             8998589998989-99999887538724788977689997236889---------97489999999874-489889---3


Q ss_pred             CCCCCCCHHHH
Q ss_conf             98632102110
Q 003717          199 AGQEEIHDMEE  209 (800)
Q Consensus       199 ~~q~~i~~~ee  209 (800)
                      +..++|..+-+
T Consensus        83 gR~i~V~~~~~   93 (104)
T d1wg5a_          83 HRYIEIFKSSR   93 (104)
T ss_dssp             SSCCEEEEECT
T ss_pred             CEEEEEEECCH
T ss_conf             35999998897

>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=96.68  E-value=0.0005  Score=39.64  Aligned_cols=65  Identities=8%  Similarity=0.106  Sum_probs=47.1

Q ss_pred             CCCCCCCCCCCCCCCHHH---CCCCCCCCCEEE---ECCCCCCCC---C-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCC
Q ss_conf             733479988888852000---011467642366---015899972---1-111333689999643441021235464146
Q 003717          122 DATRLDTPKKLLDKDKKL---NIFFPRLRKVKT---LPFCGTGKH---K-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEG  191 (800)
Q Consensus       122 kl~is~~Lk~svsesd~L---reyFskyGKVKs---Vp~kgTGK~---K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG  191 (800)
                      +....+.|+..+++ ++|   ..+|++||+|..   ++++.++..   + |+|         |.|.+-+++..|++.|||
T Consensus         9 n~vyV~nLp~~~t~-~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aF---------V~f~~~~~A~~Ai~~lng   78 (89)
T d2cpia1           9 NLVFVVGLSQRLAD-PEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAY---------VTYIRSEDALRAIQCVNN   78 (89)
T ss_dssp             SCEEEEEECTTTCC-HHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEE---------EEESSHHHHHHHHHHHTT
T ss_pred             CEEEEECCCCCCCH-HHHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCCEEEE---------EECCCCHHHHHHHHHHCC
T ss_conf             88999798976387-89998898763558825877720267687777653799---------851541229999998589


Q ss_pred             CCCCC
Q ss_conf             81026
Q 003717          192 KQIHH  196 (800)
Q Consensus       192 ~~i~n  196 (800)
                      ..+..
T Consensus        79 ~~~~g   83 (89)
T d2cpia1          79 VVVDG   83 (89)
T ss_dssp             EEETT
T ss_pred             CEECC
T ss_conf             99999

>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=96.68  E-value=0.0002  Score=42.00  Aligned_cols=67  Identities=12%  Similarity=0.151  Sum_probs=49.3

Q ss_pred             CCCCCCCCCHHHCCCCCCCCCEEE---ECCCCCC---CCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCC
Q ss_conf             988888852000011467642366---0158999---721-111333689999643441021235464146810268998
Q 003717          128 TPKKLLDKDKKLNIFFPRLRKVKT---LPFCGTG---KHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPAAG  200 (800)
Q Consensus       128 ~Lk~svsesd~LreyFskyGKVKs---Vp~kgTG---K~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n~~  200 (800)
                      .|+..+++ ++|+.+|++||.|..   ++++.++   +++ |||         |.|.+-+++..|+..|||..+.   +.
T Consensus         5 nLp~~~t~-~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~af---------V~f~~~~~A~~A~~~~~~~~~~---g~   71 (85)
T d2cpfa1           5 NLNFSTTE-ETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGF---------VEYKKPEQAQKALKQLQGHTVD---GH   71 (85)
T ss_dssp             SCCTTCCH-HHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEE---------EEESSHHHHHHHHHHSTTCEET---TE
T ss_pred             CCCCCCCH-HHHHHHHHHHCCCCCCCEECCCCCCCCCCCCEEEE---------EEECCHHHHHHHHHHHCCCEEC---CE
T ss_conf             89997989-99999999839803221000233235453313789---------9989999999999982998899---99


Q ss_pred             CCCCCHH
Q ss_conf             6321021
Q 003717          201 QEEIHDM  207 (800)
Q Consensus       201 q~~i~~~  207 (800)
                      ...|..+
T Consensus        72 ~i~V~~a   78 (85)
T d2cpfa1          72 KLEVRIS   78 (85)
T ss_dssp             ECEEECS
T ss_pred             EEEEEEC
T ss_conf             9799988

>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=96.67  E-value=0.00014  Score=42.91  Aligned_cols=71  Identities=8%  Similarity=0.048  Sum_probs=53.1

Q ss_pred             CCCCCCCCCCCCCCHHHCCCCCCCCCEE---EECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCC
Q ss_conf             3347998888885200001146764236---60158999721-1113336899996434410212354641468102689
Q 003717          123 ATRLDTPKKLLDKDKKLNIFFPRLRKVK---TLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPA  198 (800)
Q Consensus       123 l~is~~Lk~svsesd~LreyFskyGKVK---sVp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n  198 (800)
                      +++. .|+..+++ ++|+.+|++||.|.   .++...+|+++ |||         |.|.+.+++..|+..|||..+.   
T Consensus         4 l~v~-nLp~~~t~-~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~af---------V~f~~~e~A~~Ai~~l~g~~~~---   69 (81)
T d2ghpa1           4 LWMT-NFPPSYTQ-RNIRDLLQDINVVALSIRLPSLRFNTSRRFAY---------IDVTSKEDARYCVEKLNGLKIE---   69 (81)
T ss_dssp             EEEE-CCCTTCCH-HHHHHHHHHTTCCCCEEECC-------CCEEE---------EECSSHHHHHHHHHHHTTCEET---
T ss_pred             EEEE-CCCCCCCH-HHHHHHHHHHCCEEEEEEECCCCCCCCCCEEE---------EEECCHHHHHHHHHHHCCCEEC---
T ss_conf             9997-97986989-99999999829687642200011234552158---------9989999999999986997889---


Q ss_pred             CCCCCCCHH
Q ss_conf             986321021
Q 003717          199 AGQEEIHDM  207 (800)
Q Consensus       199 ~~q~~i~~~  207 (800)
                      +....|.-+
T Consensus        70 g~~i~V~~a   78 (81)
T d2ghpa1          70 GYTLVTKVS   78 (81)
T ss_dssp             TEECEEEEC
T ss_pred             CEEEEEEEC
T ss_conf             999999974

>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=96.64  E-value=0.00018  Score=42.30  Aligned_cols=63  Identities=11%  Similarity=0.092  Sum_probs=48.2

Q ss_pred             CCCCCCCCCCCCHHHCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCC
Q ss_conf             4799888888520000114676423660158999721111333689999643441021235464146810268
Q 003717          125 RLDTPKKLLDKDKKLNIFFPRLRKVKTLPFCGTGKHKYSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHP  197 (800)
Q Consensus       125 is~~Lk~svsesd~LreyFskyGKVKsVp~kgTGK~KYGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~  197 (800)
                      +.+.|...+++ +.|+.+|++||.|..+.........|||         |.|.+.++|..|+..+||..+...
T Consensus        11 ~V~NL~~~vte-~~L~~~F~~~G~i~~~~i~~~~~~g~aF---------V~f~~~e~A~~Ai~~ln~~~l~~~   73 (108)
T d2adba1          11 IVENLFYPVTL-DVLHQIFSKFGTVLKIITFTKNNQFQAL---------LQYADPVSAQHAKLSLDGQNIYNA   73 (108)
T ss_dssp             ESCSCCSTTHH-HHHHHHHTTTSCEEEEEEEEETTEEEEE---------EEESCHHHHHHHHHHHHSCCSSTT
T ss_pred             EEECCCCCCCH-HHHHHHHCCCCCEEEEEEEEECCCCEEE---------EEECCHHHHHHHHHHHCCCEECCC
T ss_conf             99392999989-9998887039758997998508998189---------998999999999999778870469

>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=96.61  E-value=6e-05  Score=45.22  Aligned_cols=71  Identities=13%  Similarity=0.204  Sum_probs=51.9

Q ss_pred             CCCCCCCCCCCCCCCHHHCCCCCCCCCEEEECC--CCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCC
Q ss_conf             733479988888852000011467642366015--8999721-1113336899996434410212354641468102689
Q 003717          122 DATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPF--CGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPA  198 (800)
Q Consensus       122 kl~is~~Lk~svsesd~LreyFskyGKVKsVp~--kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n  198 (800)
                      .+++ +.|+..+++ ++|+.+|.+||.|..+..  +.+|+++ |+|         |.|.+.+++..|++ |||..+.   
T Consensus        15 ~ifV-~nL~~~~te-~~l~~~F~~~G~i~~~~v~~~~~g~~kg~af---------v~F~~~e~a~~Al~-~~g~~~~---   79 (91)
T d1fjeb1          15 NLFI-GNLNPNKSV-AELKVAISELFAKNDLAVVDVRTGTNRKFGY---------VDFESAEDLEKALE-LTGLKVF---   79 (91)
T ss_dssp             EEEE-ECCCTTSCH-HHHHHHHHHHHHHHTCCCCEEEEETTTTEEE---------EEESSHHHHHHHHH-GGGEEET---
T ss_pred             EEEE-ECCCCCCHH-HHHHHHHHCCCCEEEEEEEECCCCCCCEEEE---------EEECCHHHHHHHHH-CCCCEEC---
T ss_conf             8999-576576128-8999998637847875410068998537767---------86389999999982-3994889---


Q ss_pred             CCCCCCCHH
Q ss_conf             986321021
Q 003717          199 AGQEEIHDM  207 (800)
Q Consensus       199 ~~q~~i~~~  207 (800)
                      |...+|..+
T Consensus        80 g~~i~V~~a   88 (91)
T d1fjeb1          80 GNEIKLEKP   88 (91)
T ss_dssp             TEEEEEECC
T ss_pred             CEEEEEEEC
T ss_conf             999899855

>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=96.61  E-value=0.00027  Score=41.22  Aligned_cols=62  Identities=15%  Similarity=0.185  Sum_probs=46.7

Q ss_pred             CCCCCCCC-CCCCCCHHHCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCC
Q ss_conf             33479988-888852000011467642366015899972111133368999964344102123546414681026
Q 003717          123 ATRLDTPK-KLLDKDKKLNIFFPRLRKVKTLPFCGTGKHKYSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHH  196 (800)
Q Consensus       123 l~is~~Lk-~svsesd~LreyFskyGKVKsVp~kgTGK~KYGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n  196 (800)
                      +++.+ |+ ..+++ ++|+.+|..||.|..+...-. +..|||         |.|.+.++|..|++.|||..++.
T Consensus         5 l~V~n-L~p~~~te-~~L~~~F~~fG~I~~v~i~~~-~kg~af---------V~f~~~~~A~~ai~~lng~~l~g   67 (109)
T d2adca1           5 LLVSN-LNPERVTP-QSLFILFGVYGDVQRVKILFN-KKENAL---------VQMADGNQAQLAMSHLNGHKLHG   67 (109)
T ss_dssp             EEEES-CCTTTCCH-HHHHHHHHHHTCEEEEEECCT-TSCCEE---------EEESCHHHHHHHHHHHTTCBCSS
T ss_pred             EEEEC-CCCCCCCH-HHHHHHHHHCCCCCEEEEEEC-CCCEEE---------EEECCHHHHHHHHHHHCCCEECC
T ss_conf             99967-99252999-999998750356404999760-342589---------99778799999999839978799

>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=96.60  E-value=0.00033  Score=40.77  Aligned_cols=58  Identities=9%  Similarity=-0.044  Sum_probs=47.2

Q ss_pred             CCCCCCCCCCHHHCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCC
Q ss_conf             99888888520000114676423660158999721111333689999643441021235464146810268
Q 003717          127 DTPKKLLDKDKKLNIFFPRLRKVKTLPFCGTGKHKYSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHP  197 (800)
Q Consensus       127 ~~Lk~svsesd~LreyFskyGKVKsVp~kgTGK~KYGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~  197 (800)
                      +.|+..+++ ++|+.+|++||.|..+.....   .|+|         |.|.+.+++..|+..|+|..++..
T Consensus         6 ~nlp~~~~~-~~l~~~F~~~G~v~~~~i~~~---g~af---------V~f~~~~~a~~Ai~~l~g~~~~g~   63 (87)
T d3begb1           6 SGLPPSGSW-QDLKDHMREAGDVCYADVYRD---GTGV---------VEFVRKEDMTYAVRKLDNTKFRSH   63 (87)
T ss_dssp             EECCSSCCT-THHHHHHGGGSCEEEEEECTT---SEEE---------EEESSHHHHHHHHHHHTTCBCCCT
T ss_pred             ECCCCCCCH-HHHHHHHHHHCCCCCCCCCCC---CEEE---------EEECCHHHHHHHHHHHCCCEECCC
T ss_conf             799985889-999998752212321100223---2135---------774888999999999687997996

>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=96.53  E-value=0.0003  Score=40.98  Aligned_cols=74  Identities=11%  Similarity=0.029  Sum_probs=52.3

Q ss_pred             CCCCCCCCCCCCCCHHHCCCCCCCCC-EEEECC---C-CCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCC
Q ss_conf             33479988888852000011467642-366015---8-999721-11133368999964344102123546414681026
Q 003717          123 ATRLDTPKKLLDKDKKLNIFFPRLRK-VKTLPF---C-GTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHH  196 (800)
Q Consensus       123 l~is~~Lk~svsesd~LreyFskyGK-VKsVp~---k-gTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n  196 (800)
                      +++++ |+..+++ ++|+.+|.+||. +..+..   + ++|+++ |||         |.|.+.+++..|+.+|++..+. 
T Consensus         4 LyV~n-Lp~~~te-~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aF---------V~F~~~~~A~~Ai~~l~~~~~~-   71 (96)
T d2disa1           4 LFIGG-IPKMKKR-EEILEEIAKVTEGVLDVIVYASAADKMKNRGFAF---------VEYESHRAAAMARRKLMPGRIQ-   71 (96)
T ss_dssp             EEEEC-CCTTSCH-HHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEE---------EEESSHHHHHHHHTTTTTCCSC-
T ss_pred             EEECC-CCCCCCH-HHHHHHHHHHCCCCEEEEEEEECCCCCCCCCEEE---------EEECCHHHHHHHHHHHCCCCEE-
T ss_conf             99949-8986889-9999999986975058998641123236787599---------9983999999999997689827-


Q ss_pred             CCCCCCCCCHHH
Q ss_conf             899863210211
Q 003717          197 PAAGQEEIHDME  208 (800)
Q Consensus       197 ~n~~q~~i~~~e  208 (800)
                      +.+....|.-+.
T Consensus        72 ~~g~~i~V~~A~   83 (96)
T d2disa1          72 LWGHQIAVDWAE   83 (96)
T ss_dssp             BTTBCCEEEESC
T ss_pred             ECCEEEEEEECC
T ss_conf             899888999718

>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=96.48  E-value=0.00013  Score=43.24  Aligned_cols=71  Identities=14%  Similarity=0.197  Sum_probs=53.1

Q ss_pred             CCCCCCCCCCCCCCHHH----CCCCCCCCCEEEECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCC
Q ss_conf             33479988888852000----0114676423660158999721-111333689999643441021235464146810268
Q 003717          123 ATRLDTPKKLLDKDKKL----NIFFPRLRKVKTLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHP  197 (800)
Q Consensus       123 l~is~~Lk~svsesd~L----reyFskyGKVKsVp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~  197 (800)
                      +++++ |+..+++ ++|    ..+|++||.|..+..+.+++++ |||         |.|.+.+++..|+.++||..+.  
T Consensus         6 l~V~n-Lp~~~t~-~dl~~~l~~~f~~~G~i~~i~~~~~~~~~g~af---------V~F~~~~~A~~A~~~~~~~~~~--   72 (91)
T d1nu4a_           6 IYINN-LNEKIKK-DELKKSLHAIFSRFGQILDILVSRSLKMRGQAF---------VIFKEVSSATNALRSMQGFPFY--   72 (91)
T ss_dssp             EEEES-CCTTSCH-HHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEE---------EEESSHHHHHHHHHHHTTCEET--
T ss_pred             EEEEC-CCCCCCH-HHHHHHHHHHHCCCCCCCCEEEEEECCCCCCEE---------EEECCHHHHHHHHHHHCCCEEC--
T ss_conf             99959-9999999-999999998703123255328854306898157---------8889999999999984998899--


Q ss_pred             CCCCCCCCHH
Q ss_conf             9986321021
Q 003717          198 AAGQEEIHDM  207 (800)
Q Consensus       198 n~~q~~i~~~  207 (800)
                       +....|.-+
T Consensus        73 -g~~l~v~~a   81 (91)
T d1nu4a_          73 -DKPMRIQYA   81 (91)
T ss_dssp             -TEECEEEEC
T ss_pred             -CEEEEEEEE
T ss_conf             -988899980

>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=96.46  E-value=0.00075  Score=38.58  Aligned_cols=70  Identities=10%  Similarity=0.044  Sum_probs=52.5

Q ss_pred             CCCCCCCCCCCCCCCHHHCCCCCCCCCEE---EECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCC
Q ss_conf             73347998888885200001146764236---60158999721-111333689999643441021235464146810268
Q 003717          122 DATRLDTPKKLLDKDKKLNIFFPRLRKVK---TLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHP  197 (800)
Q Consensus       122 kl~is~~Lk~svsesd~LreyFskyGKVK---sVp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~  197 (800)
                      -+++. .|+..+++ ++|+.||..||.+.   .++...+|+++ |+|         |.|.+.+++..|+. +||.++   
T Consensus        10 ~v~v~-nLp~~~t~-~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~af---------V~F~s~~~a~~Al~-~n~~~i---   74 (103)
T d2cpya1          10 CAHIT-NIPFSITK-MDVLQFLEGIPVDENAVHVLVDNNGQGLGQAL---------VQFKNEDDARKSER-LHRKKL---   74 (103)
T ss_dssp             EEEEE-SCCTTSCH-HHHHHHTTTSCCCSTTEEECCCTTSSCSSCEE---------EECSSHHHHHHHGG-GCSEEE---
T ss_pred             EEEEE-CCCCCCCH-HHHHHHHCCCCEEEEEEEEEECCCCCCCCCEE---------EEECCHHHHHHHHH-CCCCEE---
T ss_conf             89995-98988888-99864210222377788887689898576378---------99889999999996-398749---


Q ss_pred             CCCCCCCCH
Q ss_conf             998632102
Q 003717          198 AAGQEEIHD  206 (800)
Q Consensus       198 n~~q~~i~~  206 (800)
                      ++....|..
T Consensus        75 ~gr~i~V~~   83 (103)
T d2cpya1          75 NGREAFVHV   83 (103)
T ss_dssp             TTEEEEEEE
T ss_pred             CCCEEEEEE
T ss_conf             991899998

>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=96.46  E-value=0.0012  Score=37.36  Aligned_cols=74  Identities=11%  Similarity=0.108  Sum_probs=52.7

Q ss_pred             CCCCCCCCCCCCCCHHHCCCCCCCCCEE--EECCC-CCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCC
Q ss_conf             3347998888885200001146764236--60158-999721-1113336899996434410212354641468102689
Q 003717          123 ATRLDTPKKLLDKDKKLNIFFPRLRKVK--TLPFC-GTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPA  198 (800)
Q Consensus       123 l~is~~Lk~svsesd~LreyFskyGKVK--sVp~k-gTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n  198 (800)
                      +++ +.|+..+++ ++|+.+|..||-+.  .++.+ .+|+.+ |+|         |.|.+.+++.+|+ .+|+..+   .
T Consensus        18 v~V-~nLp~~~te-~~l~~~f~~~g~~~~~~~~~~~~~g~~~g~af---------V~f~~~e~a~~~~-~~~~~~~---~   82 (104)
T d1wi8a_          18 AFL-GNLPYDVTE-ESIKEFFRGLNISAVRLPREPSNPERLKGFGY---------AEFEDLDSLLSAL-SLNEESL---G   82 (104)
T ss_dssp             EEE-ESCCSSCCH-HHHHHHTTTSCEEEEECCBCSSCTTSBCSCEE---------EEESSHHHHHHHH-GGGTCEE---T
T ss_pred             EEE-ECCCCCCCH-HHHHHHHHHHCCCCCEEEEEECCCCCCCEEEE---------EEECCHHHHHHHH-HCCCCEE---C
T ss_conf             998-099986989-99999999832153102343114788613545---------7877999999999-8099989---9


Q ss_pred             CCCCCCCHHHHCC
Q ss_conf             9863210211027
Q 003717          199 AGQEEIHDMEELG  211 (800)
Q Consensus       199 ~~q~~i~~~ee~~  211 (800)
                      +....|..+.++.
T Consensus        83 gr~l~V~~a~~~~   95 (104)
T d1wi8a_          83 NKRIRVDVADQAQ   95 (104)
T ss_dssp             TEECEEEECCCCC
T ss_pred             CEEEEEEECCCCC
T ss_conf             9988999789988

>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=96.44  E-value=0.0022  Score=35.81  Aligned_cols=74  Identities=19%  Similarity=0.236  Sum_probs=54.1

Q ss_pred             CCCCCCCCCCCCCHHHCCCCCCCCCEE---EECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCC
Q ss_conf             347998888885200001146764236---60158999721-11133368999964344102123546414681026899
Q 003717          124 TRLDTPKKLLDKDKKLNIFFPRLRKVK---TLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPAA  199 (800)
Q Consensus       124 ~is~~Lk~svsesd~LreyFskyGKVK---sVp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n~  199 (800)
                      ...++|+..+++ ++|..||+.+|.+.   .+....+|+.+ |+|         |.|.+.+++.+|+. +||.++   .+
T Consensus        21 i~v~nLp~~~t~-~di~~~F~~~g~~~~~~~~~~~~~g~~~G~af---------VeF~~~e~a~~al~-~~~~~i---~g   86 (112)
T d1wela1          21 VYLKGLPFEAEN-KHVIDFFKKLDIVEDSIYIAYGPNGKATGEGF---------VEFRNEADYKAALC-RHKQYM---GN   86 (112)
T ss_dssp             EEEECCCTTCCH-HHHHHHSCSSCBCTTTCEEEECTTSSEEEEEE---------EEBSSSHHHHHHHT-SCSBCS---TT
T ss_pred             EEEECCCCCCCH-HHHHHHHHHCCCCCCCEEEECCCCCCEEEEEE---------EEECCHHHHHHHHH-CCCCCC---CC
T ss_conf             999469975759-99966775334443210221076543004789---------99889999999997-189847---99


Q ss_pred             CCCCCCHHHHCC
Q ss_conf             863210211027
Q 003717          200 GQEEIHDMEELG  211 (800)
Q Consensus       200 ~q~~i~~~ee~~  211 (800)
                      ..++|..+....
T Consensus        87 R~i~V~~~~~~~   98 (112)
T d1wela1          87 RFIQVHPITKKG   98 (112)
T ss_dssp             SCBEEEEECHHH
T ss_pred             EEEEEEECCHHH
T ss_conf             898999869578

>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=96.43  E-value=0.00042  Score=40.13  Aligned_cols=63  Identities=17%  Similarity=0.205  Sum_probs=49.9

Q ss_pred             CCCC-CCCCCCCCCCHHHCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCC
Q ss_conf             3347-99888888520000114676423660158999721111333689999643441021235464146810268
Q 003717          123 ATRL-DTPKKLLDKDKKLNIFFPRLRKVKTLPFCGTGKHKYSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHP  197 (800)
Q Consensus       123 l~is-~~Lk~svsesd~LreyFskyGKVKsVp~kgTGK~KYGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~  197 (800)
                      +++. +.|+..+++ +.|+.+|++||.|+.+.....  ..|+|         |.|.+.+++..|+.+|||..+...
T Consensus        21 l~V~ng~L~~~vte-~~L~~~F~~~G~i~~i~~~~~--k~~aF---------V~f~~~e~A~~A~~~lng~~i~~~   84 (101)
T d2cq2a1          21 LVVANGGLGNGVSR-NQLLPVLEKCGLVDALLMPPN--KPYSF---------ARYRTTEESKRAYVTLNGKEVVDD   84 (101)
T ss_dssp             EEEETCTGGGTCCH-HHHHHHHHHHSCEEEEECCTT--CSCEE---------EEESSHHHHHHHHHHTTTCEEECT
T ss_pred             EEEECCCCCCCCCH-HHHHHHHHHHCCCCEEEECCC--CCEEE---------EEECCHHHHHHHHHHHCCCCCCCC
T ss_conf             99977789998789-999999975276617863267--50899---------998998999999998389897799

>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=96.40  E-value=0.00064  Score=39.00  Aligned_cols=67  Identities=10%  Similarity=0.063  Sum_probs=50.4

Q ss_pred             CCCCCCCCCCCCCCCHHHCCCCCCCCCEEEECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCC
Q ss_conf             7334799888888520000114676423660158999721-111333689999643441021235464146810268998
Q 003717          122 DATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPAAG  200 (800)
Q Consensus       122 kl~is~~Lk~svsesd~LreyFskyGKVKsVp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n~~  200 (800)
                      .+++++ |+.++++ ++|+.+|.+||.|..+...   +.+ |+|         |.|.+.+++..|+..|||..+..   .
T Consensus        10 ~l~V~n-Lp~~~~~-~~l~~~F~~~G~i~~i~~~---~~k~~af---------V~f~~~~~A~~A~~~l~g~~i~g---~   72 (86)
T d2cpja1          10 RLFVGN-LPPDITE-EEMRKLFEKYGKAGEVFIH---KDKGFGF---------IRLETRTLAEIAKVELDNMPLRG---K   72 (86)
T ss_dssp             EEEEES-CCTTCCH-HHHHHHTSTTCCCSEEEEE---TTTTEEE---------EECSSSHHHHHHHHHHTTCCBTT---B
T ss_pred             EEEEEC-CCCCCCH-HHHHHHHHHHCCCEEEEEE---CCCCEEE---------EEECCHHHHHHHHHHHCCCEECC---E
T ss_conf             999979-9987989-9999999986986076342---1353699---------99889999999999819988999---8


Q ss_pred             CCCCC
Q ss_conf             63210
Q 003717          201 QEEIH  205 (800)
Q Consensus       201 q~~i~  205 (800)
                      ...|.
T Consensus        73 ~l~V~   77 (86)
T d2cpja1          73 QLRVR   77 (86)
T ss_dssp             CCEEE
T ss_pred             EEEEE
T ss_conf             88999

>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=96.36  E-value=0.00065  Score=38.97  Aligned_cols=62  Identities=15%  Similarity=0.166  Sum_probs=50.7

Q ss_pred             CCCCCCCCCCCCHHHCCCCCCCCCEE---EECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCC
Q ss_conf             47998888885200001146764236---60158999721-11133368999964344102123546414681026
Q 003717          125 RLDTPKKLLDKDKKLNIFFPRLRKVK---TLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHH  196 (800)
Q Consensus       125 is~~Lk~svsesd~LreyFskyGKVK---sVp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n  196 (800)
                      ..+.|+..+++ ++|+.+|..|+.+.   .+....+|+++ |+|         |.|.+.+++..|+..+||.++..
T Consensus        13 ~v~nLp~~~~~-~di~~~F~~~~~~~~~~~~~~~~~g~~~G~af---------V~f~~~e~a~~Ai~~l~~~~l~g   78 (86)
T d2cqpa1          13 KVQNMPFTVSI-DEILDFFYGYQVIPGSVCLKYNEKGMPTGEAM---------VAFESRDEATAAVIDLNDRPIGS   78 (86)
T ss_dssp             EEESCCTTCCH-HHHHHHTTTSCCCTTTCEEEECSSSCEEEEEE---------EEESCHHHHHHHHHHTTTCEETT
T ss_pred             EEECCCCCCCH-HHHHHHHHHCCCCEEEEEEEECCCCCCCEEEE---------EEECCCHHHHHHHHHCCCCEECC
T ss_conf             99798998989-99998775124642699997689999660899---------99828579999999808999999

>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=96.34  E-value=0.00072  Score=38.68  Aligned_cols=62  Identities=11%  Similarity=0.042  Sum_probs=46.2

Q ss_pred             CCCCCCCCCCCCCCCHHHCCCCCCCCCEEEECC-CCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCC
Q ss_conf             733479988888852000011467642366015-89997211113336899996434410212354641468102
Q 003717          122 DATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPF-CGTGKHKYSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIH  195 (800)
Q Consensus       122 kl~is~~Lk~svsesd~LreyFskyGKVKsVp~-kgTGK~KYGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~  195 (800)
                      .++++ .|+.++++ ++|+.+|.+||.|..+.. .+.+ .+|||         |.|.+.++|..|+..|+|..+.
T Consensus        12 tL~V~-NLp~~~te-~~l~~~F~~~G~v~~~~~~~~~~-~~~af---------V~f~~~~~A~~A~~~l~~~~i~   74 (88)
T d2adca2          12 TLHLS-NIPPSVSE-EDLKVLFSSNGGVVKGFKFFQKD-RKMAL---------IQMGSVEEAVQALIDLHNHDLG   74 (88)
T ss_dssp             EEEEE-CCCTTCCH-HHHHHHHHTTSCCEEEEEECSSS-TTCEE---------EEESSHHHHHHHHHHHTTCBSS
T ss_pred             EEEEE-CCCCCCCH-HHHHHHHHCCCCEEEEEEEEECC-CCEEE---------EEECCHHHHHHHHHHCCCCEEC
T ss_conf             89997-99988899-99999853369788888753024-40069---------9989999999999751697926

>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=96.31  E-value=0.00059  Score=39.24  Aligned_cols=70  Identities=9%  Similarity=0.063  Sum_probs=49.4

Q ss_pred             CCCCCCCCCCCCCCHHHCCCCCCCCCEEEECC----CCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCC
Q ss_conf             33479988888852000011467642366015----8999721-111333689999643441021235464146810268
Q 003717          123 ATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPF----CGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHP  197 (800)
Q Consensus       123 l~is~~Lk~svsesd~LreyFskyGKVKsVp~----kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~  197 (800)
                      +++.+ |+.++...+.|+.+|++||.|..+..    ..+|+++ |||         |.|.+.+++..|++ |||..+.  
T Consensus         7 l~V~n-Lp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~af---------V~f~~~~~a~~Al~-~n~~~~~--   73 (86)
T d2ghpa3           7 IMIRN-LSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAF---------MVFENKDSAERALQ-MNRSLLG--   73 (86)
T ss_dssp             EEEEE-ECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEE---------EEESSHHHHHHHGG-GTTEEET--
T ss_pred             EEEEC-CCCCCCCHHHHHHHHHHHHHCCCEEEECCCCCCCCCCEEEE---------EEECCHHHHHHHHH-CCCCEEC--
T ss_conf             99979-99774349999999775312111000002577655522656---------89889999999996-2999899--


Q ss_pred             CCCCCCCCH
Q ss_conf             998632102
Q 003717          198 AAGQEEIHD  206 (800)
Q Consensus       198 n~~q~~i~~  206 (800)
                       |....|..
T Consensus        74 -gr~l~V~~   81 (86)
T d2ghpa3          74 -NREISVSL   81 (86)
T ss_dssp             -TEEEEEEE
T ss_pred             -CEEEEEEE
T ss_conf             -99989997

>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=96.29  E-value=0.0013  Score=37.19  Aligned_cols=62  Identities=18%  Similarity=0.191  Sum_probs=48.0

Q ss_pred             CCCCCCCCCCCCCCCHHHCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCC
Q ss_conf             73347998888885200001146764236601589997211113336899996434410212354641468102
Q 003717          122 DATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPFCGTGKHKYSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIH  195 (800)
Q Consensus       122 kl~is~~Lk~svsesd~LreyFskyGKVKsVp~kgTGK~KYGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~  195 (800)
                      .+++. .|+..+++ +.|..+|.+||.|+.+++.. ++..|+|         |.|.+.+++..|+..|+|..+.
T Consensus        10 tl~V~-nLp~~~t~-~~l~~~f~~~G~i~~v~~~~-~~~g~af---------V~f~~~~~A~~A~~~l~g~~~~   71 (83)
T d2b0ga1          10 ILFLT-NLPEETNE-MMLSMLFNQFPGFKEVRLVP-NRHDIAF---------VEFTTELQSNAAKEALQGFKIT   71 (83)
T ss_dssp             EEEEE-SCCTTCCH-HHHHHHHTTSTTEEEEEECT-TTCSCEE---------EEESSHHHHHHHHHHHTTCBSS
T ss_pred             EEEEE-CCCCCCCH-HHHHHHHCCCCCEEEEEEEC-CCCEEEE---------EECCCHHHHHHHHHHHCCCEEC
T ss_conf             99998-89987779-99975423576478743101-1211489---------9519999999999983994968

>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=96.27  E-value=0.00042  Score=40.10  Aligned_cols=64  Identities=19%  Similarity=0.155  Sum_probs=50.6

Q ss_pred             CCCCCCCCCCCCCCCHHHCCCCCCCCCEEEE---CCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCC
Q ss_conf             7334799888888520000114676423660---158999721-11133368999964344102123546414681026
Q 003717          122 DATRLDTPKKLLDKDKKLNIFFPRLRKVKTL---PFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHH  196 (800)
Q Consensus       122 kl~is~~Lk~svsesd~LreyFskyGKVKsV---p~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n  196 (800)
                      .+++.+ |+..+++ ++|+.+|.+||.|..+   ....+|+++ |+|         |.|.+.+++..|++.+||..+..
T Consensus        20 tl~V~n-Lp~~~t~-~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~f---------V~f~~~~~A~~Ai~~l~g~~~~g   87 (102)
T d2cpxa1          20 VLYLKN-LSPRVTE-RDLVSLFARFQEKKGPPIQFRMMTGRMRGQAF---------ITFPNKEIAWQALHLVNGYKLYG   87 (102)
T ss_dssp             EEEEEC-CCTTCCH-HHHHHHTHHHHHSSSSCCEEEEECSSSCSEEE---------EECSSHHHHHHHHHHSTTCBCSS
T ss_pred             EEEEEC-CCCCCCH-HHHHHHHHHCCCEEEEEEECCCCCCCCCCCCE---------EEECCHHHHHHHHHHHCCCEECC
T ss_conf             999969-9998989-99999785345424677530466555553214---------77433789999999858998899

>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=96.25  E-value=0.00057  Score=39.29  Aligned_cols=69  Identities=14%  Similarity=0.202  Sum_probs=50.7

Q ss_pred             CCCCCCCCCCCCCCCHHHCCCCCCCCCEEEE---CCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCC
Q ss_conf             7334799888888520000114676423660---1589997211113336899996434410212354641468102689
Q 003717          122 DATRLDTPKKLLDKDKKLNIFFPRLRKVKTL---PFCGTGKHKYSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPA  198 (800)
Q Consensus       122 kl~is~~Lk~svsesd~LreyFskyGKVKsV---p~kgTGK~KYGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n  198 (800)
                      .++++ .|+..+++ ++|+.+|+.||.|..+   +++.++ ..|+|         |.|.+.+++..|+..++|..+..  
T Consensus        10 tl~V~-nLp~~~te-~~l~~~F~~~G~i~~v~i~~d~~~~-~~~af---------V~f~~~~~A~~A~~~l~~~~~~g--   75 (90)
T d2cqia1          10 TLYVG-NLSRDVTE-VLILQLFSQIGPCKSCKMITEHTSN-DPYCF---------VEFYEHRDAAAALAAMNGRKILG--   75 (90)
T ss_dssp             EEEEE-SCCTTCCH-HHHHHHHHHHSCEEEEEEECCCCSS-CCEEE---------EEESSHHHHHHHHHHHTTEEETT--
T ss_pred             EEEEE-CCCCCCCH-HHHHHHHHHCCCCEEEEEECCCCCC-CEEEE---------EEECCHHHHHHHHHHCCCCEECC--
T ss_conf             99998-99997989-9999999763994366441266764-10028---------88889999999999819998999--


Q ss_pred             CCCCCCC
Q ss_conf             9863210
Q 003717          199 AGQEEIH  205 (800)
Q Consensus       199 ~~q~~i~  205 (800)
                       ..+.|.
T Consensus        76 -~~i~v~   81 (90)
T d2cqia1          76 -KEVKVN   81 (90)
T ss_dssp             -EEEEEE
T ss_pred             -EEEEEE
T ss_conf             -988999

>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=96.18  E-value=0.00073  Score=38.64  Aligned_cols=72  Identities=14%  Similarity=0.056  Sum_probs=49.0

Q ss_pred             CCCCCCCCCCCCCCCHHHCCCCCCCCCEEEECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCC
Q ss_conf             7334799888888520000114676423660158999721-111333689999643441021235464146810268998
Q 003717          122 DATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPAAG  200 (800)
Q Consensus       122 kl~is~~Lk~svsesd~LreyFskyGKVKsVp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n~~  200 (800)
                      .+++++ |+..+++ ++|+.+|++||.|..+..+.  ..+ |+|         |.|.+.+++..|+.  +   -+.+++.
T Consensus         7 ~lfV~n-Lp~~~te-~~L~~~F~~~G~v~~v~~~~--~~~gfaf---------V~f~~~~~a~~a~~--~---~~~i~g~   68 (88)
T d1wf0a_           7 GVFVGR-CTGDMTE-DELREFFSQYGDVMDVFIPK--PFRAFAF---------VTFADDQIAQSLCG--E---DLIIKGI   68 (88)
T ss_dssp             EEEEES-CCSSSCH-HHHHHHSTTTSCCCEEECCS--SCCSCCE---------EECSCHHHHHHTTT--C---EEEETTE
T ss_pred             EEEEEC-CCCCCCH-HHHHHHHHHCCCCEEEEEEE--CCCCEEE---------EEECCHHHHHHHHH--C---CCEECCE
T ss_conf             999928-9988989-99988899829844999942--1376589---------99889999999972--9---8989999


Q ss_pred             CCCCCHHHHCC
Q ss_conf             63210211027
Q 003717          201 QEEIHDMEELG  211 (800)
Q Consensus       201 q~~i~~~ee~~  211 (800)
                      ++.|..+.++.
T Consensus        69 ~l~v~~a~~k~   79 (88)
T d1wf0a_          69 SVHISNAEPKH   79 (88)
T ss_dssp             EEEEECCCCCC
T ss_pred             EEEEEECCCCC
T ss_conf             96998677888

>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=96.11  E-value=0.0036  Score=34.49  Aligned_cols=62  Identities=11%  Similarity=0.069  Sum_probs=47.6

Q ss_pred             CCCCCCCCCCCCCCCHHHCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCC
Q ss_conf             733479988888852000011467642366015899972111133368999964344102123546414681026
Q 003717          122 DATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPFCGTGKHKYSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHH  196 (800)
Q Consensus       122 kl~is~~Lk~svsesd~LreyFskyGKVKsVp~kgTGK~KYGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n  196 (800)
                      .+++.+ |+..+++ +.|+.+|.+||.|..+....  ...|+|         |.|.+.+++..|++.|||..+..
T Consensus        19 tl~V~n-Lp~~~t~-~~l~~~f~~~G~i~~~~~~~--~~~~af---------V~f~~~~~A~~A~~~l~~~~i~g   80 (97)
T d1whya_          19 RLWVGG-LGPNTSL-AALAREFDRFGSIRTIDHVK--GDSFAY---------IQYESLDAAQAACAKMRGFPLGG   80 (97)
T ss_dssp             CEEEEC-CCSSCCH-HHHHHHHHTTSCEEEEEECS--SSCCEE---------EEESSHHHHHHHHHHHTTCBCSS
T ss_pred             EEEECC-CCCCCCH-HHHHHHHHHHCCCCEEEEEC--CCCEEE---------ECCCCHHHHHHHHHHHCCCEECC
T ss_conf             999848-9998989-99999997534562476402--221787---------61499999999999858889699

>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=96.11  E-value=0.00067  Score=38.88  Aligned_cols=54  Identities=7%  Similarity=0.009  Sum_probs=43.7

Q ss_pred             CCCCHHHCCCCCCCCCEEEECC--CCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCC
Q ss_conf             8852000011467642366015--8999721-11133368999964344102123546414681026
Q 003717          133 LDKDKKLNIFFPRLRKVKTLPF--CGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHH  196 (800)
Q Consensus       133 vsesd~LreyFskyGKVKsVp~--kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n  196 (800)
                      +.+ +.++.+|++||+|..+..  ..+|+++ |+|         |.|.+.++|..|+..|||.++.-
T Consensus        39 ~~e-d~l~e~f~k~G~I~~v~I~~~~~~~~~G~~f---------V~f~~~~~A~~Ai~~lng~~~~g   95 (104)
T d1jmta_          39 FFE-EVFTEMEEKYGEVEEMNVCDNLGDHLVGNVY---------VKFRREEDAEKAVIDLNNRWFNG   95 (104)
T ss_dssp             HHH-HHHHHHHHHTCCEEEEEECCSSSSSSEEEEE---------EEESCHHHHHHHHHHHTTCEETT
T ss_pred             HHH-HHHHHHHCCCCCEEEEEEECCCCCCEEEEEE---------EEEECHHHHHHHHHHHCCCEECC
T ss_conf             569-9999985057878999962189998841799---------99954037999999978988999

>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=95.95  E-value=0.001  Score=37.72  Aligned_cols=65  Identities=14%  Similarity=0.138  Sum_probs=47.5

Q ss_pred             CCCCCCCCCCCCCCCHHHCCCCCCCCCEEEECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCC
Q ss_conf             7334799888888520000114676423660158999721-111333689999643441021235464146810268998
Q 003717          122 DATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPAAG  200 (800)
Q Consensus       122 kl~is~~Lk~svsesd~LreyFskyGKVKsVp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n~~  200 (800)
                      .+++++ +  ++++ ++|+.+|++||.|..+...   +.+ |||         |.|.+.+++..|+.+|||.++..   .
T Consensus         7 ti~V~~-~--~~te-~~L~~~F~~~G~I~~v~~~---~~~~~af---------V~f~~~~~A~~Ai~~lng~~~~g---~   67 (79)
T d2bz2a1           7 TLYVYG-E--DMTP-TLLRGAFSPFGNIIDLSMD---PPRNCAF---------VTYEKMESADQAVAELNGTQVES---V   67 (79)
T ss_dssp             EEEEEC-S--SCCH-HHHHHHHSTTCCCSCEEEE---TTTTEEE---------EECSSHHHHHHHHHHHTTCBCSS---C
T ss_pred             EEEEEC-C--CCCH-HHHHHHHHCCCCCCEEEEC---CCCCEEE---------EEECCCHHHHHHHHHHCCCEECC---E
T ss_conf             999978-9--7999-9999998550756435202---6898899---------99924189999999859999999---9


Q ss_pred             CCCCC
Q ss_conf             63210
Q 003717          201 QEEIH  205 (800)
Q Consensus       201 q~~i~  205 (800)
                      ...|.
T Consensus        68 ~l~V~   72 (79)
T d2bz2a1          68 QLKVN   72 (79)
T ss_dssp             BCEEE
T ss_pred             EEEEE
T ss_conf             98999

>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=95.90  E-value=0.0011  Score=37.66  Aligned_cols=60  Identities=10%  Similarity=0.021  Sum_probs=45.0

Q ss_pred             CCCCCCCCCCCCCCHHHCCCCCCCCCEEEECC--CCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCC
Q ss_conf             33479988888852000011467642366015--8999721-111333689999643441021235464146810
Q 003717          123 ATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPF--CGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQI  194 (800)
Q Consensus       123 l~is~~Lk~svsesd~LreyFskyGKVKsVp~--kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i  194 (800)
                      +++.+ |+..+++ ++|+.+|..||.|..+..  ..+|+++ |||         |.|.+-+++..|++ ++|..+
T Consensus         9 vfV~n-lp~~~te-~~l~~~F~~~G~v~~v~l~~~~~~~~kG~af---------V~f~~~e~a~~al~-~~~~~~   71 (85)
T d1zh5a2           9 VYIKG-FPTDATL-DDIKEWLEDKGQVLNIQMRRTLHKAFKGSIF---------VVFDSIESAKKFVE-TPGQKY   71 (85)
T ss_dssp             EEEEC-CCTTCCH-HHHHHHHTTSCCEEEEEEEECTTCCEEEEEE---------EEESCHHHHHHHHT-CCCCEE
T ss_pred             EEEEC-CCCCCCH-HHHHHHHHHHCCCCCCEEEEECCCCCCEEEE---------EEECCHHHHHHHHH-HCCCEE
T ss_conf             99979-7987979-9999989875524230032102588635789---------99848999999999-789979

>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=95.86  E-value=0.0025  Score=35.38  Aligned_cols=62  Identities=6%  Similarity=-0.075  Sum_probs=48.5

Q ss_pred             CCCCCCCCCCCCCCCHHHCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCC
Q ss_conf             7334799888888520000114676423660158999721111333689999643441021235464146810268
Q 003717          122 DATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPFCGTGKHKYSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHP  197 (800)
Q Consensus       122 kl~is~~Lk~svsesd~LreyFskyGKVKsVp~kgTGK~KYGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~  197 (800)
                      .+++.+ |+..+++ ++|+.+|.+||.|+.+...-   ..|+|         |.|.+.+++..|++.|||..+...
T Consensus        17 ~i~V~N-lp~~~~~-~~L~~~F~~~G~v~~~~i~~---~g~af---------V~f~~~~~a~~Ai~~lng~~~~g~   78 (98)
T d1wg4a_          17 RVLVSG-LPPSGSW-QDLKDHMREAGDVCYADVQK---DGMGM---------VEYLRKEDMEYALRKLDDTKFRSH   78 (98)
T ss_dssp             EEEEEC-CCSSCCH-HHHHHHHTTSSCEEEEEEET---TTEEE---------EEESSHHHHHHHHHHHSSEEEECT
T ss_pred             EEEEEC-CCCCCCH-HHHHHHHHHHCCCCCCCCCC---CCEEE---------EEECCHHHHHHHHHHHCCCEECCE
T ss_conf             899977-9999989-99999997522343200133---44699---------997899999999999688996890

>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=95.86  E-value=0.002  Score=35.97  Aligned_cols=60  Identities=13%  Similarity=0.170  Sum_probs=45.5

Q ss_pred             CCCCCCCCCCCCHHHCCCCCCCCCEEEECCCCCCCCC-CCCCCCCCCCCCCCCCC-CCCHHHHHHHHCCCCCCCC
Q ss_conf             4799888888520000114676423660158999721-11133368999964344-1021235464146810268
Q 003717          125 RLDTPKKLLDKDKKLNIFFPRLRKVKTLPFCGTGKHK-YSFQRVEAPPLPKYFCD-CEEHSAAFHAAEGKQIHHP  197 (800)
Q Consensus       125 is~~Lk~svsesd~LreyFskyGKVKsVp~kgTGK~K-YGFg~ve~Ps~pV~F~s-fEea~aA~eAmNG~~i~n~  197 (800)
                      +.+.|+..+++ ++|+.+|++||.|..+...   +.+ |||         |.|.+ .+++..|+.++|+..+...
T Consensus        15 fvgnL~~~~te-e~Lk~~F~~fG~V~~v~i~---~~kg~gf---------V~F~~~~~~A~~a~~~~~~~~l~~~   76 (113)
T d1owxa_          15 FSGDLDDQTCR-EDLHILFSNHGEIKWIDFV---RGAKEGI---------ILFKEKAKEALGKAKDANNGNLQLR   76 (113)
T ss_dssp             EEESCCSSCCH-HHHHHHTCSSCCEEEEECC---TTCSEEE---------EEESSCHHHHHHHHHHTTTSCBCTT
T ss_pred             EECCCCCCCCH-HHHHHHHHHCCCHHEEEEE---CCCCEEE---------EEECCCHHHHHHHHHHHCCCCEECC
T ss_conf             98799987879-9999999835774148874---5886689---------9966827899999998348833157

>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=95.85  E-value=0.004  Score=34.20  Aligned_cols=73  Identities=14%  Similarity=0.168  Sum_probs=51.4

Q ss_pred             CCCCCCCCCCCCCCHHHCCCCCCCCCEEE-ECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCC
Q ss_conf             33479988888852000011467642366-0158999721-111333689999643441021235464146810268998
Q 003717          123 ATRLDTPKKLLDKDKKLNIFFPRLRKVKT-LPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPAAG  200 (800)
Q Consensus       123 l~is~~Lk~svsesd~LreyFskyGKVKs-Vp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n~~  200 (800)
                      .+....|+.++++ ++|+.+|..++-+.+ +....+|+++ |+|         |.|.+.+++..|++ +|+..+..   .
T Consensus        17 ~v~v~nLp~~~te-~dl~~~F~~~~~~~v~~~~~~~g~~~G~af---------VeF~~~~~a~~Al~-~~~~~i~g---R   82 (102)
T d1weza_          17 CVHMRGLPYRATE-NDIYNFFSPLNPMRVHIEIGPDGRVTGEAD---------VEFATHEDAVAAMA-KDKANMQH---R   82 (102)
T ss_dssp             EEEEESCCTTCCH-HHHHHSSCSCCCSEEEEEESSSSCEEEEEE---------EECSSSHHHHHHHT-TSSCCSSS---S
T ss_pred             EEEEECCCCCCCH-HHHHHHHHCCCCCEEEEEEECCCCCEEEEE---------EEECCHHHHHHHHH-CCCCEECC---E
T ss_conf             8998089986889-999878742475224667724786047778---------99879999999997-29998999---9


Q ss_pred             CCCCCHHHH
Q ss_conf             632102110
Q 003717          201 QEEIHDMEE  209 (800)
Q Consensus       201 q~~i~~~ee  209 (800)
                      .++|..+..
T Consensus        83 ~I~V~~s~~   91 (102)
T d1weza_          83 YVELFLNST   91 (102)
T ss_dssp             CCEEEEECC
T ss_pred             EEEEEECCC
T ss_conf             999997588

>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=95.83  E-value=0.00047  Score=39.82  Aligned_cols=72  Identities=13%  Similarity=-0.022  Sum_probs=50.5

Q ss_pred             CCCCCCCCCCCCCCHHHCCCCCCCCCEEEECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCC
Q ss_conf             334799888888520000114676423660158999721-1113336899996434410212354641468102689986
Q 003717          123 ATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPAAGQ  201 (800)
Q Consensus       123 l~is~~Lk~svsesd~LreyFskyGKVKsVp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n~~q  201 (800)
                      +++++ |+.++++ ++|+.+|.+||.+.....   ++.+ |||         |.|.+.+++..|++.|||.+.  .+|..
T Consensus         4 l~V~n-Lp~~~te-~~L~~~F~~~G~i~~~~~---~~~rg~aF---------V~f~~~~~A~~Ai~~lng~~~--~~G~~   67 (80)
T d2cqha1           4 LYIGN-LSPAVTA-DDLRQLFGDRKLPLAGQV---LLKSGYAF---------VDYPDQNWAIRAIETLSGKVE--LHGKI   67 (80)
T ss_dssp             EEEEC-CCTTCCH-HHHHHHHHHTTCCCSSCE---EEETTEEE---------ECCSCHHHHHHHHHHHTTTCE--ETTEE
T ss_pred             EEEEC-CCCCCCH-HHHHHHHHHHCCEEEEEE---ECCCCEEE---------EEECCHHHHHHHHHHHCCCEE--ECCEE
T ss_conf             99979-9998999-999999998096897378---61266499---------998887879999998179969--99989


Q ss_pred             CCCCHHHHC
Q ss_conf             321021102
Q 003717          202 EEIHDMEEL  210 (800)
Q Consensus       202 ~~i~~~ee~  210 (800)
                      ..|..+.++
T Consensus        68 i~V~~a~~k   76 (80)
T d2cqha1          68 MEVDYSVSK   76 (80)
T ss_dssp             CEEEECCCC
T ss_pred             EEEEECCCC
T ss_conf             899975885

>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=95.81  E-value=0.00074  Score=38.62  Aligned_cols=69  Identities=13%  Similarity=0.150  Sum_probs=50.2

Q ss_pred             CCCCCCCCCCCCCCHHHCCCCCCCCCEEE--------ECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCC
Q ss_conf             33479988888852000011467642366--------0158999721-11133368999964344102123546414681
Q 003717          123 ATRLDTPKKLLDKDKKLNIFFPRLRKVKT--------LPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQ  193 (800)
Q Consensus       123 l~is~~Lk~svsesd~LreyFskyGKVKs--------Vp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~  193 (800)
                      +++ +.|+..+++ ++|+.+|.+||.+..        +.+..+++.+ |+|         |.|.+.|++..|+. |||..
T Consensus         4 lyV-gNLp~~~te-~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~af---------V~f~~~e~a~~a~~-l~g~~   71 (90)
T d1u2fa_           4 LYV-GNIPFGITE-EAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAF---------LEFRSVDETTQAMA-FDGII   71 (90)
T ss_dssp             EEE-CSCCTTCCT-THHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEE---------EEESSCTTTTTGGG-GSSCC
T ss_pred             EEE-CCCCCCCCH-HHHHHHHHHHCCEEEEEEECCCEEEECCCCCCCEEEE---------EEECCHHHHHHHHH-HCCCE
T ss_conf             999-699976245-8988889860857799994256056644699762899---------98389999999986-19958


Q ss_pred             CCCCCCCCCCCCH
Q ss_conf             0268998632102
Q 003717          194 IHHPAAGQEEIHD  206 (800)
Q Consensus       194 i~n~n~~q~~i~~  206 (800)
                      +.   |..++|.+
T Consensus        72 ~~---Gr~l~V~r   81 (90)
T d1u2fa_          72 FQ---GQSLKIRR   81 (90)
T ss_dssp             SS---SSCCCCBC
T ss_pred             EC---CEEEEECC
T ss_conf             89---98889788

>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=95.80  E-value=0.0011  Score=37.68  Aligned_cols=62  Identities=16%  Similarity=0.178  Sum_probs=47.5

Q ss_pred             CCCCCCCCCCCCCCCHHHCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCC
Q ss_conf             733479988888852000011467642366015899972111133368999964344102123546414681026
Q 003717          122 DATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPFCGTGKHKYSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHH  196 (800)
Q Consensus       122 kl~is~~Lk~svsesd~LreyFskyGKVKsVp~kgTGK~KYGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n  196 (800)
                      .+++++ |+..+++ ++|+.+|.+||.|..+...-.  ..|||         |.|.+.+++..|+..|||..+..
T Consensus        20 ~l~v~n-L~~~~te-~~L~~~F~~fG~i~~v~i~~~--kg~af---------V~f~~~~~A~~Ai~~l~~~~i~g   81 (96)
T d1x4ga1          20 TVYCGG-IASGLTD-QLMRQTFSPFGQIMEIRVFPE--KGYSF---------VRFSTHESAAHAIVSVNGTTIEG   81 (96)
T ss_dssp             EEEEEC-CSSCCCH-HHHHHHHHHHSCEEEEEEETT--TTEEE---------EEESSHHHHHHHHHHHTTCEETT
T ss_pred             EEEECC-CCCCCCH-HHHHHHHHHHCCCEEEEEEEC--CEEEE---------EEECCHHHHHHHHHHHCCCEECC
T ss_conf             999908-9998999-999999998299669999701--30899---------99899999999999819999999

>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=95.76  E-value=0.0013  Score=37.18  Aligned_cols=64  Identities=11%  Similarity=0.139  Sum_probs=44.9

Q ss_pred             CCCCCCCCCHHHCCCCCCCCCEEEECCC--CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             9888888520000114676423660158--99972111133368999964344102123546414681026899863210
Q 003717          128 TPKKLLDKDKKLNIFFPRLRKVKTLPFC--GTGKHKYSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPAAGQEEIH  205 (800)
Q Consensus       128 ~Lk~svsesd~LreyFskyGKVKsVp~k--gTGK~KYGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n~~q~~i~  205 (800)
                      .|+..+++ ++|+.+|..||.|+.++..  ..+..+|+|         |.|.+-+++..|+. +++.++   .+.+..|.
T Consensus         7 nlp~~~t~-~~l~~~F~~~G~I~~v~~~~~~~~~~~~af---------V~F~~~~~a~~Al~-~~~~~i---~g~~i~V~   72 (75)
T d2ghpa2           7 NLPKSYNQ-NKVYKYFKHCGPIIHVDVADSLKKNFRFAR---------IEFARYDGALAAIT-KTHKVV---GQNEIIVS   72 (75)
T ss_dssp             EECTTCCH-HHHHHHHGGGSCEEEEEEEECTTSSSEEEE---------EEESSHHHHHHHHT-TTTCEE---TTEECEEE
T ss_pred             CCCCCCCH-HHHHHHHHCCCCEEEEEEEEECCCCCEEEE---------EEECCHHHHHHHHH-HCCCEE---CCEEEEEE
T ss_conf             99999988-999998712881699999750233316999---------99832677688887-369699---99999999

>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=95.65  E-value=0.0011  Score=37.55  Aligned_cols=72  Identities=17%  Similarity=0.155  Sum_probs=52.1

Q ss_pred             CCCCCCCCCCCCCCCCHHHCCCCCCCCCEEEECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCC
Q ss_conf             87334799888888520000114676423660158999721-11133368999964344102123546414681026899
Q 003717          121 KDATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPAA  199 (800)
Q Consensus       121 pkl~is~~Lk~svsesd~LreyFskyGKVKsVp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n~  199 (800)
                      ..+++++ |+..+++ ++|+.+|.+||.+..+..   ++++ |+|         +.|.+.+++..|+..|||..+.   +
T Consensus         9 k~l~V~n-Lp~~~te-~~l~~~F~~~g~i~~~~~---~~~rg~af---------V~f~~~~~A~~Ai~~l~~~~i~---g   71 (86)
T d2cpda1           9 KILYVRN-LMLSTSE-EMIEKEFNNIKPGAVERV---KKIRDYAF---------VHFSNREDAVEAMKALNGKVLD---G   71 (86)
T ss_dssp             CEEEEES-CCTTCCH-HHHHHHHHTTSTTCEEEE---EECSSEEE---------EEESSHHHHHHHHHHHSSEEET---T
T ss_pred             CEEEECC-CCCCCCH-HHHHHHHCCCCEEEEEEE---CCCCEEEE---------EEECCHHHHHHHHHHCCCCEEC---C
T ss_conf             9999929-8997889-999986206532655797---55427999---------9869999999999980998999---9


Q ss_pred             CCCCCCHHHH
Q ss_conf             8632102110
Q 003717          200 GQEEIHDMEE  209 (800)
Q Consensus       200 ~q~~i~~~ee  209 (800)
                      ....|.-+-|
T Consensus        72 ~~i~V~~akP   81 (86)
T d2cpda1          72 SPIEVTLAKP   81 (86)
T ss_dssp             EEEEEECCCC
T ss_pred             EEEEEEECCC
T ss_conf             8989996607

>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=95.41  E-value=0.0027  Score=35.21  Aligned_cols=68  Identities=10%  Similarity=-0.028  Sum_probs=47.4

Q ss_pred             CCCCCCCCCCCCCCHHHCCCCCCCCCEEEECCCCCCCC-CCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCC
Q ss_conf             33479988888852000011467642366015899972-11113336899996434410212354641468102689986
Q 003717          123 ATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPFCGTGKH-KYSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPAAGQ  201 (800)
Q Consensus       123 l~is~~Lk~svsesd~LreyFskyGKVKsVp~kgTGK~-KYGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n~~q  201 (800)
                      +++ +.|+..+++ ++|..+|.+||.|..+...   +. .|+|         |.|.+.++|..|+..+++..+.. +|..
T Consensus        11 l~V-~nLp~~~t~-~~L~~~f~~~G~i~~v~~~---~~~~~af---------V~f~~~e~A~~a~~~~~~~~~~~-~g~~   75 (88)
T d2cq1a1          11 LHI-RKLPGEVTE-TEVIALGLPFGKVTNILML---KGKNQAF---------LELATEEAAITMVNYYSAVTPHL-RNQP   75 (88)
T ss_dssp             EEE-ESCCTTCCH-HHHHHTTTTTSCEEEEEEE---TTTTEEE---------EEESSHHHHHHHHHHHHHSCCEE-TTEE
T ss_pred             EEE-ECCCCCCCH-HHHHHHHHCCCCCCCCCCC---CCCEEEE---------EEECCHHHHHHHHHHHCCCCCCC-CCCE
T ss_conf             999-679988889-9999887502422220002---3441799---------98489999999999980599745-9977


Q ss_pred             CCCC
Q ss_conf             3210
Q 003717          202 EEIH  205 (800)
Q Consensus       202 ~~i~  205 (800)
                      +.|.
T Consensus        76 l~v~   79 (88)
T d2cq1a1          76 IYIQ   79 (88)
T ss_dssp             CEEE
T ss_pred             EEEE
T ss_conf             9999

>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=95.39  E-value=0.0017  Score=36.41  Aligned_cols=65  Identities=6%  Similarity=-0.000  Sum_probs=47.4

Q ss_pred             CCCCCCCCCCCCCCCHHHCCCCCCCCC-EEEECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCC
Q ss_conf             733479988888852000011467642-3660158999721-11133368999964344102123546414681026899
Q 003717          122 DATRLDTPKKLLDKDKKLNIFFPRLRK-VKTLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPAA  199 (800)
Q Consensus       122 kl~is~~Lk~svsesd~LreyFskyGK-VKsVp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n~  199 (800)
                      .+++.+ |+.++++ ++|+.+|.+||- +..     +++.+ |+|         |.|.+.+++..|+..|||..+.   +
T Consensus         7 ~i~V~n-Lp~~~t~-~~l~~lF~~~G~~~~~-----~~~~kg~af---------V~f~~~~~A~~Ai~~ln~~~~~---G   67 (88)
T d1wg1a_           7 GILVKN-LPQDSNC-QEVHDLLKDYDLKYCY-----VDRNKRTAF---------VTLLNGEQAQNAIQMFHQYSFR---G   67 (88)
T ss_dssp             CEEEES-CCSSCCH-HHHHHHTCSSCCCCEE-----EEGGGTEEE---------ECCSCHHHHHHHHHHHTTEEET---T
T ss_pred             EEEEEC-CCCCCCH-HHHHHHHHHCCCEEEE-----EECCCCCEE---------EEECCHHHHHHHHHHHCCCEEC---C
T ss_conf             999969-9986375-7887778860960353-----011577148---------9988999999999985899899---9


Q ss_pred             CCCCCC
Q ss_conf             863210
Q 003717          200 GQEEIH  205 (800)
Q Consensus       200 ~q~~i~  205 (800)
                      .+..|.
T Consensus        68 ~~l~V~   73 (88)
T d1wg1a_          68 KDLIVQ   73 (88)
T ss_dssp             EEEEEE
T ss_pred             EEEEEE
T ss_conf             898999

>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=95.07  E-value=0.022  Score=29.76  Aligned_cols=69  Identities=17%  Similarity=0.253  Sum_probs=52.5

Q ss_pred             CCEEEEECCCCCCCH---------HHHHHHHHCCCCEEEEEEECCCCCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEE
Q ss_conf             849999079988998---------89998530389624999965699767999936899889999998459947679377
Q 003717           13 QTRIYVGGLGEKVTD---------DDLAKVFSSLGEVKAVDIVRTKGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRL   83 (800)
Q Consensus        13 ~rtLFVGNLp~sVTE---------EdLrelFskFGeV~sVrVIRdTGRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkL   83 (800)
                      ..+|-|.-..+...+         ..|.+.|..||+|.-++++.+    --+|+|..  -..|.+|+. ++|.++.||.|
T Consensus        15 DgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d----~mwVTF~d--G~SAL~al~-l~g~~v~G~~l   87 (95)
T d1ufwa_          15 DATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG----QMLVTFAD--SHSALSVLD-VDGMKVKGRAV   87 (95)
T ss_dssp             TCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT----EEEEECSC--SHHHHHHHH-GGGSEETTEEE
T ss_pred             CCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCEEEEEEEECC----EEEEEECC--CHHHHHHHC-CCCEEECCEEE
T ss_conf             867999961688311565888999999999863781999999588----29999878--687998752-57819715699


Q ss_pred             EEEEC
Q ss_conf             99742
Q 003717           84 RLERA   88 (800)
Q Consensus        84 kVe~A   88 (800)
                      .|..-
T Consensus        88 ~It~~   92 (95)
T d1ufwa_          88 KISGP   92 (95)
T ss_dssp             EEECC
T ss_pred             EEECC
T ss_conf             99657

>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=94.97  E-value=0.0068  Score=32.79  Aligned_cols=68  Identities=9%  Similarity=-0.018  Sum_probs=48.5

Q ss_pred             CCCCCCCCCCCCCCHHHCCCCCCCCCEEEECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCC
Q ss_conf             334799888888520000114676423660158999721-1113336899996434410212354641468102689986
Q 003717          123 ATRLDTPKKLLDKDKKLNIFFPRLRKVKTLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHPAAGQ  201 (800)
Q Consensus       123 l~is~~Lk~svsesd~LreyFskyGKVKsVp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~n~~q  201 (800)
                      +++. .|+..+++ ++|..+|.+||.|..+.+.   +.| |+|         |.|.+.+++..|++.+++..+. ..+..
T Consensus        18 l~v~-nlp~~~te-~~l~~~F~~fG~I~~~~~~---~~k~~Af---------V~f~~~e~A~~ai~~~~~~~~~-~~g~~   82 (104)
T d1wexa_          18 VHVR-GLCESVVE-ADLVEALEKFGTICYVMMM---PFKRQAL---------VEFENIDSAKECVTFAADVPVY-IAGQQ   82 (104)
T ss_dssp             EEEE-SCCSSCCH-HHHHHHHTTTSCEEEEEEE---TTTTEEE---------EEESSHHHHHHHHHHHHHSCCB-SSSSB
T ss_pred             EEEE-CCCCCCCH-HHHHHHHHHCCCCEEEEEE---ECCEEEE---------EEECCHHHHHHHHHHHCCCCCE-EEEEE
T ss_conf             9991-89999979-9999766025653499997---3110379---------9868999999999987479948-70378


Q ss_pred             CCCC
Q ss_conf             3210
Q 003717          202 EEIH  205 (800)
Q Consensus       202 ~~i~  205 (800)
                      ++|.
T Consensus        83 l~v~   86 (104)
T d1wexa_          83 AFFN   86 (104)
T ss_dssp             CEEE
T ss_pred             EEEE
T ss_conf             8999

>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=94.44  E-value=0.0028  Score=35.14  Aligned_cols=54  Identities=13%  Similarity=0.100  Sum_probs=41.4

Q ss_pred             CCCCCCCCCHHHCCCCCCCCCEEEECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCC
Q ss_conf             9888888520000114676423660158999721-1113336899996434410212354641468102
Q 003717          128 TPKKLLDKDKKLNIFFPRLRKVKTLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIH  195 (800)
Q Consensus       128 ~Lk~svsesd~LreyFskyGKVKsVp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~  195 (800)
                      .|+.++++ ++|+.+|++||- ..+.   .++.+ |+|         +.|.+-+++..|+..|||..+.
T Consensus         5 nLp~~~t~-~~l~~~F~~~g~-~~~~---~~~~~g~af---------v~f~~~~~A~~Ai~~ln~~~~~   59 (75)
T d1wi6a1           5 GLPGDVTN-QEVHDLLSDYEL-KYCF---VDKYKGTAF---------VTLLNGEQAEAAINTFHQSRLR   59 (75)
T ss_dssp             CCCTTCCH-HHHHHHTTTSCE-EEEE---EETTTTEEE---------EEESSHHHHHHHHHHHTTEESS
T ss_pred             CCCCCCCH-HHHHHHHHCCCC-CCEE---ECCCCEEEE---------EEECCHHHHHHHHHHHCCCCCC
T ss_conf             99996789-999998743252-2115---546321699---------9987778888888985796679

>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=94.34  E-value=0.1  Score=25.64  Aligned_cols=60  Identities=13%  Similarity=0.117  Sum_probs=51.8

Q ss_pred             HHHHHHHHCCCCEEEEEEECC-CCCCEEEEEECCCCHHHHHHHHHHCCCCEECCEEEEEEECC
Q ss_conf             899985303896249999656-99767999936899889999998459947679377997424
Q 003717           28 DDLAKVFSSLGEVKAVDIVRT-KGRSFGYVDFFPSSHKSLSKLFSTYNGCVWKGGRLRLERAK   89 (800)
Q Consensus        28 EdLrelFskFGeV~sVrVIRd-TGRGFGFVeFaS~D~EDAeKAIeeLNG~eLdGRkLkVe~Ak   89 (800)
                      ..|...|.++|.|..+.+..- .+.-.|-|...+  ..+|..|+..|+..+|++++|.|.++.
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 QLLQEAFARHGKVKSVELSPHTDYQLKAVVQMEN--LQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESS--HHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHHHEEEEEEEEEECCCCCEEEEEECCC--HHHHHHHHHHHHHHHCCCEEEEEEEEC
T ss_conf             9999998852158999998636896899998487--788999999987874287079999842

>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=94.27  E-value=0.006  Score=33.13  Aligned_cols=72  Identities=10%  Similarity=-0.014  Sum_probs=48.0

Q ss_pred             CCCCCCCCCCCCCCC----HHHCCCCCCCCCEEEECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCC
Q ss_conf             733479988888852----0000114676423660158999721-11133368999964344102123546414681026
Q 003717          122 DATRLDTPKKLLDKD----KKLNIFFPRLRKVKTLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHH  196 (800)
Q Consensus       122 kl~is~~Lk~svses----d~LreyFskyGKVKsVp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n  196 (800)
                      .+++.+ |..++.+.    +.|+.+|..||.|..+...   +.+ |+|         |.|.+.++|..|+.+|||..+..
T Consensus         7 ~L~v~n-l~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~---k~~~~af---------V~f~~~~~A~~Ai~~lng~~~~g   73 (104)
T d1weya_           7 GLIACV-ANDDVFSESETRAKFESLFRTYDKDTTFQYF---KSFKRVR---------INFSNPLSAADARLRLHKTEFLG   73 (104)
T ss_dssp             EEEEEC-CCGGGGSTTTHHHHHHHHHHTTCSSCEEEEE---TTTTEEE---------EECSSTTHHHHHHHTSTTSEETT
T ss_pred             EEEEEE-CCCHHCCCHHHHHHHHHHHCCCCCCEEEEEE---CCCCEEE---------EEECCHHHHHHHHHHHCCCCCCC
T ss_conf             089995-8901137188899999872035552689996---6887899---------99899999999999855013389


Q ss_pred             CCCCCCCCCHHHH
Q ss_conf             8998632102110
Q 003717          197 PAAGQEEIHDMEE  209 (800)
Q Consensus       197 ~n~~q~~i~~~ee  209 (800)
                         ..+.|.-+..
T Consensus        74 ---~~l~v~~a~~   83 (104)
T d1weya_          74 ---KEMKLYFAQT   83 (104)
T ss_dssp             ---EECEEECCCC
T ss_pred             ---CEEEEEECCC
T ss_conf             ---8768853446

>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=94.01  E-value=0.025  Score=29.41  Aligned_cols=59  Identities=10%  Similarity=-0.020  Sum_probs=40.6

Q ss_pred             CCCCCCCCCC-CCCCCHHHCCCCCCCCCEEEECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHH--HCCCCC
Q ss_conf             7334799888-888520000114676423660158999721-111333689999643441021235464--146810
Q 003717          122 DATRLDTPKK-LLDKDKKLNIFFPRLRKVKTLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHA--AEGKQI  194 (800)
Q Consensus       122 kl~is~~Lk~-svsesd~LreyFskyGKVKsVp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eA--mNG~~i  194 (800)
                      .+++++ |+. .+++ ++|..+|++||.|..+...   +.+ |+|         |.|.+.++|..|++.  +++..+
T Consensus        20 ~l~v~n-Lp~~~~te-~~l~~~F~~fG~V~~v~~~---~~k~~af---------V~f~~~~~A~~Ai~~~~~~~~~~   82 (99)
T d1x4fa1          20 VIHLSN-LPHSGYSD-SAVLKLAEPYGKIKNYILM---RMKSQAF---------IEMETREDAMAMVDHCLKKALWF   82 (99)
T ss_dssp             EEEEES-CCCSSCCS-HHHHTTTTTTSCCSEEEEE---TTTTEEE---------EECSSHHHHHHHHHHHHHSCCCS
T ss_pred             EEEEEC-CCCCCCCH-HHHHHHHCCCCCEEEEEEE---ECCCCEE---------EEECCHHHHHHHHHHHHCCCCEE
T ss_conf             899937-86775389-9998665344530489876---0477279---------99635689999999973689648

>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=92.02  E-value=0.021  Score=29.81  Aligned_cols=50  Identities=14%  Similarity=0.216  Sum_probs=38.9

Q ss_pred             HHHCCCCCCCCCEEEECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCC
Q ss_conf             0000114676423660158999721-11133368999964344102123546414681026
Q 003717          137 KKLNIFFPRLRKVKTLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHH  196 (800)
Q Consensus       137 d~LreyFskyGKVKsVp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n  196 (800)
                      ++++..|++||+|..+.... +.++ |+|         |.|.+.++|..|+.+|||..+..
T Consensus        34 edv~~~~~~~G~V~~v~~~~-~~~~G~~f---------V~f~~~e~A~~A~~~lng~~~~g   84 (99)
T d2dita1          34 EDLRVECSKFGQIRKLLLFD-RHPDGVAS---------VSFRDPEEADYCIQTLDGRWFGG   84 (99)
T ss_dssp             HHHHHHGGGTSCCSEEEEET-TCTTCEEE---------EECSCHHHHHHHHHHSTTCEETT
T ss_pred             HHHHHHHCCCCCEEEEECCC-CCCCCEEE---------EEECCHHHHHHHHHHHCCCEECC
T ss_conf             99998726766079996347-78864799---------99898999999999868969899

>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=91.70  E-value=0.28  Score=23.02  Aligned_cols=66  Identities=12%  Similarity=0.292  Sum_probs=54.9

Q ss_pred             CCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEECC--C---C-CCEEEEEECCCCHHHHHHHHHHCCCCEECC
Q ss_conf             849999079988998899985303896249999656--9---9-767999936899889999998459947679
Q 003717           13 QTRIYVGGLGEKVTDDDLAKVFSSLGEVKAVDIVRT--K---G-RSFGYVDFFPSSHKSLSKLFSTYNGCVWKG   80 (800)
Q Consensus        13 ~rtLFVGNLp~sVTEEdLrelFskFGeV~sVrVIRd--T---G-RGFGFVeFaS~D~EDAeKAIeeLNG~eLdG   80 (800)
                      .++|-|..||+..+++++.+.++..|.+........  +   . -.-|||.|.+  .++...-...++|+.+.+
T Consensus         1 ~tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~--~~~v~~F~~~f~g~~F~D   72 (91)
T d1uw4a_           1 LSKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKN--QEDIILFRDRFDGYVFLD   72 (91)
T ss_dssp             CCEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESS--SHHHHHHHHHHTTCEEEC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHCCCCCEEEEEEECCCCCCCCCCCEEEEEEECC--HHHHHHHHHHCCCCEEEC
T ss_conf             966999369798999999998577674589988589867899744589998689--999999998729818982

>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=89.83  E-value=0.086  Score=26.16  Aligned_cols=54  Identities=9%  Similarity=0.027  Sum_probs=39.4

Q ss_pred             HHHCCCCCCCCCEEEECCC---CCCCC-CCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCC
Q ss_conf             0000114676423660158---99972-1111333689999643441021235464146810268
Q 003717          137 KKLNIFFPRLRKVKTLPFC---GTGKH-KYSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQIHHP  197 (800)
Q Consensus       137 d~LreyFskyGKVKsVp~k---gTGK~-KYGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i~n~  197 (800)
                      ++++..|.+||.|..+..+   ..... ..|+.       +|.|.+.++|..|+..|||..+..+
T Consensus        29 edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~v-------fV~f~~~e~A~~A~~~l~Gr~f~gR   86 (104)
T d1o0pa_          29 EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKI-------FVEFTSVFDCQKAMQGLTGRKFANR   86 (104)
T ss_dssp             HHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEE-------EEEESCHHHHHHHHHHHSSCCSSSS
T ss_pred             HHHHHHHCCCCCEEEEEEEECCCCCCCCCCEEE-------EEEECCHHHHHHHHHHHCCCEECCE
T ss_conf             999999616682577897523777765773289-------9998999999999999789998991

>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=89.26  E-value=0.06  Score=27.09  Aligned_cols=59  Identities=10%  Similarity=0.002  Sum_probs=40.3

Q ss_pred             CCCCCCCCCC-CCCCHHHCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCC
Q ss_conf             3347998888-88520000114676423660158999721111333689999643441021235464146810
Q 003717          123 ATRLDTPKKL-LDKDKKLNIFFPRLRKVKTLPFCGTGKHKYSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQI  194 (800)
Q Consensus       123 l~is~~Lk~s-vsesd~LreyFskyGKVKsVp~kgTGK~KYGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i  194 (800)
                      +.+.+ |+.. +++ ++|..+|.+||.|..+.....  ..|+|         |.|.+.++|..|+.++++..+
T Consensus        11 v~v~n-l~~~~~t~-~eL~~lF~~fG~I~~i~i~~~--k~~af---------V~f~~~~~A~~A~~~l~~~~~   70 (89)
T d1x4da1          11 VHIMD-FQRGKNLR-YQLLQLVEPFGVISNHLILNK--INEAF---------IEMATTEDAQAAVDYYTTTPA   70 (89)
T ss_dssp             EEEES-CCCSSSHH-HHHHTTTGGGSCEEEEEECSS--SSCEE---------EEESSHHHHHHHHHHHHHSCC
T ss_pred             EEEEC-CCCCCCCH-HHHHHHHHHHCCEEEEEEECC--CEEEE---------EEECCHHHHHHHHHHHHHCCC
T ss_conf             99978-99876789-999999986387278876044--22899---------997460557999998750888

>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=83.44  E-value=0.2  Score=23.95  Aligned_cols=51  Identities=6%  Similarity=0.068  Sum_probs=36.3

Q ss_pred             CCCCCCCCHHHCCCCCCCCCEEEECCCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCC
Q ss_conf             888888520000114676423660158999721-111333689999643441021235464146810
Q 003717          129 PKKLLDKDKKLNIFFPRLRKVKTLPFCGTGKHK-YSFQRVEAPPLPKYFCDCEEHSAAFHAAEGKQI  194 (800)
Q Consensus       129 Lk~svsesd~LreyFskyGKVKsVp~kgTGK~K-YGFg~ve~Ps~pV~F~sfEea~aA~eAmNG~~i  194 (800)
                      ++.+..  +.+..+|.+||.|..++..   +.+ |+|         |.|.+-+++..|+. +||..+
T Consensus        12 ~p~~~~--~~il~~F~~~G~I~~~~~~---~~~~~~f---------V~f~~~~~A~~Al~-~nG~~~   63 (81)
T d1wwha1          12 FPQASA--SYILLQFAQYGNILKHVMS---NTGNWMH---------IRYQSKLQARKALS-KDGRIF   63 (81)
T ss_dssp             CCGGGH--HHHHHHHHTTSCEEEEEEC---SSSSEEE---------EEESSHHHHHHHHT-TTTCEE
T ss_pred             CCHHHH--HHHHHHHHHHHHHHEEEEC---CCCCEEE---------EEECCCHHHHHHHH-CCCCEE
T ss_conf             885777--9999999742011068954---8998899---------99763279999986-078757